TRAP (Tandem Repeats Analysis Program)

TRF Version 4.00

Sequence: contig00000333

tutorial_data.fasta.s2.2.5.7.80.10.25.1000.txt.html

Found at i: i:2808 original size:7 final size:7

Alignment explanation

Indices: 2786--2829 Score: 79 Period size: 7 Copynumber: 6.1 Consensus size: 7 2776 AGGCAAGATC 2786 TAGGGTT 1 TAGGGTT 2793 TAGGNGTT 1 TAGG-GTT 2801 TAGGGTT 1 TAGGGTT 2808 TAGGGTT 1 TAGGGTT 2815 TAGGGTT 1 TAGGGTT 2822 TAGGGTT 1 TAGGGTT 2829 T 1 T 2830 GTTCTTTGCA Statistics Matches: 36, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 7 29 0.81 8 7 0.19 ACGTcount: A:0.14, C:0.00, G:0.41, T:0.43 Consensus pattern (7 bp): TAGGGTT Left flanking sequence: Indices 2286 -- 2785 TTTTTTAATAAAAAAATTAAACTGTATTCCAAAAGAATGGAGGCATGAGATCAATTTCAGATTGC AATTCAAGATAAACTCATTTTTATTAATTTGCTCAATTTGCTGTTGAGGAATTAAAAATTCAATC AAACTCTTACATTTAAACAATTTAAAAAATTCAACTTTTATAGTTTTGTAATTCACTTGTCTTTG TGTCCAAATNAGTTGAAATGAATAAATCAGAGGCAAGCAGCANGCAATTAAACACCAGCAAAGCT CAATAGTTAAACAGCAGCAGACAGCTGCAGCAGCAGCAGTAGTAGCAGCACCAGTAGCAGCATCA GCAGCAGTAGTAGTAGTAGTAGTAGCAGCAGCAGCAGTAGTAGCAGCAGCAGTAGCAGCAGGAGC AGCAGTAGCANGTAGCAGCAACTGTGTAAAACGAATTCCGGAAGGGCCGACTCAATAGGCTGCTG CAGCAGCAAGTCCGATCTAATACATAAATAATACAAGGCAAGATC Right flanking sequence: Indices 2830 -- 3329 GTTCTTTGCATTATCCAAAGTGAACAAGAAGAAATCAAAAAAAAAATTAAAACGAATTCAAATAA ATCCATTCTTGCTGCAAACAAACCAGCACATTTGCTTTCTAATTAATGCTAAACCTAAACCCTAA ACCATAAACCCTCAACCCTAAACTCTAAACGCTAAACCCTAAACCCTAATGCTAAACCCTTATGT TAGCAAACNGGATGGCATCTTTATAGGATAAATANTGAAANTGCATCTGAAGTTGTTTGGTTTTC CATTTCGCACTTTGAGTGCAAACCCTAACCCGTAAACCCTAAACCCTAAACCCTAAACCCCGAAC CCTAAACCCTAGCCTCCTAGCCCCTGTAACAGCTCTGCGTGTGTTTCCGAATTCATTCTTTGGCA CTTCTTTGATTTTGCAATTCAAATCATTTATAATTTCAATTTATTTCAAATATCTTTTATTTTAT TTATTTTAAAAGAAGTTAAAACCCCGCTGCGGCCGCTGGCTGCCG Found at i:2960 original size:7 final size:7 Alignment explanation

