mothur > fastq.info(file=MM1.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM2.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM3.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM4.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM5.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM6.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM7.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM8.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM9.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM10.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM11.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM12.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM13.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM14.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM15.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM16.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM17.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM18.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM19.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM20.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM21.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM22.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM23.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM24.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM25.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM26.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM27.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM28.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM29.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM30.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM31.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM32.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM33.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM34.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM35.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM36.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM37.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM38.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM39.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM40.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM41.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM42.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM43.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM44.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM45.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM46.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM47.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM48.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM49.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM50.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM51.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM52.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM53.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM54.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM55.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM56.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM57.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM58.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM59.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM60.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM61.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM62.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM63.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM64.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM65.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM66.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM67.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM68.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM69.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM70.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM71.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM72.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM73.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM74.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)
fastq.info(file=MM75.file, oligos=primers.oligos, checkorient=t, fasta=f, qfile=f, format=illumina1.8+)

make.contigs(ffastq=MM61.F230_forward.fastq, rfastq=MM61.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM62.F230_forward.fastq, rfastq=MM62.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM63.F230_forward.fastq, rfastq=MM63.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM64.F230_forward.fastq, rfastq=MM64.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM65.F230_forward.fastq, rfastq=MM65.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM66.F230_forward.fastq, rfastq=MM66.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM67.F230_forward.fastq, rfastq=MM67.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM68.F230_forward.fastq, rfastq=MM68.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM69.F230_forward.fastq, rfastq=MM69.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM70.F230_forward.fastq, rfastq=MM70.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM71.F230_forward.fastq, rfastq=MM71.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM72.F230_forward.fastq, rfastq=MM72.F230_reverse.fastq, trimoverlap=T)

make.contigs(ffastq=MM73.F230_forward.fastq, rfastq=MM73.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM74.F230_forward.fastq, rfastq=MM74.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM75.F230_forward.fastq, rfastq=MM75.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM60.F230_forward.fastq, rfastq=MM60.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM59.F230_forward.fastq, rfastq=MM59.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM58.F230_forward.fastq, rfastq=MM58.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM57.F230_forward.fastq, rfastq=MM57.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM56.F230_forward.fastq, rfastq=MM56.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM55.F230_forward.fastq, rfastq=MM55.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM54.F230_forward.fastq, rfastq=MM54.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM53.F230_forward.fastq, rfastq=MM53.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM52.F230_forward.fastq, rfastq=MM52.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM51.F230_forward.fastq, rfastq=MM51.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM50.F230_forward.fastq, rfastq=MM50.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM49.F230_forward.fastq, rfastq=MM49.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM48.F230_forward.fastq, rfastq=MM48.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM47.F230_forward.fastq, rfastq=MM47.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM46.F230_forward.fastq, rfastq=MM46.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM45.F230_forward.fastq, rfastq=MM45.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM44.F230_forward.fastq, rfastq=MM44.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM43.F230_forward.fastq, rfastq=MM43.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM42.F230_forward.fastq, rfastq=MM42.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM41.F230_forward.fastq, rfastq=MM41.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM40.F230_forward.fastq, rfastq=MM40.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM39.F230_forward.fastq, rfastq=MM39.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM38.F230_forward.fastq, rfastq=MM38.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM37.F230_forward.fastq, rfastq=MM37.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM36.F230_forward.fastq, rfastq=MM36.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM35.F230_forward.fastq, rfastq=MM35.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM34.F230_forward.fastq, rfastq=MM34.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM33.F230_forward.fastq, rfastq=MM33.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM32.F230_forward.fastq, rfastq=MM32.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM31.F230_forward.fastq, rfastq=MM31.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM30.F230_forward.fastq, rfastq=MM30.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM29.F230_forward.fastq, rfastq=MM29.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM28.F230_forward.fastq, rfastq=MM28.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM27.F230_forward.fastq, rfastq=MM27.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM26.F230_forward.fastq, rfastq=MM26.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM25.F230_forward.fastq, rfastq=MM25.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM24.F230_forward.fastq, rfastq=MM24.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM23.F230_forward.fastq, rfastq=MM23.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM22.F230_forward.fastq, rfastq=MM22.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM21.F230_forward.fastq, rfastq=MM21.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM20.F230_forward.fastq, rfastq=MM20.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM19.F230_forward.fastq, rfastq=MM19.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM18.F230_forward.fastq, rfastq=MM18.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM17.F230_forward.fastq, rfastq=MM17.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM16.F230_forward.fastq, rfastq=MM16.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM15.F230_forward.fastq, rfastq=MM15.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM14.F230_forward.fastq, rfastq=MM14.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM13.F230_forward.fastq, rfastq=MM13.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM12.F230_forward.fastq, rfastq=MM12.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM11.F230_forward.fastq, rfastq=MM11.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM10.F230_forward.fastq, rfastq=MM10.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM9.F230_forward.fastq, rfastq=MM9.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM8.F230_forward.fastq, rfastq=MM8.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM7.F230_forward.fastq, rfastq=MM7.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM6.F230_forward.fastq, rfastq=MM6.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM5.F230_forward.fastq, rfastq=MM5.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM4.F230_forward.fastq, rfastq=MM4.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM3.F230_forward.fastq, rfastq=MM3.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM2.F230_forward.fastq, rfastq=MM2.F230_reverse.fastq, trimoverlap=T)
make.contigs(ffastq=MM1.F230_forward.fastq, rfastq=MM1.F230_reverse.fastq, trimoverlap=T)

make.contigs(ffastq=MM61.BE_forward.fastq, rfastq=MM61.BE_reverse.fastq)
make.contigs(ffastq=MM62.BE_forward.fastq, rfastq=MM62.BE_reverse.fastq)
make.contigs(ffastq=MM63.BE_forward.fastq, rfastq=MM63.BE_reverse.fastq)
make.contigs(ffastq=MM64.BE_forward.fastq, rfastq=MM64.BE_reverse.fastq)
make.contigs(ffastq=MM65.BE_forward.fastq, rfastq=MM65.BE_reverse.fastq)
make.contigs(ffastq=MM66.BE_forward.fastq, rfastq=MM66.BE_reverse.fastq)
make.contigs(ffastq=MM67.BE_forward.fastq, rfastq=MM67.BE_reverse.fastq)
make.contigs(ffastq=MM68.BE_forward.fastq, rfastq=MM68.BE_reverse.fastq)
make.contigs(ffastq=MM69.BE_forward.fastq, rfastq=MM69.BE_reverse.fastq)
make.contigs(ffastq=MM70.BE_forward.fastq, rfastq=MM70.BE_reverse.fastq)
make.contigs(ffastq=MM71.BE_forward.fastq, rfastq=MM71.BE_reverse.fastq)
make.contigs(ffastq=MM72.BE_forward.fastq, rfastq=MM72.BE_reverse.fastq)
make.contigs(ffastq=MM73.BE_forward.fastq, rfastq=MM73.BE_reverse.fastq)
make.contigs(ffastq=MM74.BE_forward.fastq, rfastq=MM74.BE_reverse.fastq)
make.contigs(ffastq=MM75.BE_forward.fastq, rfastq=MM75.BE_reverse.fastq)
make.contigs(ffastq=MM60.BE_forward.fastq, rfastq=MM60.BE_reverse.fastq)
make.contigs(ffastq=MM59.BE_forward.fastq, rfastq=MM59.BE_reverse.fastq)
make.contigs(ffastq=MM58.BE_forward.fastq, rfastq=MM58.BE_reverse.fastq)
make.contigs(ffastq=MM57.BE_forward.fastq, rfastq=MM57.BE_reverse.fastq)
make.contigs(ffastq=MM56.BE_forward.fastq, rfastq=MM56.BE_reverse.fastq)
make.contigs(ffastq=MM55.BE_forward.fastq, rfastq=MM55.BE_reverse.fastq)
make.contigs(ffastq=MM54.BE_forward.fastq, rfastq=MM54.BE_reverse.fastq)
make.contigs(ffastq=MM53.BE_forward.fastq, rfastq=MM53.BE_reverse.fastq)
make.contigs(ffastq=MM52.BE_forward.fastq, rfastq=MM52.BE_reverse.fastq)
make.contigs(ffastq=MM51.BE_forward.fastq, rfastq=MM51.BE_reverse.fastq)
make.contigs(ffastq=MM50.BE_forward.fastq, rfastq=MM50.BE_reverse.fastq)
make.contigs(ffastq=MM49.BE_forward.fastq, rfastq=MM49.BE_reverse.fastq)
make.contigs(ffastq=MM48.BE_forward.fastq, rfastq=MM48.BE_reverse.fastq)
make.contigs(ffastq=MM47.BE_forward.fastq, rfastq=MM47.BE_reverse.fastq)
make.contigs(ffastq=MM46.BE_forward.fastq, rfastq=MM46.BE_reverse.fastq)
make.contigs(ffastq=MM45.BE_forward.fastq, rfastq=MM45.BE_reverse.fastq)
make.contigs(ffastq=MM44.BE_forward.fastq, rfastq=MM44.BE_reverse.fastq)
make.contigs(ffastq=MM43.BE_forward.fastq, rfastq=MM43.BE_reverse.fastq)
make.contigs(ffastq=MM42.BE_forward.fastq, rfastq=MM42.BE_reverse.fastq)
make.contigs(ffastq=MM41.BE_forward.fastq, rfastq=MM41.BE_reverse.fastq)
make.contigs(ffastq=MM40.BE_forward.fastq, rfastq=MM40.BE_reverse.fastq)
make.contigs(ffastq=MM39.BE_forward.fastq, rfastq=MM39.BE_reverse.fastq)
make.contigs(ffastq=MM38.BE_forward.fastq, rfastq=MM38.BE_reverse.fastq)
make.contigs(ffastq=MM37.BE_forward.fastq, rfastq=MM37.BE_reverse.fastq)
make.contigs(ffastq=MM36.BE_forward.fastq, rfastq=MM36.BE_reverse.fastq)
make.contigs(ffastq=MM35.BE_forward.fastq, rfastq=MM35.BE_reverse.fastq)
make.contigs(ffastq=MM34.BE_forward.fastq, rfastq=MM34.BE_reverse.fastq)
make.contigs(ffastq=MM33.BE_forward.fastq, rfastq=MM33.BE_reverse.fastq)
make.contigs(ffastq=MM32.BE_forward.fastq, rfastq=MM32.BE_reverse.fastq)
make.contigs(ffastq=MM31.BE_forward.fastq, rfastq=MM31.BE_reverse.fastq)
make.contigs(ffastq=MM30.BE_forward.fastq, rfastq=MM30.BE_reverse.fastq)
make.contigs(ffastq=MM29.BE_forward.fastq, rfastq=MM29.BE_reverse.fastq)
make.contigs(ffastq=MM28.BE_forward.fastq, rfastq=MM28.BE_reverse.fastq)
make.contigs(ffastq=MM27.BE_forward.fastq, rfastq=MM27.BE_reverse.fastq)
make.contigs(ffastq=MM26.BE_forward.fastq, rfastq=MM26.BE_reverse.fastq)
make.contigs(ffastq=MM25.BE_forward.fastq, rfastq=MM25.BE_reverse.fastq)
make.contigs(ffastq=MM24.BE_forward.fastq, rfastq=MM24.BE_reverse.fastq)
make.contigs(ffastq=MM23.BE_forward.fastq, rfastq=MM23.BE_reverse.fastq)
make.contigs(ffastq=MM22.BE_forward.fastq, rfastq=MM22.BE_reverse.fastq)
make.contigs(ffastq=MM21.BE_forward.fastq, rfastq=MM21.BE_reverse.fastq)
make.contigs(ffastq=MM20.BE_forward.fastq, rfastq=MM20.BE_reverse.fastq)
make.contigs(ffastq=MM19.BE_forward.fastq, rfastq=MM19.BE_reverse.fastq)
make.contigs(ffastq=MM18.BE_forward.fastq, rfastq=MM18.BE_reverse.fastq)
make.contigs(ffastq=MM17.BE_forward.fastq, rfastq=MM17.BE_reverse.fastq)
make.contigs(ffastq=MM16.BE_forward.fastq, rfastq=MM16.BE_reverse.fastq)
make.contigs(ffastq=MM15.BE_forward.fastq, rfastq=MM15.BE_reverse.fastq)
make.contigs(ffastq=MM14.BE_forward.fastq, rfastq=MM14.BE_reverse.fastq)
make.contigs(ffastq=MM13.BE_forward.fastq, rfastq=MM13.BE_reverse.fastq)
make.contigs(ffastq=MM12.BE_forward.fastq, rfastq=MM12.BE_reverse.fastq)
make.contigs(ffastq=MM11.BE_forward.fastq, rfastq=MM11.BE_reverse.fastq)
make.contigs(ffastq=MM10.BE_forward.fastq, rfastq=MM10.BE_reverse.fastq)
make.contigs(ffastq=MM9.BE_forward.fastq, rfastq=MM9.BE_reverse.fastq)
make.contigs(ffastq=MM8.BE_forward.fastq, rfastq=MM8.BE_reverse.fastq)
make.contigs(ffastq=MM7.BE_forward.fastq, rfastq=MM7.BE_reverse.fastq)
make.contigs(ffastq=MM6.BE_forward.fastq, rfastq=MM6.BE_reverse.fastq)
make.contigs(ffastq=MM5.BE_forward.fastq, rfastq=MM5.BE_reverse.fastq)
make.contigs(ffastq=MM4.BE_forward.fastq, rfastq=MM4.BE_reverse.fastq)
make.contigs(ffastq=MM3.BE_forward.fastq, rfastq=MM3.BE_reverse.fastq)
make.contigs(ffastq=MM2.BE_forward.fastq, rfastq=MM2.BE_reverse.fastq)
make.contigs(ffastq=MM1.BE_forward.fastq, rfastq=MM1.BE_reverse.fastq)

add the header row to the contigs.report-files

screen.seqs(fasta=MM61.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM61.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM62.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM62.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM63.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM63.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM64.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM64.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM65.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM65.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM66.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM66.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM67.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM67.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM68.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM68.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM69.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM69.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM70.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM70.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM71.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM71.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM72.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM72.F230_forward.contigs.report, minoverlap=25)

