added Shell examples

Shell-examples/441E-590.fasta

+>441E-590 Nov_16c-2001/Nov16c/441E-590.SEQ trimmed
+CTCCACGCGGTGGCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCGGCA
+CGAGGCGTCGACGTTCTACGACACGTCGTGCCCCAGGGCTCTGGCCACCATCAAGAGCGG
+CGTGGCGGCAGCCGTGAGCAGCGATCCCCGCATGGGCGCCTCCCTGCTCAGGCTGCACTT
+CCACGACTGCTTTGTCCAAGGCTGTGACGCGTCTGTTCTTCTGTCCGGCATGGAACAAAA
+CGCGGGTCCGAACGTGGGGTCGCTGAGGGGCTTCGGCGTCATCGACAACATCAAGACCCA
+GCTGGAGAGTATATGCAAGCAGACCGTCTCCTGCGCCGACATCCTCACCGTCGCCGCCCG
+CGACTCCGTTGTCGCCCTTGGAGGGCCATCGTGGACTGTCCCGCTGGGGAGACGGGACTC
+CACCACCGCAAGTGCCTCGCTGGCGAACAGTGACCTCCCTGGCCCGAGCTCTAGCCGGTC
+ACAGCTCGAGGCCGCGTTCCTCAAGAAGAACCTTAACACGGTCGACATGGTCGCGCTCTC
+AGGCGCGCACCACATCGGGAAGNCCAGTGCTCCAACTTTCGGACTCGGATCTACGGGGGT
+GACAACAACATCAAACACTGGCTTCCGACGTCTCTCAAGGNCAAACTGCCCCCCAGTCCC
+GGGGGGCAAACAACCAAACCTTGGNCGNAACCNTGGGAACACNNANCGAACGCCCCCAAA
+NGGCGTTTTCNGAACAAAACGGCCCTTNACTTNCAACCCAAAACCCTTCCCTTGGTCAAC
+AAAAAAAAAANGGGGGNTTCCCCTTGGGNAACTTCGNGGAAANCCAAANGGNGGGGTTTC
+TTTTAAAAACAAAC

Shell-examples/441E-620.fasta

+>441E-620 Nov_16c-2001/Nov16c/441E-620.SEQ
+CGCGGTGGTGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCGGCACGAGG
+AGCAATCCTTACGGTGAAAGAACACACTGAGCCTACGTACGTAGCTAGATAGATTTGTGA
+GCCATGGCTTCCAGCTCTGGCTGTAGGGCCTGGCATTGCTTGCTTGCCCTCTTCCTCCTC
+TCCTCTTCCGCGTATGGTCAGCTGTCGCCGTCGTTCTACGCCAAGAGCTGCCCGACGCTG
+CAGCTCATCGTGCGGGCCACCATGATCAAGGCGCTCCTCGCCGAGCGCCGAATGGGCGCC
+TCCCTCCTCAGGCTCCACTTCCACGACTGCTTTGTCCAAGGCTGTGACGGGTCCATTCTC
+TTGGATGACGTGGGTAGCTTCGTTGGCGAGAAGACGGCCTTTCCGAACGTGGATTCGGTG
+CGGGGCTACGAGGTGATCGACGAGATCAAGAAGAACGTGGAGCTGCTCTGCCCTGGCATC
+GTCTCCTGCGCCGACATCGCCGCCCTCGCAGCACGGGACGGCAACTTTCCTGCTAGGCGG
+GGCCCAGCTGGTCGGTGCCGCTCGGCCGCCGGGACTCAAACGACGGCCAGCTTGACTGAG
+GCGAACAGCGACCTCCCGGCGCCAAGCTTAAAGCCTGGGCCCTACTCATCAAAGCGTTCG
+ACAAGAACCAGCCTGAGCCCGCAGGACCTCACTGCGCCTGTCCGGNGCGCAAAACCATCG
+GCTTNTTCCCAATGNCCTCAACTTCCGCGACACATCTAACAACGGCACCCAACAATCGAC
+CCGGGCGNTTCNCCANCCNTGCGCAAAGCGCAACCTGGCCCCGGCCCAGG