Indices: 2943--3019 Score: 98 Period size: 7 Copynumber: 11.3 Consensus size: 7 2933 CTAATTAATG 2943 CTAAA-C 1 CTAAACC 2949 CTAAACC 1 CTAAACC 2956 CTAAACC 1 CTAAACC * 2963 ATAAACC 1 CTAAACC * 2970 CTCAACC 1 CTAAACC * 2977 CTAAACT 1 CTAAACC * 2984 CTAAACG 1 CTAAACC 2991 CTAAACC 1 CTAAACC 2998 CTAAACC 1 CTAAACC ** 3005 CT-AATG 1 CTAAACC 3011 CTAAACC 1 CTAAACC 3018 CT 1 CT 3020 TATGTTAGCA Statistics Matches: 58, Mismatches: 11, Indels: 3 0.81 0.15 0.04 Matches are distributed among these distances: 6 9 0.16 7 49 0.84 ACGTcount: A:0.42, C:0.38, G:0.03, T:0.18 Consensus pattern (7 bp): CTAAACC Left flanking sequence: Indices 2443 -- 2942 AATTCAACTTTTATAGTTTTGTAATTCACTTGTCTTTGTGTCCAAATNAGTTGAAATGAATAAAT CAGAGGCAAGCAGCANGCAATTAAACACCAGCAAAGCTCAATAGTTAAACAGCAGCAGACAGCTG CAGCAGCAGCAGTAGTAGCAGCACCAGTAGCAGCATCAGCAGCAGTAGTAGTAGTAGTAGTAGCA GCAGCAGCAGTAGTAGCAGCAGCAGTAGCAGCAGGAGCAGCAGTAGCANGTAGCAGCAACTGTGT AAAACGAATTCCGGAAGGGCCGACTCAATAGGCTGCTGCAGCAGCAAGTCCGATCTAATACATAA ATAATACAAGGCAAGATCTAGGGTTTAGGNGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTGTT CTTTGCATTATCCAAAGTGAACAAGAAGAAATCAAAAAAAAAATTAAAACGAATTCAAATAAATC CATTCTTGCTGCAAACAAACCAGCACATTTGCTTTCTAATTAATG Right flanking sequence: Indices 3020 -- 3519 TATGTTAGCAAACNGGATGGCATCTTTATAGGATAAATANTGAAANTGCATCTGAAGTTGTTTGG TTTTCCATTTCGCACTTTGAGTGCAAACCCTAACCCGTAAACCCTAAACCCTAAACCCTAAACCC CGAACCCTAAACCCTAGCCTCCTAGCCCCTGTAACAGCTCTGCGTGTGTTTCCGAATTCATTCTT TGGCACTTCTTTGATTTTGCAATTCAAATCATTTATAATTTCAATTTATTTCAAATATCTTTTAT TTTATTTATTTTAAAAGAAGTTAAAACCCCGCTGCGGCCGCTGGCTGCCGACTTTGGCGAACTTG AATTTCAAGTGTCTGCACGAGTTGAACTCAGAACTTGAACGAAGAGGGGAAACTGCGCATTTCTG GGGCTAAAAAGGCCGAAAGAGACAAAAATAAATGAATAAATTGAATAAAAGTGCAGATAAATGGA GAATTCGAGGAAGATATTCACAAAATCGAGATCTTTTCCTCGGAG Found at i:3134 original size:7 final size:7 Alignment explanation

Indices: 3109--3165 Score: 86 Period size: 7 Copynumber: 8.1 Consensus size: 7 3099 CTTTGAGTGC 3109 AAACCCT 1 AAACCCT * * 3116 AACCCGT 1 AAACCCT 3123 AAACCCT 1 AAACCCT 3130 AAACCCT 1 AAACCCT 3137 AAACCCT 1 AAACCCT * 3144 AAACCCC 1 AAACCCT * 3151 GAACCCT 1 AAACCCT 3158 AAACCCT 1 AAACCCT 3165 A 1 A 3166 GCCTCCTAGC Statistics Matches: 42, Mismatches: 8, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 7 42 1.00 ACGTcount: A:0.40, C:0.44, G:0.04, T:0.12 Consensus pattern (7 bp): AAACCCT Left flanking sequence: Indices 2609 -- 3108 CAGCAGCAGTAGTAGTAGTAGTAGTAGCAGCAGCAGCAGTAGTAGCAGCAGCAGTAGCAGCAGGA GCAGCAGTAGCANGTAGCAGCAACTGTGTAAAACGAATTCCGGAAGGGCCGACTCAATAGGCTGC TGCAGCAGCAAGTCCGATCTAATACATAAATAATACAAGGCAAGATCTAGGGTTTAGGNGTTTAG GGTTTAGGGTTTAGGGTTTAGGGTTTGTTCTTTGCATTATCCAAAGTGAACAAGAAGAAATCAAA AAAAAAATTAAAACGAATTCAAATAAATCCATTCTTGCTGCAAACAAACCAGCACATTTGCTTTC TAATTAATGCTAAACCTAAACCCTAAACCATAAACCCTCAACCCTAAACTCTAAACGCTAAACCC TAAACCCTAATGCTAAACCCTTATGTTAGCAAACNGGATGGCATCTTTATAGGATAAATANTGAA ANTGCATCTGAAGTTGTTTGGTTTTCCATTTCGCACTTTGAGTGC Right flanking sequence: Indices 3166 -- 3665 GCCTCCTAGCCCCTGTAACAGCTCTGCGTGTGTTTCCGAATTCATTCTTTGGCACTTCTTTGATT TTGCAATTCAAATCATTTATAATTTCAATTTATTTCAAATATCTTTTATTTTATTTATTTTAAAA GAAGTTAAAACCCCGCTGCGGCCGCTGGCTGCCGACTTTGGCGAACTTGAATTTCAAGTGTCTGC ACGAGTTGAACTCAGAACTTGAACGAAGAGGGGAAACTGCGCATTTCTGGGGCTAAAAAGGCCGA AAGAGACAAAAATAAATGAATAAATTGAATAAAAGTGCAGATAAATGGAGAATTCGAGGAAGATA TTCACAAAATCGAGATCTTTTCCTCGGAGTTTCTTCGGATGAGGCGTTGCTGTTTCCAAAACGAA CACAGCAACTCGCGGGCACTGCGGAGCCGATTCGGCGCCAAAATTAACGCTTTTTAGCGTCATCT GCGTCAAATTGAACGGCGAAACCGAATTAATTACNAAAAACTAAA Found at i:4403 original size:3 final size:3 Alignment explanation