screen.seqs(fasta=MM73.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM73.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM74.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM74.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM75.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM75.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM60.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM60.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM59.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM59.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM58.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM58.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM57.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM57.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM56.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM56.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM55.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM55.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM54.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM54.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM53.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM53.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM52.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM52.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM51.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM51.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM50.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM50.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM49.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM49.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM48.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM48.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM47.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM47.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM46.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM46.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM45.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM45.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM44.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM44.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM43.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM43.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM42.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM42.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM41.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM41.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM40.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM40.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM39.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM39.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM38.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM38.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM37.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM37.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM36.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM36.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM35.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM35.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM34.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM34.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM33.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM33.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM32.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM32.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM31.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM31.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM30.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM30.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM29.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM29.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM28.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM28.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM27.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM27.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM26.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM26.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM25.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM25.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM24.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM24.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM23.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM23.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM22.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM22.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM21.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM21.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM20.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM20.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM19.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM19.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM18.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM18.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM17.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM17.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM16.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM16.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM15.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM15.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM14.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM14.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM13.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM13.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM12.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM12.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM11.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM11.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM10.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM10.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM9.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM9.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM8.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM8.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM7.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM7.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM6.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM6.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM5.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM5.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM4.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM4.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM3.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM3.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM2.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM2.F230_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM1.F230_forward.trim.contigs.fasta, maxambig=0, minlength=250, maxlength=340, contigsreport=MM1.F230_forward.contigs.report, minoverlap=25)

screen.seqs(fasta=MM61.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM61.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM62.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM62.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM63.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM63.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM64.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM64.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM65.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM65.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM66.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM66.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM67.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM67.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM68.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM68.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM69.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM69.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM70.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM70.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM71.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM71.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM72.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM72.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM73.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM73.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM74.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM74.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM75.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM75.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM60.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM60.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM59.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM59.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM58.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM58.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM57.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM57.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM56.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM56.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM55.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM55.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM54.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM54.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM53.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM53.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM52.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM52.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM51.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM51.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM50.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM50.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM49.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM49.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM48.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM48.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM47.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM47.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM46.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM46.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM45.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM45.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM44.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM44.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM43.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM43.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM42.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM42.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM41.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM41.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM40.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM40.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM39.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM39.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM38.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM38.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM37.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM37.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM36.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM36.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM35.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM35.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM34.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM34.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM33.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM33.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM32.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM32.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM31.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM31.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM30.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM30.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM29.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM29.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM28.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM28.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM27.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM27.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM26.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM26.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM25.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM25.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM24.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM24.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM23.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM23.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM22.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM22.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM21.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM21.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM20.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM20.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM19.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM19.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM18.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM18.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM17.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM17.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM16.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM16.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM15.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM15.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM14.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM14.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM13.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM13.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM12.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM12.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM11.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM11.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM10.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM10.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM9.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM9.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM8.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM8.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM7.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM7.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM6.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM6.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM5.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM5.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM4.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM4.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM3.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM3.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM2.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM2.BE_forward.contigs.report, minoverlap=25)
screen.seqs(fasta=MM1.BE_forward.trim.contigs.fasta, maxambig=0, minlength=330, maxlength=375, contigsreport=MM1.BE_forward.contigs.report, minoverlap=25)

primers removed:
trim.seqs(fasta=MM72.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM71.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM70.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM69.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM68.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM67.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM66.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM65.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM64.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM63.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM62.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM61.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)

trim.seqs(fasta=MM73.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM74.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM75.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM60.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM59.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM58.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM57.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM56.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM55.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM54.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM53.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM52.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM51.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM50.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM49.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM48.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM47.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM46.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM45.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM44.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM43.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM42.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM41.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM40.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM39.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM38.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM37.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM36.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM35.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM34.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM33.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM32.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM31.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM30.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM29.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM28.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM27.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM26.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM25.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM24.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM23.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM22.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM21.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM20.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM19.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM18.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM17.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM16.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM15.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM14.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM13.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM12.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM11.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM10.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM9.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM8.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM7.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM6.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM5.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM4.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM3.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM2.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)
trim.seqs(fasta=MM1.F230_forward.trim.contigs.good.fasta, oligos=F230.oligos)

trim.seqs(fasta=MM72.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM71.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM70.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM69.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM68.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM67.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM66.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM65.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM64.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM63.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM62.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM61.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM73.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM74.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM75.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM60.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM59.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM58.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM57.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM56.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM55.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM54.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM53.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM52.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM51.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM50.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM49.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM48.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM47.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM46.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM45.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM44.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM43.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM42.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM41.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM40.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM39.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM38.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM37.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM36.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM35.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM34.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM33.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM32.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM31.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM30.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM29.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM28.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM27.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM26.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM25.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM24.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM23.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM22.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM21.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM20.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM19.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM18.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM17.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM16.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM15.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM14.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM13.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM12.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM11.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM10.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM9.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM8.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM7.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM6.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM5.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM4.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM3.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM2.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)
trim.seqs(fasta=MM1.BE_forward.trim.contigs.good.fasta, oligos=BE.oligos)

usearch -derep_fulllength MM72.F230_forward.trim.contigs.good.trim.fasta -relabel MM72. -fastaout MM72.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM71.F230_forward.trim.contigs.good.trim.fasta -relabel MM71. -fastaout MM71.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM70.F230_forward.trim.contigs.good.trim.fasta -relabel MM70. -fastaout MM70.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM69.F230_forward.trim.contigs.good.trim.fasta -relabel MM69. -fastaout MM69.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM68.F230_forward.trim.contigs.good.trim.fasta -relabel MM68. -fastaout MM68.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM67.F230_forward.trim.contigs.good.trim.fasta -relabel MM67. -fastaout MM67.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM66.F230_forward.trim.contigs.good.trim.fasta -relabel MM66. -fastaout MM66.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM65.F230_forward.trim.contigs.good.trim.fasta -relabel MM65. -fastaout MM65.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM64.F230_forward.trim.contigs.good.trim.fasta -relabel MM64. -fastaout MM64.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM63.F230_forward.trim.contigs.good.trim.fasta -relabel MM63. -fastaout MM63.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM62.F230_forward.trim.contigs.good.trim.fasta -relabel MM62. -fastaout MM62.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM61.F230_forward.trim.contigs.good.trim.fasta -relabel MM61. -fastaout MM61.F230_uniques.fasta -sizeout

usearch -derep_fulllength MM73.F230_forward.trim.contigs.good.trim.fasta -relabel MM73. -fastaout MM73.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM74.F230_forward.trim.contigs.good.trim.fasta -relabel MM74. -fastaout MM74.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM75.F230_forward.trim.contigs.good.trim.fasta -relabel MM75. -fastaout MM75.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM60.F230_forward.trim.contigs.good.trim.fasta -relabel MM60. -fastaout MM60.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM59.F230_forward.trim.contigs.good.trim.fasta -relabel MM59. -fastaout MM59.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM58.F230_forward.trim.contigs.good.trim.fasta -relabel MM58. -fastaout MM58.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM57.F230_forward.trim.contigs.good.trim.fasta -relabel MM57. -fastaout MM57.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM56.F230_forward.trim.contigs.good.trim.fasta -relabel MM56. -fastaout MM56.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM55.F230_forward.trim.contigs.good.trim.fasta -relabel MM55. -fastaout MM55.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM54.F230_forward.trim.contigs.good.trim.fasta -relabel MM54. -fastaout MM54.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM53.F230_forward.trim.contigs.good.trim.fasta -relabel MM53. -fastaout MM53.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM52.F230_forward.trim.contigs.good.trim.fasta -relabel MM52. -fastaout MM52.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM51.F230_forward.trim.contigs.good.trim.fasta -relabel MM51. -fastaout MM51.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM50.F230_forward.trim.contigs.good.trim.fasta -relabel MM50. -fastaout MM50.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM49.F230_forward.trim.contigs.good.trim.fasta -relabel MM49. -fastaout MM49.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM48.F230_forward.trim.contigs.good.trim.fasta -relabel MM48. -fastaout MM48.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM47.F230_forward.trim.contigs.good.trim.fasta -relabel MM47. -fastaout MM47.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM46.F230_forward.trim.contigs.good.trim.fasta -relabel MM46. -fastaout MM46.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM45.F230_forward.trim.contigs.good.trim.fasta -relabel MM45. -fastaout MM45.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM44.F230_forward.trim.contigs.good.trim.fasta -relabel MM44. -fastaout MM44.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM43.F230_forward.trim.contigs.good.trim.fasta -relabel MM43. -fastaout MM43.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM42.F230_forward.trim.contigs.good.trim.fasta -relabel MM42. -fastaout MM42.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM41.F230_forward.trim.contigs.good.trim.fasta -relabel MM41. -fastaout MM41.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM40.F230_forward.trim.contigs.good.trim.fasta -relabel MM40. -fastaout MM40.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM39.F230_forward.trim.contigs.good.trim.fasta -relabel MM39. -fastaout MM39.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM38.F230_forward.trim.contigs.good.trim.fasta -relabel MM38. -fastaout MM38.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM37.F230_forward.trim.contigs.good.trim.fasta -relabel MM37. -fastaout MM37.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM36.F230_forward.trim.contigs.good.trim.fasta -relabel MM36. -fastaout MM36.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM35.F230_forward.trim.contigs.good.trim.fasta -relabel MM35. -fastaout MM35.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM34.F230_forward.trim.contigs.good.trim.fasta -relabel MM34. -fastaout MM34.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM33.F230_forward.trim.contigs.good.trim.fasta -relabel MM33. -fastaout MM33.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM32.F230_forward.trim.contigs.good.trim.fasta -relabel MM32. -fastaout MM32.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM31.F230_forward.trim.contigs.good.trim.fasta -relabel MM31. -fastaout MM31.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM30.F230_forward.trim.contigs.good.trim.fasta -relabel MM30. -fastaout MM30.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM29.F230_forward.trim.contigs.good.trim.fasta -relabel MM29. -fastaout MM29.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM28.F230_forward.trim.contigs.good.trim.fasta -relabel MM28. -fastaout MM28.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM27.F230_forward.trim.contigs.good.trim.fasta -relabel MM27. -fastaout MM27.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM26.F230_forward.trim.contigs.good.trim.fasta -relabel MM26. -fastaout MM26.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM25.F230_forward.trim.contigs.good.trim.fasta -relabel MM25. -fastaout MM25.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM24.F230_forward.trim.contigs.good.trim.fasta -relabel MM24. -fastaout MM24.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM23.F230_forward.trim.contigs.good.trim.fasta -relabel MM23. -fastaout MM23.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM22.F230_forward.trim.contigs.good.trim.fasta -relabel MM22. -fastaout MM22.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM21.F230_forward.trim.contigs.good.trim.fasta -relabel MM21. -fastaout MM21.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM20.F230_forward.trim.contigs.good.trim.fasta -relabel MM20. -fastaout MM20.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM19.F230_forward.trim.contigs.good.trim.fasta -relabel MM19. -fastaout MM19.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM18.F230_forward.trim.contigs.good.trim.fasta -relabel MM18. -fastaout MM18.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM17.F230_forward.trim.contigs.good.trim.fasta -relabel MM17. -fastaout MM17.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM16.F230_forward.trim.contigs.good.trim.fasta -relabel MM16. -fastaout MM16.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM15.F230_forward.trim.contigs.good.trim.fasta -relabel MM15. -fastaout MM15.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM14.F230_forward.trim.contigs.good.trim.fasta -relabel MM14. -fastaout MM14.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM13.F230_forward.trim.contigs.good.trim.fasta -relabel MM13. -fastaout MM13.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM12.F230_forward.trim.contigs.good.trim.fasta -relabel MM12. -fastaout MM12.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM11.F230_forward.trim.contigs.good.trim.fasta -relabel MM11. -fastaout MM11.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM10.F230_forward.trim.contigs.good.trim.fasta -relabel MM10. -fastaout MM10.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM9.F230_forward.trim.contigs.good.trim.fasta -relabel MM9. -fastaout MM9.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM8.F230_forward.trim.contigs.good.trim.fasta -relabel MM8. -fastaout MM8.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM7.F230_forward.trim.contigs.good.trim.fasta -relabel MM7. -fastaout MM7.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM6.F230_forward.trim.contigs.good.trim.fasta -relabel MM6. -fastaout MM6.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM5.F230_forward.trim.contigs.good.trim.fasta -relabel MM5. -fastaout MM5.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM4.F230_forward.trim.contigs.good.trim.fasta -relabel MM4. -fastaout MM4.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM3.F230_forward.trim.contigs.good.trim.fasta -relabel MM3. -fastaout MM3.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM2.F230_forward.trim.contigs.good.trim.fasta -relabel MM2. -fastaout MM2.F230_uniques.fasta -sizeout
usearch -derep_fulllength MM1.F230_forward.trim.contigs.good.trim.fasta -relabel MM1. -fastaout MM1.F230_uniques.fasta -sizeout