Shell-examples/441E1189.fasta

+>441E-1189 wei8feb28/441E1189.SEQ trimmed
+ACTCACGCGGTGGCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCGGCA
+CGAGGCACTCCACCAGTAAAGAAGTGCAGGCAACTAGCTAGCTAACCATGGCCGCCTCTG
+CCTCTTGCATTTCACTGGTGGTGCTCGTGGCTCTGGCCACGGTGGCGTCGGCGCAGCTGT
+CGCCGACGTTCTACGACACGTCGTGCCCCAGGGCCCTGGCCACCATCAAGAGCGGCGTCA
+TGGCCGCCGTGAGCAGCGACCCTCGGATGGGCGCGTCGCTGCTCCGGCTGCACTTCCACG
+ACTGCTTCGTCCAAGGCTGTGACGCGTCTGTTCTGCTGTCTGGCATGGAACAAAACGCTC
+TCCCGAACAACGGGTCACTGCGGGGCTTCGGCGTCATCGACAGCATCAAGACACAGATCG
+AGGCCATCTGCGCCCAGACCGTCTCCTGCGCCGACATCCTCACCGTCGCTGCCCGTGACT
+CCGTCGTCGCCCTCGGAGGGCCATCATGGACAGTCCCTCTGGGAAGAAGGGATTCCATAG
+ATGCAAACGAGGCGGCGGCAAACANCGACCTCCCANGCCCTACGTCTANCCGTTCAGATC
+TTGANCTGGCATTCAGCAACAAGGGCCTCCTTACGGNCGACATGGTGGNCCTCTCCGGCG
+GCGCANACCATCNGNCAAGGCGCANTGNCGGGNANCTTNAAAGGACAAGGATCTTACAAA
+TGGAGACCCAANATTCGACCNACNAACCTTCNGCCCAANTTCTTNTTCCGGGGCCAAAAT
+TGGCCCCCCGG

Shell-examples/441E1197.fasta

+>441E-1197 wei8feb28/441E1197.SEQ trimmed
+CTCACTCGGAGGCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCGGCAC
+GAGGCACCACTCCACCAGTAAAGAAGTGCAGGCAACTAGCTAGCTAACCATGGCCGCCTC
+TGCCTCTTGCATTTCACTGGTGGTGCTCGTGGCTCTGGCCACGGTGGCGTCGGCGCAGCT
+GTCGCCGACGTTCTACGACACGTCGTGCCCCAGGGCCCTGGCCACCATCAAGAGCGGCGT
+CATGGCCGCCGTGAGCAGCGACCCTCGGATGGGCGCGTCGCTGCTCCGGCTGCACTTCCA
+CGACTGCTTCGTCCAAGGCTGTGACGCGTCTGTTCTGCTGTCTGGCATGGAACAAAACGC
+TCTCCCGAACAACGGGTCACTGCGGGGCTTCGGCGTCATCGACAGCATCAAGACACAGAT
+CGAGGCCATCTGCGCCCAGACCGTCTCCTGCGCCGACATCCTCACCGTCGCTGCCCGTGA
+CTCCGTCGTCGCCCTCGGAGGGCCATCATGGACAGTCCCTCTGGGAAGAAGGGATTCCAT
+ANATGNAAACGAGGNGGTGGCAAACAGCGACTCCCAGCCCTACGTCTAGCCGTTCAGATC
+TTGAG