Indices: 4395--4439 Score: 74 Period size: 3 Copynumber: 14.7 Consensus size: 3 4385 GCAAATAGCC * 4395 CAG CAG CAG CAG NCAG CAG CAG CAG CAA CAG CAG CAG CAG CAG CA 1 CAG CAG CAG CAG -CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA 4440 ACTAAAATCA Statistics Matches: 39, Mismatches: 2, Indels: 2 0.91 0.05 0.05 Matches are distributed among these distances: 3 36 0.92 4 3 0.08 ACGTcount: A:0.36, C:0.33, G:0.29, T:0.00 Consensus pattern (3 bp): CAG Left flanking sequence: Indices 3895 -- 4394 CGCNGGCCCCCGNCTGTCTTTGATCGGATCGGACTTGTTCGGGGCTCTTTTTCTCTTCTTTTTCT CTCCTTTTGAATTCTTCTTTTNCCAAAATTAATTTTATTTTACTTTAAGAACTTCAAACTCTCCG GGACGCCCCTTGTTGCTGCTTTTCTCNCCGAGGCNCACGGACCCCCCAGCGCCAAAANTGNCCTG CAGACTGCAAAGAAAATGCAGCAGCAGCAGACGCAGCAGCANGATCCGCAGCAGCAGCAGCAGCA ACAGCANGCAGCAACAGCAGCNAGCAGCAGNCAGCAAANAAACCCAGNACNAGCTCNGCCCAATG CCGGAGGGGATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAGAGGTAAATAAATTAATTTTAA AAGAATTTCTTTTTTTCCCTTTAAAANTCTTCTAAAGCACTTTTCTCTCAACTCCAGTCTTCACT TTTCNTTCACTTTGTTTCCCNTCGCCAGCCCNGCAGCAAATAGCC Right flanking sequence: Indices 4440 -- 4939 ACTAAAATCATTTGCTTCAGCGCCTCGAGGCGTTTTTGCTGCTACTCGATTTCTGTTTTTANTAA TTTCTTTAATTCTTTTTANTTTTTTAATTTGGAATTTAATTCCATTTGCTTTCCACTCTTTTGCT GCTGCTCATTTCCTTAATTCTTTTTGCTGCTGCTCCTGCTTCCCTTTTTGCTGCTGCTGCTTCGT TTTTTGCGGCAGTTGATTCCCCTCTTGCTGCTGCTGCTTTGCCTTTTGCTGCTGCTGCTTCGCCT TTTGCTGCTGCTGATTCCCCTCTTGCTGCTGCTGTTTCTTTTGCTGCTGCTGATTCCCCTCTTGC TAATGCTGTTTCTTTTGCTGCTGCTGCTTCNTTCTCTTGCTGCCGCNTGCTGCTTTTGCGTTTGC TGCTGCTGNCTCCCCCNTNCTTGCTGCTGCTGCTTTTCCTTTTGTTGCTGNCTGCTTCTCCTCTT GCNTGCTGCTGCTGCTTTTCCTTTTGCTGCCGCTGCTCCCCCTCT Found at i:4602 original size:3 final size:3 Alignment explanation