usearch -derep_fulllength MM72.BE_forward.trim.contigs.good.trim.fasta -relabel MM72. -fastaout MM72.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM71.BE_forward.trim.contigs.good.trim.fasta -relabel MM71. -fastaout MM71.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM70.BE_forward.trim.contigs.good.trim.fasta -relabel MM70. -fastaout MM70.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM69.BE_forward.trim.contigs.good.trim.fasta -relabel MM69. -fastaout MM69.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM68.BE_forward.trim.contigs.good.trim.fasta -relabel MM68. -fastaout MM68.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM67.BE_forward.trim.contigs.good.trim.fasta -relabel MM67. -fastaout MM67.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM66.BE_forward.trim.contigs.good.trim.fasta -relabel MM66. -fastaout MM66.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM65.BE_forward.trim.contigs.good.trim.fasta -relabel MM65. -fastaout MM65.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM64.BE_forward.trim.contigs.good.trim.fasta -relabel MM64. -fastaout MM64.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM63.BE_forward.trim.contigs.good.trim.fasta -relabel MM63. -fastaout MM63.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM62.BE_forward.trim.contigs.good.trim.fasta -relabel MM62. -fastaout MM62.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM61.BE_forward.trim.contigs.good.trim.fasta -relabel MM61. -fastaout MM61.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM73.BE_forward.trim.contigs.good.trim.fasta -relabel MM73. -fastaout MM73.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM74.BE_forward.trim.contigs.good.trim.fasta -relabel MM74. -fastaout MM74.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM75.BE_forward.trim.contigs.good.trim.fasta -relabel MM75. -fastaout MM75.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM60.BE_forward.trim.contigs.good.trim.fasta -relabel MM60. -fastaout MM60.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM59.BE_forward.trim.contigs.good.trim.fasta -relabel MM59. -fastaout MM59.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM58.BE_forward.trim.contigs.good.trim.fasta -relabel MM58. -fastaout MM58.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM57.BE_forward.trim.contigs.good.trim.fasta -relabel MM57. -fastaout MM57.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM56.BE_forward.trim.contigs.good.trim.fasta -relabel MM56. -fastaout MM56.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM55.BE_forward.trim.contigs.good.trim.fasta -relabel MM55. -fastaout MM55.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM54.BE_forward.trim.contigs.good.trim.fasta -relabel MM54. -fastaout MM54.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM53.BE_forward.trim.contigs.good.trim.fasta -relabel MM53. -fastaout MM53.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM52.BE_forward.trim.contigs.good.trim.fasta -relabel MM52. -fastaout MM52.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM51.BE_forward.trim.contigs.good.trim.fasta -relabel MM51. -fastaout MM51.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM50.BE_forward.trim.contigs.good.trim.fasta -relabel MM50. -fastaout MM50.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM49.BE_forward.trim.contigs.good.trim.fasta -relabel MM49. -fastaout MM49.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM48.BE_forward.trim.contigs.good.trim.fasta -relabel MM48. -fastaout MM48.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM47.BE_forward.trim.contigs.good.trim.fasta -relabel MM47. -fastaout MM47.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM46.BE_forward.trim.contigs.good.trim.fasta -relabel MM46. -fastaout MM46.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM45.BE_forward.trim.contigs.good.trim.fasta -relabel MM45. -fastaout MM45.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM44.BE_forward.trim.contigs.good.trim.fasta -relabel MM44. -fastaout MM44.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM43.BE_forward.trim.contigs.good.trim.fasta -relabel MM43. -fastaout MM43.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM42.BE_forward.trim.contigs.good.trim.fasta -relabel MM42. -fastaout MM42.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM41.BE_forward.trim.contigs.good.trim.fasta -relabel MM41. -fastaout MM41.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM40.BE_forward.trim.contigs.good.trim.fasta -relabel MM40. -fastaout MM40.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM39.BE_forward.trim.contigs.good.trim.fasta -relabel MM39. -fastaout MM39.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM38.BE_forward.trim.contigs.good.trim.fasta -relabel MM38. -fastaout MM38.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM37.BE_forward.trim.contigs.good.trim.fasta -relabel MM37. -fastaout MM37.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM36.BE_forward.trim.contigs.good.trim.fasta -relabel MM36. -fastaout MM36.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM35.BE_forward.trim.contigs.good.trim.fasta -relabel MM35. -fastaout MM35.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM34.BE_forward.trim.contigs.good.trim.fasta -relabel MM34. -fastaout MM34.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM33.BE_forward.trim.contigs.good.trim.fasta -relabel MM33. -fastaout MM33.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM32.BE_forward.trim.contigs.good.trim.fasta -relabel MM32. -fastaout MM32.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM31.BE_forward.trim.contigs.good.trim.fasta -relabel MM31. -fastaout MM31.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM30.BE_forward.trim.contigs.good.trim.fasta -relabel MM30. -fastaout MM30.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM29.BE_forward.trim.contigs.good.trim.fasta -relabel MM29. -fastaout MM29.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM28.BE_forward.trim.contigs.good.trim.fasta -relabel MM28. -fastaout MM28.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM27.BE_forward.trim.contigs.good.trim.fasta -relabel MM27. -fastaout MM27.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM26.BE_forward.trim.contigs.good.trim.fasta -relabel MM26. -fastaout MM26.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM25.BE_forward.trim.contigs.good.trim.fasta -relabel MM25. -fastaout MM25.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM24.BE_forward.trim.contigs.good.trim.fasta -relabel MM24. -fastaout MM24.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM23.BE_forward.trim.contigs.good.trim.fasta -relabel MM23. -fastaout MM23.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM22.BE_forward.trim.contigs.good.trim.fasta -relabel MM22. -fastaout MM22.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM21.BE_forward.trim.contigs.good.trim.fasta -relabel MM21. -fastaout MM21.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM20.BE_forward.trim.contigs.good.trim.fasta -relabel MM20. -fastaout MM20.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM19.BE_forward.trim.contigs.good.trim.fasta -relabel MM19. -fastaout MM19.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM18.BE_forward.trim.contigs.good.trim.fasta -relabel MM18. -fastaout MM18.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM17.BE_forward.trim.contigs.good.trim.fasta -relabel MM17. -fastaout MM17.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM16.BE_forward.trim.contigs.good.trim.fasta -relabel MM16. -fastaout MM16.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM15.BE_forward.trim.contigs.good.trim.fasta -relabel MM15. -fastaout MM15.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM14.BE_forward.trim.contigs.good.trim.fasta -relabel MM14. -fastaout MM14.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM13.BE_forward.trim.contigs.good.trim.fasta -relabel MM13. -fastaout MM13.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM12.BE_forward.trim.contigs.good.trim.fasta -relabel MM12. -fastaout MM12.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM11.BE_forward.trim.contigs.good.trim.fasta -relabel MM11. -fastaout MM11.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM10.BE_forward.trim.contigs.good.trim.fasta -relabel MM10. -fastaout MM10.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM9.BE_forward.trim.contigs.good.trim.fasta -relabel MM9. -fastaout MM9.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM8.BE_forward.trim.contigs.good.trim.fasta -relabel MM8. -fastaout MM8.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM7.BE_forward.trim.contigs.good.trim.fasta -relabel MM7. -fastaout MM7.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM6.BE_forward.trim.contigs.good.trim.fasta -relabel MM6. -fastaout MM6.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM5.BE_forward.trim.contigs.good.trim.fasta -relabel MM5. -fastaout MM5.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM4.BE_forward.trim.contigs.good.trim.fasta -relabel MM4. -fastaout MM4.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM3.BE_forward.trim.contigs.good.trim.fasta -relabel MM3. -fastaout MM3.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM2.BE_forward.trim.contigs.good.trim.fasta -relabel MM2. -fastaout MM2.BE_uniques.fasta -sizeout
usearch -derep_fulllength MM1.BE_forward.trim.contigs.good.trim.fasta -relabel MM1. -fastaout MM1.BE_uniques.fasta -sizeout

usearch -cluster_otus MM72.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM72.F230_otus.fa
usearch -cluster_otus MM71.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM71.F230_otus.fa
usearch -cluster_otus MM70.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM70.F230_otus.fa
usearch -cluster_otus MM69.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM69.F230_otus.fa
usearch -cluster_otus MM68.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM68.F230_otus.fa
usearch -cluster_otus MM67.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM67.F230_otus.fa
usearch -cluster_otus MM66.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM66.F230_otus.fa
usearch -cluster_otus MM65.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM65.F230_otus.fa
usearch -cluster_otus MM64.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM64.F230_otus.fa
usearch -cluster_otus MM63.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM63.F230_otus.fa
usearch -cluster_otus MM62.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM62.F230_otus.fa
usearch -cluster_otus MM61.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM61.F230_otus.fa

usearch -cluster_otus MM73.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM73.F230_otus.fa
usearch -cluster_otus MM74.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM74.F230_otus.fa
usearch -cluster_otus MM75.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM75.F230_otus.fa
usearch -cluster_otus MM60.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM60.F230_otus.fa
usearch -cluster_otus MM59.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM59.F230_otus.fa
usearch -cluster_otus MM58.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM58.F230_otus.fa
usearch -cluster_otus MM57.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM57.F230_otus.fa
usearch -cluster_otus MM56.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM56.F230_otus.fa
usearch -cluster_otus MM55.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM55.F230_otus.fa
usearch -cluster_otus MM54.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM54.F230_otus.fa
usearch -cluster_otus MM53.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM53.F230_otus.fa
usearch -cluster_otus MM52.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM52.F230_otus.fa
usearch -cluster_otus MM51.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM51.F230_otus.fa
usearch -cluster_otus MM50.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM50.F230_otus.fa
usearch -cluster_otus MM49.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM49.F230_otus.fa
usearch -cluster_otus MM48.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM48.F230_otus.fa
usearch -cluster_otus MM47.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM47.F230_otus.fa
usearch -cluster_otus MM46.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM46.F230_otus.fa
usearch -cluster_otus MM45.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM45.F230_otus.fa
usearch -cluster_otus MM44.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM44.F230_otus.fa
usearch -cluster_otus MM43.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM43.F230_otus.fa
usearch -cluster_otus MM42.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM42.F230_otus.fa
usearch -cluster_otus MM41.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM41.F230_otus.fa
usearch -cluster_otus MM40.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM40.F230_otus.fa
usearch -cluster_otus MM39.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM39.F230_otus.fa
usearch -cluster_otus MM38.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM38.F230_otus.fa
usearch -cluster_otus MM37.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM37.F230_otus.fa
usearch -cluster_otus MM36.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM36.F230_otus.fa
usearch -cluster_otus MM35.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM35.F230_otus.fa
usearch -cluster_otus MM34.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM34.F230_otus.fa
usearch -cluster_otus MM33.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM33.F230_otus.fa
usearch -cluster_otus MM32.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM32.F230_otus.fa
usearch -cluster_otus MM31.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM31.F230_otus.fa
usearch -cluster_otus MM30.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM30.F230_otus.fa
usearch -cluster_otus MM29.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM29.F230_otus.fa
usearch -cluster_otus MM28.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM28.F230_otus.fa
usearch -cluster_otus MM27.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM27.F230_otus.fa
usearch -cluster_otus MM26.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM26.F230_otus.fa
usearch -cluster_otus MM25.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM25.F230_otus.fa
usearch -cluster_otus MM24.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM24.F230_otus.fa
usearch -cluster_otus MM23.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM23.F230_otus.fa
usearch -cluster_otus MM22.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM22.F230_otus.fa
usearch -cluster_otus MM21.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM21.F230_otus.fa
usearch -cluster_otus MM20.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM20.F230_otus.fa
usearch -cluster_otus MM19.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM19.F230_otus.fa
usearch -cluster_otus MM18.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM18.F230_otus.fa
usearch -cluster_otus MM17.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM17.F230_otus.fa
usearch -cluster_otus MM16.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM16.F230_otus.fa
usearch -cluster_otus MM15.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM15.F230_otus.fa
usearch -cluster_otus MM14.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM14.F230_otus.fa
usearch -cluster_otus MM13.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM13.F230_otus.fa
usearch -cluster_otus MM12.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM12.F230_otus.fa
usearch -cluster_otus MM11.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM11.F230_otus.fa
usearch -cluster_otus MM10.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM10.F230_otus.fa
usearch -cluster_otus MM9.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM9.F230_otus.fa
usearch -cluster_otus MM8.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM8.F230_otus.fa
usearch -cluster_otus MM7.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM7.F230_otus.fa
usearch -cluster_otus MM6.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM6.F230_otus.fa
usearch -cluster_otus MM5.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM5.F230_otus.fa
usearch -cluster_otus MM4.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM4.F230_otus.fa
usearch -cluster_otus MM3.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM3.F230_otus.fa
usearch -cluster_otus MM2.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM2.F230_otus.fa
usearch -cluster_otus MM1.F230_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM1.F230_otus.fa

usearch -cluster_otus MM72.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM72.BE_otus.fa
usearch -cluster_otus MM71.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM71.BE_otus.fa
usearch -cluster_otus MM70.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM70.BE_otus.fa
usearch -cluster_otus MM69.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM69.BE_otus.fa
usearch -cluster_otus MM68.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM68.BE_otus.fa
usearch -cluster_otus MM67.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM67.BE_otus.fa
usearch -cluster_otus MM66.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM66.BE_otus.fa
usearch -cluster_otus MM65.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM65.BE_otus.fa
usearch -cluster_otus MM64.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM64.BE_otus.fa
usearch -cluster_otus MM63.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM63.BE_otus.fa
usearch -cluster_otus MM62.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM62.BE_otus.fa
usearch -cluster_otus MM61.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM61.BE_otus.fa
usearch -cluster_otus MM73.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM73.BE_otus.fa
usearch -cluster_otus MM74.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM74.BE_otus.fa
usearch -cluster_otus MM75.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM75.BE_otus.fa
usearch -cluster_otus MM60.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM60.BE_otus.fa
usearch -cluster_otus MM59.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM59.BE_otus.fa
usearch -cluster_otus MM58.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM58.BE_otus.fa
usearch -cluster_otus MM57.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM57.BE_otus.fa
usearch -cluster_otus MM56.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM56.BE_otus.fa
usearch -cluster_otus MM55.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM55.BE_otus.fa
usearch -cluster_otus MM54.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM54.BE_otus.fa
usearch -cluster_otus MM53.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM53.BE_otus.fa
usearch -cluster_otus MM52.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM52.BE_otus.fa
usearch -cluster_otus MM51.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM51.BE_otus.fa
usearch -cluster_otus MM50.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM50.BE_otus.fa
usearch -cluster_otus MM49.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM49.BE_otus.fa
usearch -cluster_otus MM48.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM48.BE_otus.fa
usearch -cluster_otus MM47.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM47.BE_otus.fa
usearch -cluster_otus MM46.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM46.BE_otus.fa
usearch -cluster_otus MM45.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM45.BE_otus.fa
usearch -cluster_otus MM44.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM44.BE_otus.fa
usearch -cluster_otus MM43.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM43.BE_otus.fa
usearch -cluster_otus MM42.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM42.BE_otus.fa
usearch -cluster_otus MM41.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM41.BE_otus.fa
usearch -cluster_otus MM40.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM40.BE_otus.fa
usearch -cluster_otus MM39.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM39.BE_otus.fa
usearch -cluster_otus MM38.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM38.BE_otus.fa
usearch -cluster_otus MM37.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM37.BE_otus.fa
usearch -cluster_otus MM36.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM36.BE_otus.fa
usearch -cluster_otus MM35.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM35.BE_otus.fa
usearch -cluster_otus MM34.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM34.BE_otus.fa
usearch -cluster_otus MM33.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM33.BE_otus.fa
usearch -cluster_otus MM32.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM32.BE_otus.fa
usearch -cluster_otus MM31.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM31.BE_otus.fa
usearch -cluster_otus MM30.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM30.BE_otus.fa
usearch -cluster_otus MM29.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM29.BE_otus.fa
usearch -cluster_otus MM28.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM28.BE_otus.fa
usearch -cluster_otus MM27.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM27.BE_otus.fa
usearch -cluster_otus MM26.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM26.BE_otus.fa
usearch -cluster_otus MM25.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM25.BE_otus.fa
usearch -cluster_otus MM24.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM24.BE_otus.fa
usearch -cluster_otus MM23.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM23.BE_otus.fa
usearch -cluster_otus MM22.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM22.BE_otus.fa
usearch -cluster_otus MM21.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM21.BE_otus.fa
usearch -cluster_otus MM20.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM20.BE_otus.fa
usearch -cluster_otus MM19.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM19.BE_otus.fa
usearch -cluster_otus MM18.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM18.BE_otus.fa
usearch -cluster_otus MM17.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM17.BE_otus.fa
usearch -cluster_otus MM16.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM16.BE_otus.fa
usearch -cluster_otus MM15.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM15.BE_otus.fa
usearch -cluster_otus MM14.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM14.BE_otus.fa
usearch -cluster_otus MM13.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM13.BE_otus.fa
usearch -cluster_otus MM12.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM12.BE_otus.fa
usearch -cluster_otus MM11.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM11.BE_otus.fa
usearch -cluster_otus MM10.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM10.BE_otus.fa
usearch -cluster_otus MM9.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM9.BE_otus.fa
usearch -cluster_otus MM8.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM8.BE_otus.fa
usearch -cluster_otus MM7.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM7.BE_otus.fa
usearch -cluster_otus MM6.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM6.BE_otus.fa
usearch -cluster_otus MM5.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM5.BE_otus.fa
usearch -cluster_otus MM4.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM4.BE_otus.fa
usearch -cluster_otus MM3.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM3.BE_otus.fa
usearch -cluster_otus MM2.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM2.BE_otus.fa
usearch -cluster_otus MM1.BE_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM1.BE_otus.fa