Shell-examples/441E1210.fasta

+>441E-1210 wei8feb28/441E1210.SEQ trimmed
+AAACTGGACTCATCCGGTGGCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAA
+TTCGGCACGAGGAACAAGTGCAGGTAGCACGCATAGCTCTGGTCTTGTAGCTAGGTAGCT
+AACCATGGCCATGGGTTCTGCCTCTCGCATTTCTCTGGTGGTGCTCGTGGCTCTGGCCAC
+GGCGGCGTCCGGGCAGCTGTCGTCGACGTTCTACGACACGTCGTGCCCCAGGGCTCTGGC
+CACCATCAAGAGCGGCGTGGCGGCAGCCGTGAGCAGCGATCCCCGCATGGGCGCCTCCCT
+GCTCAGGCTGCACTTCCACGACTGCTTTGTCCAAGGCTGTGACGCGTCTGTTCTTCTGTC
+CGGCATGGAACAAAACGCGGGTCCGAACGTGGGGTCGCTGAGGGGCTTCGGCGTCATCGA
+CAACATCAAGACCAGCTGGAGAGTATATGCAAGCAGACCGTCTCCTGCGCCGACATCCTC
+ACCGTCGCCGCCCGCGANTCCGTTGTCGCCCTTGGAGGGCCATCGTGGACTGTCCCGCTG
+GGGAGACGGGACTCCACCACCGCAAGTGCCTCGCTGGCGAACAGTGACCTCCCTGGNCCG
+AGCTCTANNCGGTCACAGCTCNAGGCCGCGTTCCTCAAGAAGAACCTTAACACGGTCGAA
+ATGGTCGCGCTCTCANGGGCGCACACCCATCGGGAAAGGCCCANTGCTCCCAACTTTTCG
+GACTCGGAATCTACCGGNGGTGACNACCAAACATNNAACAACTGGCCTTTCCNGAACGTC
+TCTCAAAGGGCCAACTNGNCCCCCANTCCCGGGGGGGAAAAAACCCAAANCCTGGGNGGA
+AANCTTGGGAAAACNAAANAACNCCCCCAAACGNCNGTTTCGAAAAAACGCCCTAAA

Shell-examples/441E2117.fasta

+>441E-2117 Dec22/Dec22/441E2117.SEQ trimmed
+TTCCAAAGCAAAGCTGNCTCTCACCGCGGTGTCGGCCGCTCTAGAACTAGTGGATCCCCC
+GGGCTGCAGGAATTCGGCACGAGGCCTGGCCCGAGCTCTAGCCGGTCACAGCTCGAGGCC
+GCGTTCCTCAAGAAGAACCTTAACACGGTCGACATGGTCGCGCTCTCAGGCGCGCACACC
+ATCGGGAAGGCCCAGTGCTCCAACTTTCGGACTCGGATCTACGGCGGTGACACCAACATC
+AACACTGCCTTCGCGACGTCTCTCAAGGCCAACTGCCCCCAGTCCGGCGGCAACACCAAC
+CTGGCGAACCTGGACACGACGACGCCCAACGCGTTCGACAACGCCTACTACACCAACCTC
+CTGTCACAGAAAGGGCTCCTGCACTCGGACCAGGTGCTCTTCAACAACGACACCACCGAC
+AACACCGTCCGCAACTTTGCGTCCAACGCGGCGGCCTTCAGCAGCGCCTTCACGACGGCC
+ATGATCAAGATGGGAAACATCGCGCCGCTCACCGGGACGCAGGGCCAGATCAGGCTCAGC
+TGCTCCAAGGTGAACTCGTGGATGGACGTATGCGTCGGCAGCACGACACGTGAATGAATA
+AGGCCCCCCAAAACANTGGCCAATACCACTTATCATACCAGCACTTGAATTGTGTATTTT
+CAAAGCATGTGCNGCAGCACATCATGCATGCNTCAACGTATGTNAACGANGGGTTGAATC
+CTCAAATTCTCATGCNAAAAGGCAAGGGAGGAATTTACTATNAATCCTACCCTTACACGG
+GAATGGAAAGATGTAAACNCCTNTTTGTGGAAAATTTGGGCGNTGGAAATGGCNCCNNGC
+TCCCATTTATTTGGTAAAAAAAAAAAAAAAAAAAAACT