Indices: 4594--4609 Score: 25 Period size: 3 Copynumber: 5.3 Consensus size: 3 4584 TAATTCTTTT * 4594 TGC TGC TGC TCC TGC T 1 TGC TGC TGC TGC TGC T 4610 TCCCTTTTTG Statistics Matches: 11, Mismatches: 2, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 3 11 1.00 ACGTcount: A:0.00, C:0.38, G:0.25, T:0.38 Consensus pattern (3 bp): TGC Left flanking sequence: Indices 4094 -- 4593 CTGCAAAGAAAATGCAGCAGCAGCAGACGCAGCAGCANGATCCGCAGCAGCAGCAGCAGCAACAG CANGCAGCAACAGCAGCNAGCAGCAGNCAGCAAANAAACCCAGNACNAGCTCNGCCCAATGCCGG AGGGGATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAGAGGTAAATAAATTAATTTTAAAAGA ATTTCTTTTTTTCCCTTTAAAANTCTTCTAAAGCACTTTTCTCTCAACTCCAGTCTTCACTTTTC NTTCACTTTGTTTCCCNTCGCCAGCCCNGCAGCAAATAGCCCAGCAGCAGCAGNCAGCAGCAGCA GCAACAGCAGCAGCAGCAGCAACTAAAATCATTTGCTTCAGCGCCTCGAGGCGTTTTTGCTGCTA CTCGATTTCTGTTTTTANTAATTTCTTTAATTCTTTTTANTTTTTTAATTTGGAATTTAATTCCA TTTGCTTTCCACTCTTTTGCTGCTGCTCATTTCCTTAATTCTTTT Right flanking sequence: Indices 4610 -- 5109 TCCCTTTTTGCTGCTGCTGCTTCGTTTTTTGCGGCAGTTGATTCCCCTCTTGCTGCTGCTGCTTT GCCTTTTGCTGCTGCTGCTTCGCCTTTTGCTGCTGCTGATTCCCCTCTTGCTGCTGCTGTTTCTT TTGCTGCTGCTGATTCCCCTCTTGCTAATGCTGTTTCTTTTGCTGCTGCTGCTTCNTTCTCTTGC TGCCGCNTGCTGCTTTTGCGTTTGCTGCTGCTGNCTCCCCCNTNCTTGCTGCTGCTGCTTTTCCT TTTGTTGCTGNCTGCTTCTCCTCTTGCNTGCTGCTGCTGCTTTTCCTTTTGCTGCCGCTGCTCCC CCTCTTGCNTNGCNTGCTCCTTCCCTTCTTGCTGCTTCTGCTTCCCTTTTTGCTGTTGTTGCTTT CCGTCTTGCTGCNTGGTGTNTCCTTCTTTTGCTGCTGCTGCTTCCGCTCTTGCTGCTGCTGCTGT CCCTGCTGCTCCTTCCGCTCTTGCTGCTGCTGCTTCCTCTTTTGC Found at i:5333 original size:4 final size:4 Alignment explanation

Indices: 5295--5334 Score: 45 Period size: 4 Copynumber: 10.2 Consensus size: 4 5285 AATGATTATC * * * * 5295 ATTT A-TT ATTA ATTA ATTA ATTA ATTT ATTT ATTT ATTT A 1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A 5335 NTNTTATTNN Statistics Matches: 33, Mismatches: 2, Indels: 2 0.89 0.05 0.05 Matches are distributed among these distances: 3 3 0.09 4 30 0.91 ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62 Consensus pattern (4 bp): ATTT Left flanking sequence: Indices 4795 -- 5294 NTTCTCTTGCTGCCGCNTGCTGCTTTTGCGTTTGCTGCTGCTGNCTCCCCCNTNCTTGCTGCTGC TGCTTTTCCTTTTGTTGCTGNCTGCTTCTCCTCTTGCNTGCTGCTGCTGCTTTTCCTTTTGCTGC CGCTGCTCCCCCTCTTGCNTNGCNTGCTCCTTCCCTTCTTGCTGCTTCTGCTTCCCTTTTTGCTG TTGTTGCTTTCCGTCTTGCTGCNTGGTGTNTCCTTCTTTTGCTGCTGCTGCTTCCGCTCTTGCTG CTGCTGCTGTCCCTGCTGCTCCTTCCGCTCTTGCTGCTGCTGCTTCCTCTTTTGCTGCTGCTGCT CCCCGTTTTCCTGCTGCTGCCTCACCTTTTGCTGCTGCTGCTCCTTTTTTTGCTGCTGCTGCCTC GCCTTTTGCTGCTGCTGCGTCCCGTTTGCTGCTGCTGCTGCTGCTGCACTTCGCGTTNTTTGCTG CAGCGCAGCCTCCACTCCCCTTCAAGTTGCAAAAAAATGATTATC Right flanking sequence: Indices 5335 -- 5725 NTNTTATTNNTAATTCAGGATTGTCNTGTGGCCCCCCACCTGTTCTGGGACACACAGCCAGTGGT GAAGGCAGCGGAGCGGGCGGCGCTGGCCCCACAGGTGCAGCAAAGTGGAAATGAATTTNAAATTC TTTTTTCGATTTTGGAATTAAAAGAGAATAAATGAATAATTAATTTAAATCAAGCANATTTGGGA AATCCAGNCGGAGACGAAGATGCANGCAAATCCNGGCAAAAAGATNCTTCNGGAATTCACNTTTA CCNGCAGCAAAATAANCTCCCNAGNCAGCAAAACGNCTATTTGCTGCTGCAGCAAAACAAATTCC GTTTTCTGCTCCCCTTTGTCCCTTTATCCCGCCTTATCTTCCTAATGCAGCAGCAGCAGCAGCAG A Found at