mothur> merge.files(input=MM61.F230_otus.fa-MM62.F230_otus.fa-MM63.F230_otus.fa-MM64.F230_otus.fa-MM65.F230_otus.fa-MM66.F230_otus.fa-MM67.F230_otus.fa-MM68.F230_otus.fa-MM69.F230_otus.fa-MM70.F230_otus.fa-MM71.F230_otus.fa-MM72.F230_otus.fa-MM73.F230_otus.fa-MM74.F230_otus.fa-MM75.F230_otus.fa-MM60.F230_otus.fa-MM59.F230_otus.fa-MM58.F230_otus.fa-MM57.F230_otus.fa-MM56.F230_otus.fa-MM55.F230_otus.fa-MM54.F230_otus.fa-MM53.F230_otus.fa-MM52.F230_otus.fa-MM51.F230_otus.fa-MM50.F230_otus.fa-MM49.F230_otus.fa-MM48.F230_otus.fa-MM47.F230_otus.fa-MM46.F230_otus.fa-MM45.F230_otus.fa-MM44.F230_otus.fa-MM43.F230_otus.fa-MM42.F230_otus.fa-MM41.F230_otus.fa-MM40.F230_otus.fa-MM39.F230_otus.fa-MM38.F230_otus.fa-MM37.F230_otus.fa-MM36.F230_otus.fa-MM35.F230_otus.fa-MM34.F230_otus.fa-MM33.F230_otus.fa-MM32.F230_otus.fa-MM31.F230_otus.fa-MM30.F230_otus.fa-MM29.F230_otus.fa-MM28.F230_otus.fa-MM27.F230_otus.fa-MM26.F230_otus.fa-MM25.F230_otus.fa-MM24.F230_otus.fa-MM23.F230_otus.fa-MM22.F230_otus.fa-MM21.F230_otus.fa-MM20.F230_otus.fa-MM19.F230_otus.fa-MM18.F230_otus.fa-MM17.F230_otus.fa-MM16.F230_otus.fa-MM15.F230_otus.fa-MM14.F230_otus.fa-MM13.F230_otus.fa-MM12.F230_otus.fa-MM11.F230_otus.fa-MM10.F230_otus.fa-MM9.F230_otus.fa-MM8.F230_otus.fa-MM7.F230_otus.fa-MM6.F230_otus.fa-MM5.F230_otus.fa-MM4.F230_otus.fa-MM3.F230_otus.fa-MM2.F230_otus.fa-MM1.F230_otus.fa, output=otusALL_F230.fa)
mothur> merge.files(input=MM61.BE_otus.fa-MM62.BE_otus.fa-MM63.BE_otus.fa-MM64.BE_otus.fa-MM65.BE_otus.fa-MM66.BE_otus.fa-MM67.BE_otus.fa-MM68.BE_otus.fa-MM69.BE_otus.fa-MM70.BE_otus.fa-MM71.BE_otus.fa-MM72.BE_otus.fa-MM73.BE_otus.fa-MM74.BE_otus.fa-MM75.BE_otus.fa-MM60.BE_otus.fa-MM59.BE_otus.fa-MM58.BE_otus.fa-MM57.BE_otus.fa-MM56.BE_otus.fa-MM55.BE_otus.fa-MM54.BE_otus.fa-MM53.BE_otus.fa-MM52.BE_otus.fa-MM51.BE_otus.fa-MM50.BE_otus.fa-MM49.BE_otus.fa-MM48.BE_otus.fa-MM47.BE_otus.fa-MM46.BE_otus.fa-MM45.BE_otus.fa-MM44.BE_otus.fa-MM43.BE_otus.fa-MM42.BE_otus.fa-MM41.BE_otus.fa-MM40.BE_otus.fa-MM39.BE_otus.fa-MM38.BE_otus.fa-MM37.BE_otus.fa-MM36.BE_otus.fa-MM35.BE_otus.fa-MM34.BE_otus.fa-MM33.BE_otus.fa-MM32.BE_otus.fa-MM31.BE_otus.fa-MM30.BE_otus.fa-MM29.BE_otus.fa-MM28.BE_otus.fa-MM27.BE_otus.fa-MM26.BE_otus.fa-MM25.BE_otus.fa-MM24.BE_otus.fa-MM23.BE_otus.fa-MM22.BE_otus.fa-MM21.BE_otus.fa-MM20.BE_otus.fa-MM19.BE_otus.fa-MM18.BE_otus.fa-MM17.BE_otus.fa-MM16.BE_otus.fa-MM15.BE_otus.fa-MM14.BE_otus.fa-MM13.BE_otus.fa-MM12.BE_otus.fa-MM11.BE_otus.fa-MM10.BE_otus.fa-MM9.BE_otus.fa-MM8.BE_otus.fa-MM7.BE_otus.fa-MM6.BE_otus.fa-MM5.BE_otus.fa-MM4.BE_otus.fa-MM3.BE_otus.fa-MM2.BE_otus.fa-MM1.BE_otus.fa, output=otusALL_BE.fa)

usearch -sortbysize otusALL_F230.fa -fastaout otusALL_F230_sorted.fa
usearch -sortbysize otusALL_BE.fa -fastaout otusALL_BE_sorted.fa

usearch -cluster_otus otusALL_F230_sorted.fa -minsize 1 -otu_radius_pct 3.0 -sizein -otus otusALL_F230_sorted_clustered_3.0.fa  -sizeout -log cluster_otusALL_F230clustered3.0.log
usearch -cluster_otus otusALL_BE_sorted.fa -minsize 1 -otu_radius_pct 3.0 -sizein -otus otusALL_BE_sorted_clustered_3.0.fa  -sizeout -log cluster_otusALL_BEclustered3.0.log

usearch -usearch_global otusALL_F230.fa -db otusALL_F230_sorted_clustered_3.0.fa -strand plus -id 0.97 -mothur_shared_out otutab_3.0_F230.shared
usearch -usearch_global otusALL_BE.fa -db otusALL_BE_sorted_clustered_3.0.fa -strand plus -id 0.97 -mothur_shared_out otutab_3.0_BE.shared

Removed 42 BE-OTUs based on their presence only or mainly in negative samples
Removed 42 F230-OTUs based on their presence only or mainly in negative samples

blastn -db nt -query E:\EBAI\Benthics\otusALL_F230_sorted_clustered_3.0.negaway.fa -evalue 1e-20 -num_descriptions 100 -num_alignments 100 -out E:\EBAI\Benthics\otusALL_F230_sorted_clustered_3.0.taxonomy.txt -remote
blastn -db nt -query E:\EBAI\Benthics\otusALL_BE_sorted_clustered_3.0.negaway.fa -evalue 1e-20 -num_descriptions 100 -num_alignments 100 -out E:\EBAI\Benthics\otusALL_BE_sorted_clustered_3.0.taxonomy.txt -remote

MEGAN 6.5.10:
import otusALL_F230_sorted_clustered_3.0.taxonomy.txt
minimum bit score 100.0 (low because we want all metazoa to be separate)
top percentage 8.0
Minimum support percentage 0.0001
minimum support 1

Total: 2895
Not assigned:  4(0.14%)
No hits  654(22.6%)

Export readName_to_taxonPath to files otusALL_F230_sorted_clustered.taxonomy-eukaryota.txt, otusALL_BE_sorted_clustered.taxonomy-bacteria.txt, otusALL_BE_sorted_clustered.taxonomy-notassigned.txt and otusALL_BE_sorted_clustered.taxonomy-nohits.txt (merkkaa no hits-haara ja sit export; merkkaa eukaryota, avaa subtree, select subtree ja sit export)
"-signs removed from the files
Results put together with OTU-table, manually..
1581 Metazoa

MEGAN 6.5.10:
import otusALL_BE_sorted_clustered_3.0.taxonomy.txt
minimum bit score 100.0 (low because we want all metazoa to be separate)
top percentage 8.0
Minimum support percentage 0.0001
minimum support 1

Total: 4938
Not assigned:  11(0.22%)
No hits  1272(25.8%)

Export readName_to_taxonPath to files otusALL_F230_sorted_clustered.taxonomy-eukaryota.txt, otusALL_BE_sorted_clustered.taxonomy-bacteria.txt, otusALL_BE_sorted_clustered.taxonomy-notassigned.txt and otusALL_BE_sorted_clustered.taxonomy-nohits.txt (merkkaa no hits-haara ja sit export; merkkaa eukaryota, avaa subtree, select subtree ja sit export)
"-signs removed from the files
Results put together with OTU-table, manually..
1367 Metazoa

Since we are interested in Metazoa and monitoring them, we used this data to take out only Metazoa sequences.

mothur > get.seqs(accnos=BE_Metazoa.accnos, fasta=otusALL_BE_sorted_clustered_3.0.negaway.fa)
output = otusALL_BE_sorted_clustered_3.0.negaway.pick.fa, only metazoa sequences

mothur > get.seqs(accnos=F230_Metazoa.accnos, fasta=otusALL_F230_sorted_clustered_3.0.negaway.fa)
output = otusALL_F230_sorted_clustered_3.0.negaway.pick.fa, only metazoa sequences

Can be translated to aminoacids (frame 2) using http://www.bioinformatics.org/sms2/translate.html
otusALL_BE_sorted_clustered_3.0.negaway.pick.translated.fa
otusALL_F230_sorted_clustered_3.0.negaway.pick.translated.fa

Translated aligned using MAFFT online tool and checked for inconsistences (non-COI reads) (mafft muuttanee stop-codonit deleetioksi ellei laita allow any symbol)
otusALL_BE_sorted_clustered_3.0.negaway.pick.translated.aligned.fa
318 stop codons
otusALL_F230_sorted_clustered_3.0.negaway.pick.translated.aligned.fa
598 stop codons

we are looking for invertebrates, so I removed all seqs that had stop codons in invertebrate code.
otusALL_F230_sorted_clustered_3.0.negaway.pick.translated.aligned.stopsremoved.fa
otusALL_F230_sorted_clustered_3.0.negaway.pick.translated.aligned.stopsremoved.removed.fa (154 seqs)

otusALL_BE_sorted_clustered_3.0.negaway.pick.translated.aligned.stopsremoved.fa
otusALL_BE_sorted_clustered_3.0.negaway.pick.translated.aligned.stopsremoved.removed.fa (106 seqs)

good qualitys in otusALL_BE_.pick.translated.aligned.stopsremoved.fa checked for non-COIs, those still removed.
no obvious non-CO1s left.

mothur > get.seqs(accnos=no_stops_BE.accnos, fasta=otusALL_BE_sorted_clustered_3.0.negaway.pick.fa)
output = otusALL_BE_sorted_clustered_3.0.negaway.pick.pick.fa, stops removed file, 1261 seqs left.
mothur > get.seqs(accnos=no_stops_F230.accnos, fasta=otusALL_F230_sorted_clustered_3.0.negaway.pick.fa)
output = otusALL_F230_sorted_clustered_3.0.negaway.pick.pick.fa, stops removed file, 1427 seqs left.

Metazoa blasted against BOLD v.4 Species Level Barcode Records (2,669,681 Sequences/174,315 Species/64,199 Interim Species). Put together.
mothur > get.seqs(accnos=F230_nomatch.accnos, fasta=otusALL_F230_sorted_clustered_3.0.negaway.pick.pick.fa)
mothur > get.seqs(accnos=BE_nomatch.accnos, fasta=otusALL_BE_sorted_clustered_3.0.negaway.pick.pick.fa)

No match reads blasted against BOLD v.4 all barcode records (4,737,393 Sequences).