Shell-examples/441E2135.fasta

+>441E-2135 Dec22/Dec22/441E2135.SEQ trimmed
+AAAACTGGATCTCACCGCGGTGGCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAG
+GGAATTCGGCACGAGGGCTCACTGTGCCGGGCTTGCGAGGGTGAGCGATACCAGCTAGCC
+ACAGCGCACGCACGACGGCCATGGCGAGCAGCGGCGGGCTGGCCGGTCTGGCGGTGCTGC
+TCACCGCCGTGCTGTGCCTGCAGCTGCCGGTCCACAGCCGCGCGCAGCTGCGCGTGGGGT
+TCTACAACACCACCTGCCCCAACGCCGAGGCCATCGTCCGGCAGGCCGTCACGGCCGCCT
+TCGCCACCAACCCCGGCGTCGCCGCCGGCCTCATCCGCCTCCACTTCCACGACTGCTTCG
+TCGAGGGCTGTGATTCATCGGTGCTCCTGTCCGTCAACCCCGGCGGAGGCACGACGGAGC
+GCGAGGCAGCGCCGAACAACCCGAGCCTGCGCGGCTTCGCGGTCGTGGACGCCGCCAGGG
+CGGCATTGGAGCAGAGCTGCCCGCGCACGGTGTCATGCGCCGACATCCTGGCCTTCGCCG
+CCCGGGACAGCGTGAACATCACCGGCAGCAACGCCTTCTACCAGGTCCCTTCCGGCCGCC
+GCGACGGGAACTCTCGACCGACACCGGCGCGTTCACCCTCCCGGGGCCGAACCTGACGGC
+GGACGGCCTCNTCAGGGGGTTCCGGACGGAACCTGACCGCCGAAGGNNATGGTGGTCTGT
+CGGGCTCCCAACAATGGGGGGCTCCCACTGCAACTNCTTTATTCGTCCGGAAACCGGGAA
+CC

Shell-examples/441E2315.fasta

+>441E-2315 wei7feb26/441E2315.SEQ trimmed
+TGGTGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCGGCACGAGGGGAGA
+AGNTTATATCTCATTATTATGTATACAACTATAAGTAGGATNGATAGNAATTCTCCATGC
+CTTTGCATGAGAAAGNGGGAATTCGATTGCNACATAATATGNGGATGCATGCATGATTTG
+CTGCTGCTCGCACATAAACTACACATTTCAAGTGCTGGTATTNATATTGGCCACTGGNTC
+TGTGNCCTTATTCCTTCNTCAGGTGTCGCGNNTGCGAGCGAAGNCGANNAACANANTCGC
+CTCNTNNCGATCANACNCGAANTACCNNCCCTGNACANACACTNACCCNTGNATNCNANC
+CTGCNCCTCTNCCGNCTCTGNNCNACANNCATNTGACCCNCANTACTNATNCCNNCANCA
+NTANACCCNTNCTCCCCCACNCCTCCCNNCNNCANNACACCCANACCNCTCNNANCNACC
+ATCATCCTCCCCACATAACACCNNTNANCCNCCNNCCTNCCCNTCATNCNCCNNATACNC
+TCCNTCACANCTATATATNCCCNCTACTACTNTANNCCCCATCCNNTNNCGNNCCTNANN
+ANNCTACCCATCNCTCTCCNTCTCCCTNNTCTCTNCCTCTCCTCTCNTCNACTNTTCATC
+TNCCCACACCNCTNTCCATCCNTCTNTCCCTCACCTCACTNTACATCACNCNACGCGACG
+TNNTACATCACCANTCTCTCTATCCATCATNCNCTCCTNCTNTANNACACANCCTNGCTA
+TACANCTNNCCTNTTCTNCCCACCTATATAACTTANATCNTACTTNTATNACTANCCTCA
+NTTNNTTCCTATCCTACTATCNNTNTCCTNTCATCTCCACCTNGNNCTACNCTNCTATNN
+CTNAACNCTACCAANNCCCTACCTNCNTCCTACTCCCNNCTCCACCCTCTCACACNACNT
+CTCNCTCTTCTCCTNCCCACTCTCTAATCNCACCTCCATCCNACTTATTNCCCATCTANC
+CANCATNANANCCATNCCTCNCCANNTCCCTCATANCCCTNCNACNACNANAAACCACTC
+NCCNCATCACANCCANAGCTNCNCCNCNCACCNCATACACACCAGTCCCATCT