Folmer's primers:
No contigs can be made because too long fragment. Both fragments treated separately.

fastq.info(file=MM2_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM1_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM3_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM4_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM5_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM6_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM7_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM8_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM9_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM10_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM11_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM12_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM13_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM14_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM15_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM16_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM17_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM18_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM19_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM20_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM30_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM21_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM39_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM48_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM31_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM22_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM23_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM24_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM25_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM26_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM27_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM28_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM29_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM32_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM33_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM34_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM35_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM36_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM37_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM38_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM40_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM41_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM42_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM43_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM44_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM45_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM46_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM47_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM49_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM50_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM51_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM52_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM53_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM54_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM55_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM56_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM57_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM58_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM59_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM60_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM61_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM62_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM63_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM64_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM65_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM66_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM67_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM68_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM69_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM70_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM71_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM72_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM73_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM74_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)
fastq.info(file=MM75_Folmer.file, checkorient=t, fasta=T, qfile=T, format=illumina1.8+)


trim.seqs(fasta=MM2.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM2.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM1.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM1.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM3.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM3.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM4.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM4.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM5.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM5.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM6.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM6.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM7.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM7.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM8.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM8.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM9.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM9.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM10.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM10.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM11.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM11.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM12.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM12.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM13.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM13.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM14.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM14.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM15.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM15.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM16.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM16.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM17.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM17.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM18.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM18.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM19.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM19.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM20.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM20.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM21.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM21.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM22.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM22.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM23.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM23.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM24.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM24.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM25.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM25.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM26.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM26.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM27.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM27.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM28.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM28.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM29.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM29.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM30.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM30.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM31.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM31.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM32.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM32.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM33.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM33.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM34.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM34.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM35.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM35.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM36.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM36.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM37.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM37.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM38.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM38.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM39.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM39.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM40.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM40.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM41.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM41.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM42.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM42.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM43.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM43.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM44.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM44.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM45.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM45.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM46.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM46.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM47.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM47.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM48.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM48.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM49.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM49.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM50.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM50.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM51.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM51.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM52.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM52.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM53.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM53.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM54.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM54.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM55.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM55.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM56.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM56.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM57.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM57.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM58.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM58.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM59.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM59.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM60.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM60.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM61.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM61.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM62.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM62.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM63.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM63.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM64.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM64.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM65.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM65.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM66.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM66.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM67.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM67.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM68.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM68.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM69.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM69.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM70.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM70.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM71.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM71.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM72.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM72.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM73.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM73.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM74.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM74.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM75.Folmer_forward.fasta, oligos=FolmerF.oligos, qfile=MM75.Folmer_forward.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)

trim.seqs(fasta=MM2.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM2.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM1.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM1.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM3.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM3.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM4.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM4.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM5.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM5.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM6.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM6.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM7.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM7.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM8.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM8.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM9.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM9.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM10.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM10.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM11.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM11.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM12.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM12.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM13.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM13.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM14.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM14.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM15.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM15.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM16.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM16.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM17.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM17.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM18.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM18.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM19.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM19.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM20.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM20.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM21.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM21.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM22.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM22.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM23.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM23.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM24.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM24.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM25.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM25.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM26.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM26.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM27.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM27.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM28.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM28.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM29.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM29.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM30.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM30.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM31.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM31.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM32.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM32.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM33.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM33.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM34.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM34.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM35.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM35.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM36.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM36.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM37.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM37.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM38.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM38.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM39.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM39.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM40.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM40.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM41.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM41.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM42.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM42.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM43.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM43.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM44.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM44.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM45.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM45.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM46.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM46.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM47.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM47.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM48.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM48.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM49.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM49.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM50.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM50.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM51.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM51.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM52.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM52.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM53.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM53.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM54.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM54.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM55.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM55.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM56.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM56.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM57.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM57.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM58.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM58.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM59.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM59.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM60.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM60.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM61.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM61.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM62.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM62.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM63.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM63.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM64.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM64.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM65.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM65.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM66.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM66.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM67.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM67.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM68.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM68.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM69.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM69.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM70.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM70.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM71.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM71.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM72.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM72.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM73.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM73.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM74.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM74.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)
trim.seqs(fasta=MM75.Folmer_reverse.fasta, oligos=FolmerR.oligos, qfile=MM75.Folmer_reverse.qual, maxambig=0, maxhomop=12, pdiffs=0, minlength=200, qwindowaverage=30, qwindowsize=30, processors=2)

usearch -derep_fulllength MM72.Folmer_forward.trim.fasta -relabel MM72. -fastaout MM72.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM71.Folmer_forward.trim.fasta -relabel MM71. -fastaout MM71.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM70.Folmer_forward.trim.fasta -relabel MM70. -fastaout MM70.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM69.Folmer_forward.trim.fasta -relabel MM69. -fastaout MM69.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM68.Folmer_forward.trim.fasta -relabel MM68. -fastaout MM68.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM67.Folmer_forward.trim.fasta -relabel MM67. -fastaout MM67.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM66.Folmer_forward.trim.fasta -relabel MM66. -fastaout MM66.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM65.Folmer_forward.trim.fasta -relabel MM65. -fastaout MM65.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM64.Folmer_forward.trim.fasta -relabel MM64. -fastaout MM64.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM63.Folmer_forward.trim.fasta -relabel MM63. -fastaout MM63.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM62.Folmer_forward.trim.fasta -relabel MM62. -fastaout MM62.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM61.Folmer_forward.trim.fasta -relabel MM61. -fastaout MM61.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM73.Folmer_forward.trim.fasta -relabel MM73. -fastaout MM73.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM74.Folmer_forward.trim.fasta -relabel MM74. -fastaout MM74.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM75.Folmer_forward.trim.fasta -relabel MM75. -fastaout MM75.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM60.Folmer_forward.trim.fasta -relabel MM60. -fastaout MM60.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM59.Folmer_forward.trim.fasta -relabel MM59. -fastaout MM59.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM58.Folmer_forward.trim.fasta -relabel MM58. -fastaout MM58.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM57.Folmer_forward.trim.fasta -relabel MM57. -fastaout MM57.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM56.Folmer_forward.trim.fasta -relabel MM56. -fastaout MM56.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM55.Folmer_forward.trim.fasta -relabel MM55. -fastaout MM55.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM54.Folmer_forward.trim.fasta -relabel MM54. -fastaout MM54.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM53.Folmer_forward.trim.fasta -relabel MM53. -fastaout MM53.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM52.Folmer_forward.trim.fasta -relabel MM52. -fastaout MM52.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM51.Folmer_forward.trim.fasta -relabel MM51. -fastaout MM51.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM50.Folmer_forward.trim.fasta -relabel MM50. -fastaout MM50.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM49.Folmer_forward.trim.fasta -relabel MM49. -fastaout MM49.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM48.Folmer_forward.trim.fasta -relabel MM48. -fastaout MM48.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM47.Folmer_forward.trim.fasta -relabel MM47. -fastaout MM47.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM46.Folmer_forward.trim.fasta -relabel MM46. -fastaout MM46.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM45.Folmer_forward.trim.fasta -relabel MM45. -fastaout MM45.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM44.Folmer_forward.trim.fasta -relabel MM44. -fastaout MM44.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM43.Folmer_forward.trim.fasta -relabel MM43. -fastaout MM43.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM42.Folmer_forward.trim.fasta -relabel MM42. -fastaout MM42.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM41.Folmer_forward.trim.fasta -relabel MM41. -fastaout MM41.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM40.Folmer_forward.trim.fasta -relabel MM40. -fastaout MM40.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM39.Folmer_forward.trim.fasta -relabel MM39. -fastaout MM39.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM38.Folmer_forward.trim.fasta -relabel MM38. -fastaout MM38.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM37.Folmer_forward.trim.fasta -relabel MM37. -fastaout MM37.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM36.Folmer_forward.trim.fasta -relabel MM36. -fastaout MM36.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM35.Folmer_forward.trim.fasta -relabel MM35. -fastaout MM35.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM34.Folmer_forward.trim.fasta -relabel MM34. -fastaout MM34.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM33.Folmer_forward.trim.fasta -relabel MM33. -fastaout MM33.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM32.Folmer_forward.trim.fasta -relabel MM32. -fastaout MM32.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM31.Folmer_forward.trim.fasta -relabel MM31. -fastaout MM31.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM30.Folmer_forward.trim.fasta -relabel MM30. -fastaout MM30.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM29.Folmer_forward.trim.fasta -relabel MM29. -fastaout MM29.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM28.Folmer_forward.trim.fasta -relabel MM28. -fastaout MM28.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM27.Folmer_forward.trim.fasta -relabel MM27. -fastaout MM27.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM26.Folmer_forward.trim.fasta -relabel MM26. -fastaout MM26.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM25.Folmer_forward.trim.fasta -relabel MM25. -fastaout MM25.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM24.Folmer_forward.trim.fasta -relabel MM24. -fastaout MM24.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM23.Folmer_forward.trim.fasta -relabel MM23. -fastaout MM23.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM22.Folmer_forward.trim.fasta -relabel MM22. -fastaout MM22.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM21.Folmer_forward.trim.fasta -relabel MM21. -fastaout MM21.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM20.Folmer_forward.trim.fasta -relabel MM20. -fastaout MM20.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM19.Folmer_forward.trim.fasta -relabel MM19. -fastaout MM19.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM18.Folmer_forward.trim.fasta -relabel MM18. -fastaout MM18.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM17.Folmer_forward.trim.fasta -relabel MM17. -fastaout MM17.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM16.Folmer_forward.trim.fasta -relabel MM16. -fastaout MM16.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM15.Folmer_forward.trim.fasta -relabel MM15. -fastaout MM15.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM14.Folmer_forward.trim.fasta -relabel MM14. -fastaout MM14.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM13.Folmer_forward.trim.fasta -relabel MM13. -fastaout MM13.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM12.Folmer_forward.trim.fasta -relabel MM12. -fastaout MM12.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM11.Folmer_forward.trim.fasta -relabel MM11. -fastaout MM11.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM10.Folmer_forward.trim.fasta -relabel MM10. -fastaout MM10.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM9.Folmer_forward.trim.fasta -relabel MM9. -fastaout MM9.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM8.Folmer_forward.trim.fasta -relabel MM8. -fastaout MM8.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM7.Folmer_forward.trim.fasta -relabel MM7. -fastaout MM7.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM6.Folmer_forward.trim.fasta -relabel MM6. -fastaout MM6.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM5.Folmer_forward.trim.fasta -relabel MM5. -fastaout MM5.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM4.Folmer_forward.trim.fasta -relabel MM4. -fastaout MM4.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM3.Folmer_forward.trim.fasta -relabel MM3. -fastaout MM3.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM2.Folmer_forward.trim.fasta -relabel MM2. -fastaout MM2.Folmer_forward_uniques.fasta -sizeout
usearch -derep_fulllength MM1.Folmer_forward.trim.fasta -relabel MM1. -fastaout MM1.Folmer_forward_uniques.fasta -sizeout

usearch -derep_fulllength MM72.Folmer_reverse.trim.fasta -relabel MM72. -fastaout MM72.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM71.Folmer_reverse.trim.fasta -relabel MM71. -fastaout MM71.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM70.Folmer_reverse.trim.fasta -relabel MM70. -fastaout MM70.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM69.Folmer_reverse.trim.fasta -relabel MM69. -fastaout MM69.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM68.Folmer_reverse.trim.fasta -relabel MM68. -fastaout MM68.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM67.Folmer_reverse.trim.fasta -relabel MM67. -fastaout MM67.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM66.Folmer_reverse.trim.fasta -relabel MM66. -fastaout MM66.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM65.Folmer_reverse.trim.fasta -relabel MM65. -fastaout MM65.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM64.Folmer_reverse.trim.fasta -relabel MM64. -fastaout MM64.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM63.Folmer_reverse.trim.fasta -relabel MM63. -fastaout MM63.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM62.Folmer_reverse.trim.fasta -relabel MM62. -fastaout MM62.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM61.Folmer_reverse.trim.fasta -relabel MM61. -fastaout MM61.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM73.Folmer_reverse.trim.fasta -relabel MM73. -fastaout MM73.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM74.Folmer_reverse.trim.fasta -relabel MM74. -fastaout MM74.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM75.Folmer_reverse.trim.fasta -relabel MM75. -fastaout MM75.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM60.Folmer_reverse.trim.fasta -relabel MM60. -fastaout MM60.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM59.Folmer_reverse.trim.fasta -relabel MM59. -fastaout MM59.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM58.Folmer_reverse.trim.fasta -relabel MM58. -fastaout MM58.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM57.Folmer_reverse.trim.fasta -relabel MM57. -fastaout MM57.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM56.Folmer_reverse.trim.fasta -relabel MM56. -fastaout MM56.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM55.Folmer_reverse.trim.fasta -relabel MM55. -fastaout MM55.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM54.Folmer_reverse.trim.fasta -relabel MM54. -fastaout MM54.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM53.Folmer_reverse.trim.fasta -relabel MM53. -fastaout MM53.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM52.Folmer_reverse.trim.fasta -relabel MM52. -fastaout MM52.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM51.Folmer_reverse.trim.fasta -relabel MM51. -fastaout MM51.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM50.Folmer_reverse.trim.fasta -relabel MM50. -fastaout MM50.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM49.Folmer_reverse.trim.fasta -relabel MM49. -fastaout MM49.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM48.Folmer_reverse.trim.fasta -relabel MM48. -fastaout MM48.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM47.Folmer_reverse.trim.fasta -relabel MM47. -fastaout MM47.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM46.Folmer_reverse.trim.fasta -relabel MM46. -fastaout MM46.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM45.Folmer_reverse.trim.fasta -relabel MM45. -fastaout MM45.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM44.Folmer_reverse.trim.fasta -relabel MM44. -fastaout MM44.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM43.Folmer_reverse.trim.fasta -relabel MM43. -fastaout MM43.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM42.Folmer_reverse.trim.fasta -relabel MM42. -fastaout MM42.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM41.Folmer_reverse.trim.fasta -relabel MM41. -fastaout MM41.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM40.Folmer_reverse.trim.fasta -relabel MM40. -fastaout MM40.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM39.Folmer_reverse.trim.fasta -relabel MM39. -fastaout MM39.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM38.Folmer_reverse.trim.fasta -relabel MM38. -fastaout MM38.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM37.Folmer_reverse.trim.fasta -relabel MM37. -fastaout MM37.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM36.Folmer_reverse.trim.fasta -relabel MM36. -fastaout MM36.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM35.Folmer_reverse.trim.fasta -relabel MM35. -fastaout MM35.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM34.Folmer_reverse.trim.fasta -relabel MM34. -fastaout MM34.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM33.Folmer_reverse.trim.fasta -relabel MM33. -fastaout MM33.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM32.Folmer_reverse.trim.fasta -relabel MM32. -fastaout MM32.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM31.Folmer_reverse.trim.fasta -relabel MM31. -fastaout MM31.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM30.Folmer_reverse.trim.fasta -relabel MM30. -fastaout MM30.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM29.Folmer_reverse.trim.fasta -relabel MM29. -fastaout MM29.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM28.Folmer_reverse.trim.fasta -relabel MM28. -fastaout MM28.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM27.Folmer_reverse.trim.fasta -relabel MM27. -fastaout MM27.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM26.Folmer_reverse.trim.fasta -relabel MM26. -fastaout MM26.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM25.Folmer_reverse.trim.fasta -relabel MM25. -fastaout MM25.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM24.Folmer_reverse.trim.fasta -relabel MM24. -fastaout MM24.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM23.Folmer_reverse.trim.fasta -relabel MM23. -fastaout MM23.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM22.Folmer_reverse.trim.fasta -relabel MM22. -fastaout MM22.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM21.Folmer_reverse.trim.fasta -relabel MM21. -fastaout MM21.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM20.Folmer_reverse.trim.fasta -relabel MM20. -fastaout MM20.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM19.Folmer_reverse.trim.fasta -relabel MM19. -fastaout MM19.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM18.Folmer_reverse.trim.fasta -relabel MM18. -fastaout MM18.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM17.Folmer_reverse.trim.fasta -relabel MM17. -fastaout MM17.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM16.Folmer_reverse.trim.fasta -relabel MM16. -fastaout MM16.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM15.Folmer_reverse.trim.fasta -relabel MM15. -fastaout MM15.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM14.Folmer_reverse.trim.fasta -relabel MM14. -fastaout MM14.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM13.Folmer_reverse.trim.fasta -relabel MM13. -fastaout MM13.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM12.Folmer_reverse.trim.fasta -relabel MM12. -fastaout MM12.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM11.Folmer_reverse.trim.fasta -relabel MM11. -fastaout MM11.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM10.Folmer_reverse.trim.fasta -relabel MM10. -fastaout MM10.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM9.Folmer_reverse.trim.fasta -relabel MM9. -fastaout MM9.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM8.Folmer_reverse.trim.fasta -relabel MM8. -fastaout MM8.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM7.Folmer_reverse.trim.fasta -relabel MM7. -fastaout MM7.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM6.Folmer_reverse.trim.fasta -relabel MM6. -fastaout MM6.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM5.Folmer_reverse.trim.fasta -relabel MM5. -fastaout MM5.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM4.Folmer_reverse.trim.fasta -relabel MM4. -fastaout MM4.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM3.Folmer_reverse.trim.fasta -relabel MM3. -fastaout MM3.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM2.Folmer_reverse.trim.fasta -relabel MM2. -fastaout MM2.Folmer_reverse_uniques.fasta -sizeout
usearch -derep_fulllength MM1.Folmer_reverse.trim.fasta -relabel MM1. -fastaout MM1.Folmer_reverse_uniques.fasta -sizeout

usearch -cluster_otus MM72.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM72.Folmer_forward_otus.fa
usearch -cluster_otus MM71.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM71.Folmer_forward_otus.fa
usearch -cluster_otus MM70.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM70.Folmer_forward_otus.fa
usearch -cluster_otus MM69.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM69.Folmer_forward_otus.fa
usearch -cluster_otus MM68.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM68.Folmer_forward_otus.fa
usearch -cluster_otus MM67.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM67.Folmer_forward_otus.fa
usearch -cluster_otus MM66.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM66.Folmer_forward_otus.fa
usearch -cluster_otus MM65.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM65.Folmer_forward_otus.fa
usearch -cluster_otus MM64.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM64.Folmer_forward_otus.fa
usearch -cluster_otus MM63.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM63.Folmer_forward_otus.fa
usearch -cluster_otus MM62.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM62.Folmer_forward_otus.fa
usearch -cluster_otus MM61.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM61.Folmer_forward_otus.fa
usearch -cluster_otus MM73.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM73.Folmer_forward_otus.fa
usearch -cluster_otus MM74.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM74.Folmer_forward_otus.fa
usearch -cluster_otus MM75.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM75.Folmer_forward_otus.fa
usearch -cluster_otus MM60.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM60.Folmer_forward_otus.fa
usearch -cluster_otus MM59.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM59.Folmer_forward_otus.fa
usearch -cluster_otus MM58.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM58.Folmer_forward_otus.fa
usearch -cluster_otus MM57.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM57.Folmer_forward_otus.fa
usearch -cluster_otus MM56.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM56.Folmer_forward_otus.fa
usearch -cluster_otus MM55.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM55.Folmer_forward_otus.fa
usearch -cluster_otus MM54.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM54.Folmer_forward_otus.fa
usearch -cluster_otus MM53.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM53.Folmer_forward_otus.fa
usearch -cluster_otus MM52.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM52.Folmer_forward_otus.fa
usearch -cluster_otus MM51.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM51.Folmer_forward_otus.fa
usearch -cluster_otus MM50.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM50.Folmer_forward_otus.fa
usearch -cluster_otus MM49.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM49.Folmer_forward_otus.fa
usearch -cluster_otus MM48.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM48.Folmer_forward_otus.fa
usearch -cluster_otus MM47.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM47.Folmer_forward_otus.fa
usearch -cluster_otus MM46.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM46.Folmer_forward_otus.fa
usearch -cluster_otus MM45.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM45.Folmer_forward_otus.fa
usearch -cluster_otus MM44.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM44.Folmer_forward_otus.fa
usearch -cluster_otus MM43.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM43.Folmer_forward_otus.fa
usearch -cluster_otus MM42.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM42.Folmer_forward_otus.fa
usearch -cluster_otus MM41.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM41.Folmer_forward_otus.fa
usearch -cluster_otus MM40.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM40.Folmer_forward_otus.fa
usearch -cluster_otus MM39.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM39.Folmer_forward_otus.fa
usearch -cluster_otus MM38.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM38.Folmer_forward_otus.fa
usearch -cluster_otus MM37.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM37.Folmer_forward_otus.fa
usearch -cluster_otus MM36.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM36.Folmer_forward_otus.fa
usearch -cluster_otus MM35.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM35.Folmer_forward_otus.fa
usearch -cluster_otus MM34.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM34.Folmer_forward_otus.fa
usearch -cluster_otus MM33.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM33.Folmer_forward_otus.fa
usearch -cluster_otus MM32.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM32.Folmer_forward_otus.fa
usearch -cluster_otus MM31.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM31.Folmer_forward_otus.fa
usearch -cluster_otus MM30.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM30.Folmer_forward_otus.fa
usearch -cluster_otus MM29.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM29.Folmer_forward_otus.fa
usearch -cluster_otus MM28.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM28.Folmer_forward_otus.fa
usearch -cluster_otus MM27.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM27.Folmer_forward_otus.fa
usearch -cluster_otus MM26.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM26.Folmer_forward_otus.fa
usearch -cluster_otus MM25.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM25.Folmer_forward_otus.fa
usearch -cluster_otus MM24.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM24.Folmer_forward_otus.fa
usearch -cluster_otus MM23.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM23.Folmer_forward_otus.fa
usearch -cluster_otus MM22.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM22.Folmer_forward_otus.fa
usearch -cluster_otus MM21.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM21.Folmer_forward_otus.fa
usearch -cluster_otus MM20.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM20.Folmer_forward_otus.fa
usearch -cluster_otus MM19.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM19.Folmer_forward_otus.fa
usearch -cluster_otus MM18.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM18.Folmer_forward_otus.fa
usearch -cluster_otus MM17.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM17.Folmer_forward_otus.fa
usearch -cluster_otus MM16.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM16.Folmer_forward_otus.fa
usearch -cluster_otus MM15.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM15.Folmer_forward_otus.fa
usearch -cluster_otus MM14.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM14.Folmer_forward_otus.fa
usearch -cluster_otus MM13.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM13.Folmer_forward_otus.fa
usearch -cluster_otus MM12.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM12.Folmer_forward_otus.fa
usearch -cluster_otus MM11.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM11.Folmer_forward_otus.fa
usearch -cluster_otus MM10.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM10.Folmer_forward_otus.fa
usearch -cluster_otus MM9.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM9.Folmer_forward_otus.fa
usearch -cluster_otus MM8.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM8.Folmer_forward_otus.fa
usearch -cluster_otus MM7.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM7.Folmer_forward_otus.fa
usearch -cluster_otus MM6.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM6.Folmer_forward_otus.fa
usearch -cluster_otus MM5.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM5.Folmer_forward_otus.fa
usearch -cluster_otus MM4.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM4.Folmer_forward_otus.fa
usearch -cluster_otus MM3.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM3.Folmer_forward_otus.fa
usearch -cluster_otus MM2.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM2.Folmer_forward_otus.fa
usearch -cluster_otus MM1.Folmer_forward_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM1.Folmer_forward_otus.fa

usearch -cluster_otus MM72.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM72.Folmer_reverse_otus.fa
usearch -cluster_otus MM71.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM71.Folmer_reverse_otus.fa
usearch -cluster_otus MM70.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM70.Folmer_reverse_otus.fa
usearch -cluster_otus MM69.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM69.Folmer_reverse_otus.fa
usearch -cluster_otus MM68.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM68.Folmer_reverse_otus.fa
usearch -cluster_otus MM67.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM67.Folmer_reverse_otus.fa
usearch -cluster_otus MM66.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM66.Folmer_reverse_otus.fa
usearch -cluster_otus MM65.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM65.Folmer_reverse_otus.fa
usearch -cluster_otus MM64.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM64.Folmer_reverse_otus.fa
usearch -cluster_otus MM63.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM63.Folmer_reverse_otus.fa
usearch -cluster_otus MM62.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM62.Folmer_reverse_otus.fa
usearch -cluster_otus MM61.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM61.Folmer_reverse_otus.fa
usearch -cluster_otus MM73.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM73.Folmer_reverse_otus.fa
usearch -cluster_otus MM74.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM74.Folmer_reverse_otus.fa
usearch -cluster_otus MM75.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM75.Folmer_reverse_otus.fa
usearch -cluster_otus MM60.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM60.Folmer_reverse_otus.fa
usearch -cluster_otus MM59.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM59.Folmer_reverse_otus.fa
usearch -cluster_otus MM58.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM58.Folmer_reverse_otus.fa
usearch -cluster_otus MM57.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM57.Folmer_reverse_otus.fa
usearch -cluster_otus MM56.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM56.Folmer_reverse_otus.fa
usearch -cluster_otus MM55.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM55.Folmer_reverse_otus.fa
usearch -cluster_otus MM54.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM54.Folmer_reverse_otus.fa
usearch -cluster_otus MM53.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM53.Folmer_reverse_otus.fa
usearch -cluster_otus MM52.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM52.Folmer_reverse_otus.fa
usearch -cluster_otus MM51.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM51.Folmer_reverse_otus.fa
usearch -cluster_otus MM50.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM50.Folmer_reverse_otus.fa
usearch -cluster_otus MM49.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM49.Folmer_reverse_otus.fa
usearch -cluster_otus MM48.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM48.Folmer_reverse_otus.fa
usearch -cluster_otus MM47.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM47.Folmer_reverse_otus.fa
usearch -cluster_otus MM46.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM46.Folmer_reverse_otus.fa
usearch -cluster_otus MM45.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM45.Folmer_reverse_otus.fa
usearch -cluster_otus MM44.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM44.Folmer_reverse_otus.fa
usearch -cluster_otus MM43.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM43.Folmer_reverse_otus.fa
usearch -cluster_otus MM42.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM42.Folmer_reverse_otus.fa
usearch -cluster_otus MM41.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM41.Folmer_reverse_otus.fa
usearch -cluster_otus MM40.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM40.Folmer_reverse_otus.fa
usearch -cluster_otus MM39.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM39.Folmer_reverse_otus.fa
usearch -cluster_otus MM38.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM38.Folmer_reverse_otus.fa
usearch -cluster_otus MM37.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM37.Folmer_reverse_otus.fa
usearch -cluster_otus MM36.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM36.Folmer_reverse_otus.fa
usearch -cluster_otus MM35.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM35.Folmer_reverse_otus.fa
usearch -cluster_otus MM34.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM34.Folmer_reverse_otus.fa
usearch -cluster_otus MM33.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM33.Folmer_reverse_otus.fa
usearch -cluster_otus MM32.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM32.Folmer_reverse_otus.fa
usearch -cluster_otus MM31.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM31.Folmer_reverse_otus.fa
usearch -cluster_otus MM30.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM30.Folmer_reverse_otus.fa
usearch -cluster_otus MM29.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM29.Folmer_reverse_otus.fa
usearch -cluster_otus MM28.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM28.Folmer_reverse_otus.fa
usearch -cluster_otus MM27.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM27.Folmer_reverse_otus.fa
usearch -cluster_otus MM26.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM26.Folmer_reverse_otus.fa
usearch -cluster_otus MM25.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM25.Folmer_reverse_otus.fa
usearch -cluster_otus MM24.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM24.Folmer_reverse_otus.fa
usearch -cluster_otus MM23.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM23.Folmer_reverse_otus.fa
usearch -cluster_otus MM22.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM22.Folmer_reverse_otus.fa
usearch -cluster_otus MM21.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM21.Folmer_reverse_otus.fa
usearch -cluster_otus MM20.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM20.Folmer_reverse_otus.fa
usearch -cluster_otus MM19.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM19.Folmer_reverse_otus.fa
usearch -cluster_otus MM18.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM18.Folmer_reverse_otus.fa
usearch -cluster_otus MM17.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM17.Folmer_reverse_otus.fa
usearch -cluster_otus MM16.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM16.Folmer_reverse_otus.fa
usearch -cluster_otus MM15.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM15.Folmer_reverse_otus.fa
usearch -cluster_otus MM14.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM14.Folmer_reverse_otus.fa
usearch -cluster_otus MM13.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM13.Folmer_reverse_otus.fa
usearch -cluster_otus MM12.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM12.Folmer_reverse_otus.fa
usearch -cluster_otus MM11.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM11.Folmer_reverse_otus.fa
usearch -cluster_otus MM10.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM10.Folmer_reverse_otus.fa
usearch -cluster_otus MM9.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM9.Folmer_reverse_otus.fa
usearch -cluster_otus MM8.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM8.Folmer_reverse_otus.fa
usearch -cluster_otus MM7.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM7.Folmer_reverse_otus.fa
usearch -cluster_otus MM6.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM6.Folmer_reverse_otus.fa
usearch -cluster_otus MM5.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM5.Folmer_reverse_otus.fa
usearch -cluster_otus MM4.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM4.Folmer_reverse_otus.fa
usearch -cluster_otus MM3.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM3.Folmer_reverse_otus.fa
usearch -cluster_otus MM2.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM2.Folmer_reverse_otus.fa
usearch -cluster_otus MM1.Folmer_reverse_uniques.fasta -sizein -minsize 1 -otu_radius_pct 2.0 -sizeout -otus MM1.Folmer_reverse_otus.fa