Shell-examples/441E2320.fasta

+>441E-2320 wei7feb26/441E2320.SEQ trimmed
+CACCGCGGTGGCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCGGCACG
+AGGGCGCGTCGCTGCTCCGGCTGCACTTCCACGACTGCTTCGTCCAAGGCTGTGACGCGT
+CTGTTCTGCTGTCTGGCATGGAACAAAACGCTCTCCCGAACAACGGGTCACTGCGGGGCT
+TCGGCGTCATCGACAGCATCAAGACACAGATCGAGGCCATCTGCGCCCAGACCGTCTCCT
+GCGCCGACATCCTCACCGTCGCTGCCCGTGACTCCGTCGTCGCCCTCGGAGGGCCATCAT
+GGACAGTCCCTCTGGGAAGAAGGGATTCCATAGATGCAAACGAGGCGGCGGCAAACAGCG
+ACCTCCCAGGCCCTACGTCTAGCCGTTCAGATCTTGAGCTGGCATTCAGCAACAAGGGCC
+TCCTTACGGTCGACATGGTGGCCCTCTCCGGCGCGNACACCATCGGCCAGGCGCAGTGCG
+GGACCTTCAAGGACAGGATCTACAATGAGACCAACATCGACACGACCTTCGCCACATCTC
+TCCGGGCCAACTGCCCCCGGTCCGGCGGCGACGGCAGCCTGGCGAACTGGACACGACGAC
+GGCCAACACCTTCGACAACGCCTACTACACCAACCTCATGTCACAGAAGGGGGCTCCTGC
+ACTCGGACCAGGTGCTGNTCCACAACGACACCACCGACAACACGGTCCGGAACTTTGNCG
+TCCAACCCCGGCGCATTCNACAANCGCCTTTTCACGAACGGCCCAT

Shell-examples/441E2504.fasta

+>441E-2504 08jan02wei5/441E2504.SEQ trimmed
+GAGTTCCACGCGGNGGCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCG
+GCACGAGGTCCACCAGTAAAGAAGTGCAGGCAACTAGCTAGCTAACCATGGCCGCCTCTG
+CCTCTTGCATTTCACTGGTGGTGCTCGTGGCTCTGGCCACGGTGGCGTCGGCGCAGCTGT
+CGCCGACGTTCTACGACACGTCGTGCCCCAGGGCCCTGGCCACCATCAAGAGCGGCGTCA
+TGGCCGCCGNGAGCAGCGACCCTCGGATGGGCGCGTCGCTGCTCCGGNTGCACTTCCACG
+ACTGCTTCGTCCAAGGCTGTGANNCGTCTGTTCTGNTGTCTGGCATGGAACAAAACGCTC
+TCCCGAACAACGGGTCACTGCGGGGNTTCNGCGTCCATCGACAGCATNCAANACACAGAT
+CGAGGCCATCTGCGNCCAGACCGTCTCCTGCGCCGACATCCTCACCGNCNNTGCCCGNGA
+CTCCGTCCNTCNTCCCTCGNAAGGATCTATACATGNACAGTCCCCTCTGGGNAAAAAACG
+CANNTTTNCNCAANNATCCCAACCNATAGNCGCAAGANNANACAACNACACGACCNNCAC
+CTNANNANCCCATNNNCANNCTAAGNCCGCTANACANCANNNANCTCANNCTCTNNCCAA
+CTTACNTCTANNANNNATAAGCTACCCTTCATNTNTAACTNAGACACTGAACNNNNGGAG
+NTAGNGACCAACNTCTCTCTCAGCACNNTACACANNNATNACTATCCANTATCGCCTCNA
+TCTNCCATCNTCACCTACAATNGAAGCCNCTNAANCACNCCCTNCTTCTTAANAGNGNTA
+CTCTACTGCGCTNTCTCTACNTNANNCTCACAGCNTGCACACCTNCCTTNCCCACCTCAC
+TNNGAGTANAATNCNATACGTNAANNTCTNTCCTNTCTCCGCGACTCNACCAAAACANNN
+CNATNCTCTTTTCTTNTACNCAGCTTATNCTCCCATCTTANCTTTNTCNACCCTCAACCT
+CCCTCNATCCANACNCCAACNNAANNGGNACNCTCANCTAANACNTAAAGTCCAANAAAA
+CACACATCTNNTNACNCTACCCATTCCCCCCCCCTCCCCACNCCCCCNNANTTCNCTCAC
+NCNTTACACCACNCNNTTNCNCCNACTCAANTCCANCNCNTCATCCTCTATCCTANACTC
+ANAAGCCTGCCACACCTTNTAACCCNTCCCTACTTTATNCACTAAACTCATNCNNCTACA
+ATATGCNGNTNCACTCNCCNCCNATATACTNTACCTAAGCATTCTCCTCACACACA