mothur> merge.files(input=MM61.Folmer_forward_otus.fa-MM62.Folmer_forward_otus.fa-MM63.Folmer_forward_otus.fa-MM64.Folmer_forward_otus.fa-MM65.Folmer_forward_otus.fa-MM66.Folmer_forward_otus.fa-MM67.Folmer_forward_otus.fa-MM68.Folmer_forward_otus.fa-MM69.Folmer_forward_otus.fa-MM70.Folmer_forward_otus.fa-MM71.Folmer_forward_otus.fa-MM72.Folmer_forward_otus.fa-MM74.Folmer_forward_otus.fa-MM75.Folmer_forward_otus.fa-MM60.Folmer_forward_otus.fa-MM59.Folmer_forward_otus.fa-MM58.Folmer_forward_otus.fa-MM57.Folmer_forward_otus.fa-MM56.Folmer_forward_otus.fa-MM55.Folmer_forward_otus.fa-MM54.Folmer_forward_otus.fa-MM53.Folmer_forward_otus.fa-MM52.Folmer_forward_otus.fa-MM51.Folmer_forward_otus.fa-MM50.Folmer_forward_otus.fa-MM49.Folmer_forward_otus.fa-MM48.Folmer_forward_otus.fa-MM47.Folmer_forward_otus.fa-MM46.Folmer_forward_otus.fa-MM45.Folmer_forward_otus.fa-MM44.Folmer_forward_otus.fa-MM43.Folmer_forward_otus.fa-MM42.Folmer_forward_otus.fa-MM41.Folmer_forward_otus.fa-MM40.Folmer_forward_otus.fa-MM39.Folmer_forward_otus.fa-MM38.Folmer_forward_otus.fa-MM37.Folmer_forward_otus.fa-MM36.Folmer_forward_otus.fa-MM35.Folmer_forward_otus.fa-MM34.Folmer_forward_otus.fa-MM33.Folmer_forward_otus.fa-MM32.Folmer_forward_otus.fa-MM31.Folmer_forward_otus.fa-MM30.Folmer_forward_otus.fa-MM29.Folmer_forward_otus.fa-MM28.Folmer_forward_otus.fa-MM27.Folmer_forward_otus.fa-MM26.Folmer_forward_otus.fa-MM25.Folmer_forward_otus.fa-MM24.Folmer_forward_otus.fa-MM23.Folmer_forward_otus.fa-MM22.Folmer_forward_otus.fa-MM21.Folmer_forward_otus.fa-MM20.Folmer_forward_otus.fa-MM19.Folmer_forward_otus.fa-MM18.Folmer_forward_otus.fa-MM17.Folmer_forward_otus.fa-MM16.Folmer_forward_otus.fa-MM15.Folmer_forward_otus.fa-MM14.Folmer_forward_otus.fa-MM13.Folmer_forward_otus.fa-MM12.Folmer_forward_otus.fa-MM11.Folmer_forward_otus.fa-MM10.Folmer_forward_otus.fa-MM9.Folmer_forward_otus.fa-MM8.Folmer_forward_otus.fa-MM7.Folmer_forward_otus.fa-MM6.Folmer_forward_otus.fa-MM5.Folmer_forward_otus.fa-MM4.Folmer_forward_otus.fa-MM3.Folmer_forward_otus.fa-MM2.Folmer_forward_otus.fa-MM1.Folmer_forward_otus.fa, output=otusALL_Folmer_forward.fa)
MM73 no forward reads and excluded.
mothur> merge.files(input=MM61.Folmer_reverse_otus.fa-MM62.Folmer_reverse_otus.fa-MM63.Folmer_reverse_otus.fa-MM64.Folmer_reverse_otus.fa-MM67.Folmer_reverse_otus.fa-MM68.Folmer_reverse_otus.fa-MM69.Folmer_reverse_otus.fa-MM70.Folmer_reverse_otus.fa-MM71.Folmer_reverse_otus.fa-MM72.Folmer_reverse_otus.fa-MM74.Folmer_reverse_otus.fa-MM75.Folmer_reverse_otus.fa-MM60.Folmer_reverse_otus.fa-MM59.Folmer_reverse_otus.fa-MM58.Folmer_reverse_otus.fa-MM57.Folmer_reverse_otus.fa-MM56.Folmer_reverse_otus.fa-MM55.Folmer_reverse_otus.fa-MM54.Folmer_reverse_otus.fa-MM53.Folmer_reverse_otus.fa-MM52.Folmer_reverse_otus.fa-MM51.Folmer_reverse_otus.fa-MM50.Folmer_reverse_otus.fa-MM49.Folmer_reverse_otus.fa-MM48.Folmer_reverse_otus.fa-MM47.Folmer_reverse_otus.fa-MM46.Folmer_reverse_otus.fa-MM45.Folmer_reverse_otus.fa-MM44.Folmer_reverse_otus.fa-MM43.Folmer_reverse_otus.fa-MM42.Folmer_reverse_otus.fa-MM41.Folmer_reverse_otus.fa-MM40.Folmer_reverse_otus.fa-MM39.Folmer_reverse_otus.fa-MM38.Folmer_reverse_otus.fa-MM37.Folmer_reverse_otus.fa-MM36.Folmer_reverse_otus.fa-MM35.Folmer_reverse_otus.fa-MM34.Folmer_reverse_otus.fa-MM33.Folmer_reverse_otus.fa-MM32.Folmer_reverse_otus.fa-MM31.Folmer_reverse_otus.fa-MM30.Folmer_reverse_otus.fa-MM29.Folmer_reverse_otus.fa-MM28.Folmer_reverse_otus.fa-MM27.Folmer_reverse_otus.fa-MM26.Folmer_reverse_otus.fa-MM25.Folmer_reverse_otus.fa-MM24.Folmer_reverse_otus.fa-MM23.Folmer_reverse_otus.fa-MM22.Folmer_reverse_otus.fa-MM21.Folmer_reverse_otus.fa-MM20.Folmer_reverse_otus.fa-MM19.Folmer_reverse_otus.fa-MM18.Folmer_reverse_otus.fa-MM17.Folmer_reverse_otus.fa-MM16.Folmer_reverse_otus.fa-MM15.Folmer_reverse_otus.fa-MM14.Folmer_reverse_otus.fa-MM13.Folmer_reverse_otus.fa-MM12.Folmer_reverse_otus.fa-MM11.Folmer_reverse_otus.fa-MM10.Folmer_reverse_otus.fa-MM9.Folmer_reverse_otus.fa-MM8.Folmer_reverse_otus.fa-MM7.Folmer_reverse_otus.fa-MM6.Folmer_reverse_otus.fa-MM5.Folmer_reverse_otus.fa-MM4.Folmer_reverse_otus.fa-MM3.Folmer_reverse_otus.fa-MM2.Folmer_reverse_otus.fa-MM1.Folmer_reverse_otus.fa, output=otusALL_Folmer_reverse.fa)
MM65, MM66 and MM73 no reverse reads and excluded.

usearch -sortbysize otusALL_Folmer_forward.fa -fastaout otusALL_Folmer_forward_sorted.fa
usearch -sortbysize otusALL_Folmer_reverse.fa -fastaout otusALL_Folmer_reverse_sorted.fa

usearch -cluster_otus otusALL_Folmer_forward_sorted.fa -minsize 1 -otu_radius_pct 3.0 -sizein -otus otusALL_Folmer_forward_sorted_clustered_3.0.fa  -sizeout -log cluster_otusALL_Folmerforwardclustered3.0.log
usearch -cluster_otus otusALL_Folmer_reverse_sorted.fa -minsize 1 -otu_radius_pct 3.0 -sizein -otus otusALL_Folmer_reverse_sorted_clustered_3.0.fa  -sizeout -log cluster_otusALL_Folmerreverseclustered3.0.log

usearch -usearch_global otusALL_Folmer_forward.fa -db otusALL_Folmer_forward_sorted_clustered_3.0.fa -strand plus -id 0.97 -mothur_shared_out otutab_3.0_Folmer_forward.shared
usearch -usearch_global otusALL_Folmer_reverse.fa -db otusALL_Folmer_reverse_sorted_clustered_3.0.fa -strand plus -id 0.97 -mothur_shared_out otutab_3.0_Folmer_reverse.shared

Removed 38 Folmer_forward-OTUs based on their presence only or mainly in negative samples
Removed 12 Folmer_reverse-OTUs based on their presence only or mainly in negative samples

using blast-2.6.0+:
blastn -db nt -query F:\EBAI\Benthics\otusALL_Folmer_forward_sorted_clustered_3.0.negaway.fa -evalue 1e-20 -num_descriptions 100 -num_alignments 100 -out F:\EBAI\Benthics\otusALL_Folmer_forward_sorted_clustered_3.0.taxonomy.txt -remote
blastn -db nt -query F:\EBAI\Benthics\otusALL_Folmer_reverse_sorted_clustered_3.0.negaway.fa -evalue 1e-20 -num_descriptions 100 -num_alignments 100 -out F:\EBAI\Benthics\otusALL_Folmer_reverse_sorted_clustered_3.0.taxonomy.txt -remote

MEGAN 6.7.11:
import otusALL_Folmer_reverse_sorted_clustered_3.0.taxonomy.txt
minimum bit score 100.0 (low because we want all metazoa to be separate)
top percentage 8.0
Minimum support percentage 0.0001
minimum support 1

Total: 567
Not assigned:  0(0.0%)
No hits  36(6.3%)

Export readName_to_taxonPath to files otusALL_Folmer_reverse_sorted_clustered.taxonomy-eukaryota.txt, otusALL_Folmer_reverse_sorted_clustered.taxonomy-bacteria.txt, otusALL_Folmer_reverse_sorted_clustered.taxonomy-notassigned.txt and otusALL_Folmer_reverse_sorted_clustered.taxonomy-nohits.txt (merkkaa no hits-haara ja sit export; merkkaa eukaryota, avaa subtree, select subtree ja sit export)
"-signs removed from the files
Results put together with OTU-table, manually..
422 Metazoa

MEGAN 6.7.11:
import otusALL_Folmer_forward_sorted_clustered_3.0.taxonomy.txt
minimum bit score 100.0 (low because we want all metazoa to be separate)
top percentage 8.0
Minimum support percentage 0.0001
minimum support 1

Total: 1672
Not assigned: 3 (0.02%)
No hits 302 (18.1%)

Export readName_to_taxonPath to files otusALL_Folmer_forward_sorted_clustered.taxonomy-eukaryota.txt, otusALL_Folmer_forward_sorted_clustered.taxonomy-bacteria.txt, otusALL_Folmer_forward_sorted_clustered.taxonomy-notassigned.txt and otusALL_Folmer_forward_sorted_clustered.taxonomy-nohits.txt (merkkaa no hits-haara ja sit export; merkkaa eukaryota, avaa subtree, select subtree ja sit export)
"-signs removed from the files
Results put together with OTU-table, manually..
1008 Metazoa

Since we are interested in Metazoa and monitoring them, we used this data to take out only Metazoa sequences.

mothur > get.seqs(accnos=Folmer_forward_Metazoa.accnos, fasta=otusALL_Folmer_forward_sorted_clustered_3.0.negaway.fa)
output = otusALL_Folmer_forward_sorted_clustered_3.0.negaway.pick.fa, only metazoa sequences

mothur > get.seqs(accnos=Folmer_reverse_Metazoa.accnos, fasta=otusALL_Folmer_reverse_sorted_clustered_3.0.negaway.fa)
output = otusALL_Folmer_reverse_sorted_clustered_3.0.negaway.pick.fa, only metazoa sequences

reverse made reverse compliment: otusALL_Folmer_reverse_sorted_clustered_3.0.negaway.pick.reverscompl.fa, aligned, and cut from beginning.

Can be translated to aminoacids (frame 2,invertebrate mitochondrial) using http://www.bioinformatics.org/sms2/translate.html
otusALL_Folmer_forward_sorted_clustered_3.0.negaway.pick.translated.fa
Can be translated to aminoacids (frame 3,invertebrate mitochondrial) using http://www.bioinformatics.org/sms2/translate.html
otusALL_Folmer_reverse_sorted_clustered_3.0.negaway.pick.translated.fa

Translated aligned using MAFFT online tool and checked for inconsistences (non-COI reads) (mafft muuttanee stop-codonit deleetioksi ellei laita allow any symbol)
otusALL_Folmer_forward_sorted_clustered_3.0.negaway.pick.translated.aligned.fa
218 stop codons
otusALL_Folmer_reverse_sorted_clustered_3.0.negaway.pick.translated.aligned.fa
40 stop codons

we are looking for invertebrates, so I removed all seqs that had stop codons in invertebrate code.
otusALL_Folmer_reverse_sorted_clustered_3.0.negaway.pick.translated.aligned.stopsremoved.fa
otusALL_Folmer_reverse_sorted_clustered_3.0.negaway.pick.translated.aligned.stopsremoved.removed.fa (19 seqs)
mothur > get.seqs(accnos=no_stops_Folmer_reverse.accnos, fasta=otusALL_Folmer_reverse_sorted_clustered_3.0.negaway.pick.fa)
output = otusALL_Folmer_reverse_sorted_clustered_3.0.negaway.pick.pick.fa, stops removed file, 403 seqs left.

otusALL_Folmer_forward_sorted_clustered_3.0.negaway.pick.translated.aligned.stopsremoved.fa
otusALL_Folmer_forward_sorted_clustered_3.0.negaway.pick.translated.aligned.stopsremoved.removed.fa (51 seqs)

good qualitys in otusALL_Folmer_forward_.pick.translated.aligned.stopsremoved.fa checked for non-COIs, those still removed.
no obvious non-CO1s left.

mothur > get.seqs(accnos=no_stops_Folmer_forward.accnos, fasta=otusALL_Folmer_forward_sorted_clustered_3.0.negaway.pick.fa)
output = otusALL_Folmer_forward_sorted_clustered_3.0.negaway.pick.pick.fa, stops removed file, 957 seqs left.

Metazoa blasted against BOLD v.4 Species Level Barcode Records (2,761,675 Sequences/177,412 Species/65,093 Interim Species). Put together.
Reverse made reverse complement before submission.

mothur > get.seqs(accnos=Folmer_forward_nomatch.accnos, fasta=otusALL_Folmer_forward_sorted_clustered_3.0.negaway.pick.pick.fa)
mothur > get.seqs(accnos=Folmer_reverse_nomatch.accnos, fasta=otusALL_Folmer_reverse_sorted_clustered_3.0.negaway.pick.pick.fa)

No match reads blasted against BOLD v.4 all barcode records (4,885,655 Sequences).