Shell-examples/441E877.fasta

+>441E-877 Dec21wei3/Dec21wei3/441E877.SEQ trimmed
+CTTACTCACGCGGTGGCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCG
+GCACGAGGCTCCACCAGTAAAGAAGTGCAGGCAACTAGCTAGCTAACCATGGCCGCCTCT
+GCCTCTTGCATTTCACTGGTGGTGCTCGTGGCTCTGGCCACGGTGGCGTCGGCGCAGCTG
+TCGCCGACGTTCTACGACACGTCGTGCCCCAGGGCCCTGGCCACCATCAAGAGCGGCGTC
+ATGGCCGCCGTGAGCAGCGACCCTCGGATGGGCGCGTCGCTGCTCCGGCTGCACTTCCAC
+GACTGCTTCGTCCAAGGCTGTGACGCGTCTGTTCTGCTGTCTGGCATGGAACAAAACGCT
+CTCCCGAACAACGGGTCACTGCGGGGCTTCGGCGTCATCGACAGCATCAAGACACAGATC
+GAGGCCATCTGCGCCCAGACCGTCTCCTGCGCCGACATCCTCACCGTCGCTGCCCGTGAC
+TCCGTCGTCGCCCTCGGAGGGCCATCATGGACAGTCCCTCTGGGAAGAAGGGATTCCATA
+GATGCAAACGAGGCGGCGGCAAACAGCGACCTCCCAGGCCCTACGTCTAGCCGTTCAGAT
+CTTGAGCTGGCATTCAGCAACAAGGGCCTCCTTACGGTCGACATGGTGGCCTCTCCGGNG
+CGCACACCATCGGNCAGGCGCAGTGCGGGACCTTCAAGGACAGGATCTACAATGAGACCA
+ACATCGACACGACCTTCGCCACATCTCTTCCGGGCCAAACTGCCCCCGGTCCCGGCGGNN
+GACGGNCAANCCCNGNGCGNAACCTTGGGAAACCNAANGACGGCCCCAACAACCCTTC

Shell-examples/441E935.fasta

+>441E-935 Dec22/Dec22/441E935.SEQ trimmed
+CTGGATTCTCACCGCGGTGNCGNCCGCTCTANAAACTAGTGGATCCCCCGGGCTGCAGGG
+AATTCGGCACGAGGCAGATAACAAGTGCAGGTAGCACGCATAGCTCTGGTCTTGTAGCTA
+GGTAGCTAACCATGGCCATGGGTTCTGCCTCTCGCATTTCTCTGGTGGTGCTCGTGGCTC
+TGGCCACGGCGGCGTCCGGGCAGCTGTCGTCGACGTTCTACGACACGTCGTGCCCCAGGG
+CTCTGGCCACCATCAAGAGCGGCGTGGCGGCAGCCGTGAGCAGCGATCCCCGCATGGGCG
+CCTCCCTGCTCANGCTGCACTTCCACGACTGCTTTGTCCAAGGCTGTGACGCGTCTGTTC
+TTCTGTCCGGCATGGAACAAAACGCGGGTCCGAACGTGGGGTCGCTGAGGGGCTTCGGCG
+TNATCNACAACATCAAGACCCAGCTGGAGAGTATATGCAAGCAGAACGTCTCCTGCGCCG
+ACATCCTCACCGTCGCCGCCCGCGACTCCGTTGTCNCCCTTGNAGGGCCNATCGTGGACT
+GTCCCGCTGNGGAAACGGGACTCCCACCACCCCAA

Shell-examples/441E962.fasta

+>441E-962 Dec22/Dec22/441E962.SEQ trimmed
+ATCTCACGCGGTGGCGTCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGCAACCAGA
+TAACAAGTGCAGGTAGCACGCATAGCTCTGGTCTTGTAGCTAGGTAGCTAACCATGGCCA
+TGGGTTCTGCCTCTCGCATTTCTCTGGTGGTGCTCGTGGCTCTGGCCACGGCGGCGTCCG
+GGCAGCTGTCGTCGACGTTCTACGACACGTCGTGCCCCAGGGCTCTGGCCACCATCAAGA
+GCGGCGTGGCGGCAGCCGTGAGCAGCGATCCCCGCATGGGCGCCTCCCTGCTCAGGCTGC
+ACTTCCACGACTGCTTTGTCCAAGGCTGTGACGCGTCTGTTCTTCTGTCCGGCATGGAAC
+AAAACGCGGGTCCGAACGTGGGGTCGCTGAGGGGCTTCGGCGTCATCGACAACATCAAGA
+CCAGCTGGAGAGTATATGCNAGCAGACCGTCTCCTGCGCCGACATCCTCACCGTCGCCGC
+CCGCGACTCCCGTTGTCGCCCTTGGAGGGCCCATC

Shell-examples/441EAC8.fasta

+>441E-AC8 441EAMar2502/441EAC8.Seq trimmed
+GGCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCGGCACGAGGCTACCG
+CCTCCTCCCCCCAAACTCCCAACTACCCGCTCTGCTCCTGAGTTCCGAGCCCGCCCGATC
+TCCGCCGCAGCCATCCCGCCGACGCCGCTCCGTCAGGTCACACGGGGAACCTCGCCATGG
+CCGCCGCGTCCTCCGCCACCTCCGTCCACGACTTCACCGTCAAGGATTCAAGCGGCAAGG
+ACGTCGACCTCAGCGTCTACAAGGGGAAGGTTCTTCTCATTGTTAACGTCGCATCCCAGT
+GTGGCTTAACCAACTCCAACTACACCGAGCTGAGCCAGCTGTACCCCAAGTACAAGGACC
+AAGGCTTTGAGATCTTGGCTTTCCCATGCAATCAGTTTGGTGGGCAGGAGCCTGGCACCA
+ATGATGAGATAGTTCAGTTTGCCTGCACTCGCTTCAAGGCTGAGTACCCCATTTTTGACA
+AGGTTGATGTCAACGGCAACAATGTTTCTCCCCTATACAAGTTCCTGAAGTCTAGCAAAG
+GTGGCCTTTTCGGCGACAGCATCAAGTGGAACTTCTCCAAGTTCTTGGTTGACAAGGAGG
+GTCACGTTGTGGACCGCTATGCCCCGACCACTTCCCCCCTGAGCATTGAGAAGGATATCA
+AGAACTGCTTGGGAGCTCTTANANGCGCCGCTGGCCGGACGTCTCGAGAAATTGGCACTC
+TGTATTCTAGAAACAATAATAATGGTGGNGGTGAAATAAAATCTGTANCCAGCATTTCAG
+AAGGCTGCATCTGCTATG