We are interested in the identified Metazoa, and only invertebrates; vertebrates excluded. Put together the 4 fragments that have been identified.
Each species name will have only 1 OTU, thus merging OTUs if having the same name.

Abundance threshold: all substracted 5.

1751 OTUs in total in the four fragments. After merging the OTUs (same name within 97%) and removing unidentified OTUs (OTUs not identifed using Species Level Barcode Records and which do not have species-named identity in All Barcode Records), 443 OTUs.

For Normalizations, put all fragments together and calculated minimum number of sequences, 36991 sample MM7.

mothur > sub.sample(shared=F230_BE_FolmerFR_otutab.txt, size=36991)

N of OTUs etc with PAST

Assemblage variation in R Studio:

> library(vegan)
> setwd("F:/EBAI/Benthics")
> getwd()
> Species <- read.csv("Species.csv")
*Species.csv made from subsampled species table without three first rows and then transposed. ";" replaced with "," in csv file.

dis <- vegdist(Species)
## Bray-Curtis distances between samples
groups <- factor(c(rep(1,4), rep(2,4), rep(3,4), rep(4,4), rep(5,4), rep(6,4), rep(7,4), rep(8,4), rep(9,4), rep(10,4), rep(11,4), rep(12,4), rep(13,4), rep(14,4), rep(15,4), rep(16,4), rep(17,4), rep(18,4)), labels = c("HotVoll","QiaVoll","MoVoll","MoSkran","QiaSkran","HotSkran","Mo025","Qia025","Hot025","Mo2","Qia2","Hot2","Mo75","Qia75","Hot75","Mo15","Qia15","Hot15"))
## Calculate multivariate dispersions
mod <- betadisper(dis, groups)
mod

## Draw a boxplot of the distances to centroid for each group
boxplot(mod)
head(mod)
$distances
 [1] 0.491685478 0.520738354 0.565779779 0.551172614 0.591947328 0.560897197 0.584818753 0.640907446 0.456233443 0.473063898 0.313311296 0.373041273 0.238740766 0.113282420
[15] 0.094907627 0.159202471 0.143817377 0.170018816 0.373767930 0.179970598 0.080433203 0.107397091 0.230021131 0.090678332 0.340573656 0.130377661 0.266737065 0.238469402
[29] 0.371647855 0.191611821 0.226239032 0.230262769 0.273885855 0.084066940 0.180638438 0.075383231 0.263144064 0.170358373 0.237343759 0.247871428 0.107728220 0.189007650
[43] 0.219273318 0.093281694 0.175929167 0.013045346 0.225496966 0.099855068 0.116924640 0.049580976 0.095105132 0.050953445 0.108778026 0.089887831 0.079174334 0.111259406
[57] 0.126009152 0.025701435 0.099520318 0.084315014 0.165752709 0.133521046 0.077187883 0.115403690 0.092848530 0.097676348 0.045002266 0.038891717 0.077327231 0.007420977
[71] 0.074749904 0.048000856

dis <- vegdist(Species, binary=TRUE)
## Sørensen distances between samples
groups <- factor(c(rep(1,4), rep(2,4), rep(3,4), rep(4,4), rep(5,4), rep(6,4), rep(7,4), rep(8,4), rep(9,4), rep(10,4), rep(11,4), rep(12,4), rep(13,4), rep(14,4), rep(15,4), rep(16,4), rep(17,4), rep(18,4)), labels = c("HotVoll","QiaVoll","MoVoll","MoSkran","QiaSkran","HotSkran","Mo025","Qia025","Hot025","Mo2","Qia2","Hot2","Mo75","Qia75","Hot75","Mo15","Qia15","Hot15"))
mod <- betadisper(dis, groups)
mod
boxplot(mod)
head(mod)
$distances
 [1] 0.34185070 0.41348615 0.31366410 0.39388003 0.42464688 0.35838006 0.38293048 0.74973790 0.39668639 0.22631124 0.40991635 0.08970125 0.12508977 0.20640161 0.10931582 0.19226374
[17] 0.28499095 0.20529077 0.24866299 0.21039224 0.06471512 0.16852250 0.13369296 0.09598759 0.25098331 0.17801200 0.18389795 0.16927749 0.30081462 0.29826091 0.27254360 0.16426858
[33] 0.08808145 0.07320405 0.11804131 0.15316229 0.24610894 0.17700957 0.11845024 0.17592566 0.17291899 0.27200480 0.13426134 0.17347488 0.06099071 0.06061481 0.11908984 0.05068861
[49] 0.07808178 0.07896330 0.06109428 0.03806708 0.05386107 0.05817444 0.07431871 0.06323147 0.09065703 0.02873119 0.04650581 0.05676454 0.06180107 0.11266764 0.09534289 0.08448904
[65] 0.09821640 0.06475749 0.06033942 0.06970579 0.09546880 0.04992499 0.09324365 0.05006140

Atna Metazoa SampleVal NotSub.txt includes Species Table not subsampled and Atna Metazoa SampleID.txt information about samples for bivariate correlations (Filter=Site, Storage=Extraction).
Bivariate correlations:

install.packages("poilog")
require(poilog)

source("F:/EBAI/Benthics/manuscript/bivariatecorr/Twosample.bivar.comparison.R")

# Tre samfunn - Jonsv.Meta, Atna.Meta og Atna.Id.Meta
temp.Atna.Meta<-read.table("Atna Metazoa SampleVal NotSub.txt",header=T)
temp.Atna.Meta.ID<-read.table("Atna Metazoa SampleID.txt",header=T)
temp.Atna.Meta.ID.Fi<-as.character(temp.Atna.Meta.ID[,2])
temp.Atna.Meta.ID.St<-as.character(temp.Atna.Meta.ID[,3])
temp.Atna.Meta.ID.Sa<-as.integer(temp.Atna.Meta.ID[,4])


temp.A.sample.n<-length(temp.Atna.Meta[1,])-1
temp.A.comb.n<-temp.A.sample.n*(temp.A.sample.n-1)/2
temp.n.sp<-length(temp.Atna.Meta[,1])
temp.Atna.BiCor<-rep(NA,temp.A.comb.n)
temp.Atna.S1.Fi<-rep(NA,temp.A.comb.n) #Filtration sample 1
temp.Atna.S1.St<-rep(NA,temp.A.comb.n) #Storage sample 1
temp.Atna.S1.Sa<-rep(NA,temp.A.comb.n) #Replication (sample) number sample 1
temp.Atna.S1.Sp<-rep(NA,temp.A.comb.n) #Number of species in sample 1
temp.Atna.S1.No<-rep(NA,temp.A.comb.n) #Number of individuals in sample 1
temp.Atna.S2.Fi<-rep(NA,temp.A.comb.n)
temp.Atna.S2.St<-rep(NA,temp.A.comb.n)
temp.Atna.S2.Sa<-rep(NA,temp.A.comb.n)
temp.Atna.S2.Sp<-rep(NA,temp.A.comb.n) 
temp.Atna.S2.No<-rep(NA,temp.A.comb.n) 

temp.Atna.S12.Sp<-rep(NA,temp.A.comb.n) #Number of species in sample 1 and sample 2
temp.Atna.Jacc.pa<-rep(NA,temp.A.comb.n) #Jaccard, pa
temp.Atna.Sor.pa<-rep(NA,temp.A.comb.n) #Sørensen, pa
temp.Atna.Sor.qn<-rep(NA,temp.A.comb.n) #Sørensen, quantitative
temp.Atna.Chao.ab<-rep(NA,temp.A.comb.n) #Chao, abundance based

error_pairs.A <- c()
temp.pair.n<-1

for(i in 1:(temp.A.sample.n-1)){
  for(j in (i+1):temp.A.sample.n){
    #  for(i in 1:3){
    #    for(j in (i+1):4){
    temp.s1<-temp.Atna.Meta[,i+1] #First sample
    temp.s2<-temp.Atna.Meta[,j+1] #Second sample
    temp.Atna.S1.Fi[temp.pair.n]<-temp.Atna.Meta.ID.Fi[i]
    temp.Atna.S1.St[temp.pair.n]<-temp.Atna.Meta.ID.St[i]
    temp.Atna.S1.Sa[temp.pair.n]<-temp.Atna.Meta.ID.Sa[i]
    temp.Atna.S1.Sp[temp.pair.n]<-length(temp.s1[temp.s1>0]) 
    temp.Atna.S1.No[temp.pair.n]<-sum(temp.s1) 
    temp.Atna.S2.Fi[temp.pair.n]<-temp.Atna.Meta.ID.Fi[j]
    temp.Atna.S2.St[temp.pair.n]<-temp.Atna.Meta.ID.St[j]
    temp.Atna.S2.Sa[temp.pair.n]<-temp.Atna.Meta.ID.Sa[j]
    temp.Atna.S2.Sp[temp.pair.n]<-length(temp.s2[temp.s2>0]) 
    temp.Atna.S2.No[temp.pair.n]<-sum(temp.s2) 
    
    temp.s12<-temp.s1+temp.s2
    temp.Atna.S12.Sp[temp.pair.n]<-length(temp.s12[temp.s12>0])
    
    #NBNB: Needs to remove the doble 0's before we run the estimation of the correlation
    temp.s1<-temp.s1[temp.s12>0]
    temp.s2<-temp.s2[temp.s12>0]
    temp.s12<-temp.s12[temp.s12>0]
    
    Twosample.bivar.comparison(sample1=temp.s1,sample2=temp.s2,
                               s1=paste(temp.Atna.Meta.ID.Fi[i],"-",temp.Atna.Meta.ID.St[i],"-",temp.Atna.Meta.ID.Sa[i]),
                               s2=paste(temp.Atna.Meta.ID.Fi[j],"-",temp.Atna.Meta.ID.St[j],"-",temp.Atna.Meta.ID.Sa[j]),
                               tittel="River Atna")
    
    res <- try(bipoilogMLE(temp.s1, temp.s2)) #Correlation from bivariate PoissonLognormal SAD
    if (class(res)=="list"){
      temp.Atna.BiCor[temp.pair.n] <- res$par[5]
    } else{
      res.nm <- try(bipoilogMLE(temp.s1, temp.s2, startVals=c(-1,-1,2,2,0.5),method = "Nelder-Mead"))
      if (class(res.nm)=="list"){
        temp.Atna.BiCor[temp.pair.n] <- res.nm$par[5]
      } else{
        error_pairs.A <- rbind(error_pairs.A, c(i,j))
      }
    }
    print(c(i,j,temp.pair.n))
    print(Sys.time())
    
    #Other similarity indices
    temp.A<-length(temp.s1[temp.s1>0])+length(temp.s2[temp.s2>0])-length(temp.s12[temp.s12>0])
    temp.B<-length(temp.s12[temp.s12>0])-length(temp.s2[temp.s2>0])
    temp.C<-length(temp.s12[temp.s12>0])-length(temp.s1[temp.s1>0])
    temp.Atna.Jacc.pa[temp.pair.n] <- round(temp.A/(temp.A+temp.B+temp.C),4)
    temp.Atna.Sor.pa[temp.pair.n] <- round(2*temp.A/(2*temp.A+temp.B+temp.C),4)
    
    temp<-rep(NA,length(temp.s12))
    for(k in 1:length(temp.s12)) temp[k]<-min(temp.s1[k],temp.s2[k])
    temp.Atna.Sor.qn[temp.pair.n] <- round(2*sum(temp)/(sum(temp.s1)+sum(temp.s2)),4)
    
    n1<-sum(temp.s1)
    n2<-sum(temp.s2)
    
    sam.shared.12<-cbind(temp.s1,temp.s2)
    D.12<-sam.shared.12[temp.s1>0,]
    temp.sam2<-temp.s2[temp.s1>0]
    D.12<-D.12[temp.sam2>0,]
    temp.d1<-D.12[,1]
    temp.d2<-D.12[,2]
    f.1p<-length(temp.d1[temp.d1==1])
    f.2p<-length(temp.d1[temp.d1==2])
    if(f.2p==0)	f.2p<-1
    f.p1<-length(temp.d2[temp.d2==1])
    f.p2<-length(temp.d2[temp.d2==2])
    if(f.p2==0)	f.p2<-1
    
    U.hat<-sum(temp.d1/n1)+(n2-1)/n2*f.p1/(2*f.p2)*sum(temp.d1[temp.d2==1]/n1)
    if(U.hat>1)	U.hat<-1
    V.hat<-sum(temp.d2/n2)+(n1-1)/n1*f.1p/(2*f.2p)*sum(temp.d2[temp.d1==1]/n2)
    if(V.hat>1)	V.hat<-1
    
    temp.Atna.Chao.ab[temp.pair.n]<-round((2*U.hat*V.hat/(U.hat+V.hat)),4)	#Chao's Sørensen abundance-based
    
    
    temp.pair.n<-temp.pair.n+1
  }
}

temp.Atna.Sim<-data.frame(Sam1.Filt=temp.Atna.S1.Fi,Sam1.Stor=temp.Atna.S1.St,Sam1.Samp=temp.Atna.S1.Sa,
                          Sam1.Species=temp.Atna.S1.Sp,Sam1.no.Ind=temp.Atna.S1.No,
                          Sam2.Filt=temp.Atna.S2.Fi,Sam2.Stor=temp.Atna.S2.St,Sam2.Samp=temp.Atna.S2.Sa,
                          Sam2.Species=temp.Atna.S2.Sp,Sam2.no.Ind=temp.Atna.S2.No,
                          Sam1and2.Species=temp.Atna.S12.Sp,Bivr.Corr=temp.Atna.BiCor,
                          Jaccard.pa=temp.Atna.Jacc.pa,Sorens.pa=temp.Atna.Sor.pa,
                          Sorens.quant=temp.Atna.Sor.qn,Chao.ab=temp.Atna.Chao.ab)

write.table(temp.Atna.Sim,"Atna.Similarity.txt")


##########################################################


setwd("F:/EBAI/Benthics/manuscript/ForSubmissionMBMG/Revision/BaselgaMethod")
library("betapart", lib.loc="~/R/win-library/3.5")
hot2<-read.table(file="15hot2.txt", header=T)
beta.pair(hot2, index.family="sorensen")