Shell-examples/441EBA7.fasta

+>441E-BA7 441EBMar2602/441EBMar2602/441EBA7.Seq trimmed
+CGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCGGCACGAGGCAGCGGAGTTAG
+TATTAGAACTAACACCACCATTGCCATGCTCATGAACGATGGAAATCTTGTCCTACAAAA
+TGCCTCAAACTCATCCGACATTCTATGGCAAAGTTTTGATCACCCAACAAATACTTTCCT
+CCCTGATGCTAAGATCGGCCGAGACAAGATCACTGGTTTGACTCGCCGTCTTGTTTCCAG
+TAAGAATTCAATTGACCCAGCTCGTGGTCGTTACTGTAACAAGTTAGTTCCTAACAGGTT
+GATCCTTACGCTTTTGAACTCATCCATAGTATACTGGTCTAGTGGGGAATGGAATGGACA
+GTATTTTAGCACCATTCCGGAGATGTTAAGCCACAATTTGATAGACTTCAAGTTTGTCAA
+CAACACAAATGAAGAGTACTTCACATTCAGCTTACTGAACGACACGATGATCATGCATCA
+TCTACTTGATGTTTCTGGTCAACTGAAGACTTTAATCTGGGATGAGGTCTCACAGGATTG
+GTTAGGTTCCTACTCCAACCCCAGAGCTCAGTGTGATGTCTATGCTCTGTGTGGACCATT
+CACTGTGTGCGATGACAACTCAGCTCCATATTGTAGCTGTATGAAGGGCTTCTCCATAAG
+ATCCCGGAAGATTGGGAGCTAAATGATAGAANCGATGGATGTGTGAGAAAATACTCCCTT
+AAANTGTGGCAGGTATAAGGAGTACCGCAGGAATGACCGAT

Shell-examples/441EBF1.fasta

+>441E-BF1 441EBMar2602/441EBMar2602/441EBF1.SEQ trimmed
+GCTCCACCGCGGTGGCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCGG
+CACGAGGCTCGACCTATCACAAATTCACAATTAAGTGACGTTGCATTTGAGCTAGCTAGC
+CATGGCCTCTTCGTCTCTATCAGCCGTGTTGCTCTTGTGCCTGGCCGTGGCGGCGTCGGC
+GCAGCTGTCGCCGACGTTCTACGACACGACGTGCCCGAACGCTCTGGCGACCATCAAGTC
+CGCCGTGACGGCCGCCGTGAACAAGGAGAACCGCATGGGCGCGTCGCTGCTCCGGCTGCA
+CTTCCACGATTGCTTCGTCCAAGGTTGCGACGCGTCTGTTCTGCTGTCTGGCATGGAACA
+GAACGCTATCCCGAACGTGATGTCGCTGCGAGGCTTCGAAGTCATCGACAGCATCAAGGC
+GCAGCTCGAGACCATGTGCAAGCAGACCGTCTCCTGCGCCGACATCCTCACCGTCGCCGC
+CCGCGACTCCGTCGTCGCCTTGGGAGGGCTTCGTGGACAGTTCCTCTAGGAAGGAGGGAC
+TCCACCAACGCAAACGAAGCGGCGGCGAACAACGAGCTACTCCCCCATTCTTCGACCTCG
+TCAACCTCACCCAGTCCTTCGGCGACAAGGGCTTCACCGTCACCGACTGGCGCCTCTCCG
+GGGCCACACCATCGGGCANGCACAGTGCCAGACTTCCGGGACAGGTCTACACGAGACCAA
+CTCAATCAGNTTCCGAATCGTCAAGCAATGCCCAGCGACGGTTCG

Shell-examples/DNAMAT

+# Revision of standard EDNAMAT which accounts for AGCTU plus "N"
+# We will treat N matching with any base as having a score of 0
+# i.e. neither good nor bad.  Note that N-N is given a score of
+# 0 and U-T is considered a mismatch.
+   A   C   G   N   T   U
+A  5  -4  -4   0  -4  -4
+C -4   5  -4   0  -4  -4 
+G -4  -4   5   0  -4  -4
+N  0   0   0   0   0   0
+T -4  -4  -4   0   5  -4
+U -4  -4  -4   0  -4   5