TRAP (Tandem Repeats Analysis Program)

TRF Version 4.00

Sequence: contig00000278

tutorial_data.fasta.s3.2.5.7.80.10.25.1000.txt.html

Found at i: i:1661 original size:3 final size:3

Alignment explanation

Indices: 1646--1684 Score: 71 Period size: 3 Copynumber: 13.0 Consensus size: 3 1636 ACTTNCTTCC * 1646 CAG CAG CAA CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG 1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG 1685 AGCTGTGCCG Statistics Matches: 34, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 3 34 1.00 ACGTcount: A:0.36, C:0.33, G:0.31, T:0.00 Consensus pattern (3 bp): CAG Left flanking sequence: Indices 1146 -- 1645 GCAGACCGCTACAGTCCTGCGGGTGTCGCACTATTAAATACTGCTGTTCTGTGGCAGCAGCTGCA GCAGCAGCAACCAGAGCAGCAAGTGCTGCTGCAGCAGCAGGGCAANGCAGCTACGGNAAGCTGCT NTCTGCAGCTTTTAGGAGAGGCAGGNCAGCACCTTGCTCGAAGCAGCTGAAGCAGTAGCCCTCAG CAGCAGCAGCAGCAGCAGCAGCAGCAACAGNCAGCAGCAGGGGAGAGACACTCTATGGCGTCCCC NACTGAGGGGGNTCCGCTGCGCTGCTGCTGCATTTTATTGCTTCTTCTTGCAACCCCTGGTGCTT GCTGAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGAGAAGGCTGCAACGCGGCGT TNGAGAAGCTACGAAGCTCACAGTGGGGCGAGACTGTGTCTGCTCTTGCTGCAGCTGCTGCAGCA GCCGCAGCAGCAAAGGGAACTGCAGCAGCGGTGTCACTTNCTTCC Right flanking sequence: Indices 1685 -- 2184 AGCTGTGCCGGAGACGCTGCATGCAGTGCTACGACCGTTCGTGCTGCTGCTTGATGAGAGTTAGA AGCAGTAGCTAGCAGCAGCAGCTAGCCGCAGCAGCAGCAGCGGCAGTCGCTGCTGCAGCTGCTGT AGCTGCTGCTGCTGCAGCAGCACCAGTAATTCTTAGCGTTTTATTATTGGGGTGTATGTACAGCT CGGAACCGCCCCTAGTACAATTTGCTGGTGGCTGTTNAATCCAAATCCTCGCAGCAAACCCNNTA AACCCTAAACCCTAAANCCCTGCGACACTNAAGAACGCGCTGGTCTGAGAAGCAAGAGAGCCAAT TTAAAAATTNCGAGCAGCAGACGCACTGCAGCAGCNAAAATGGTGCTGCTGTTGCTGCNTGCTGC TGCTCCTGGAAANGCACCTTGCTGCGGCTGCTGCTGCTGCTGCTACGAGTGCTNGTGCTGCAGCA GCAGCAGCAGCAGCAGNCGCGGGGCTTCCGCCNTGTACGGCACAG Found at i:1768 original size:3 final size:3 Alignment explanation

Indices: 1750--1840 Score: 59 Period size: 3 Copynumber: 29.7 Consensus size: 3 1740 GAGAGTTAGA * * * * 1750 AGC AGT AGC TAGC AGC AGC AGC TAGC CGC AGC AGC AGC AGC GGC AGT 1 AGC AGC AGC -AGC AGC AGC AGC -AGC AGC AGC AGC AGC AGC AGC AGC * * * * * * * * * * * 1797 CGC TGC TGC AGC TGC TGT AGC TGC TGC TGC TGC AGC AGC ACC AG 1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AG 1841 TAATTCTTAG Statistics Matches: 67, Mismatches: 19, Indels: 4 0.74 0.21 0.04 Matches are distributed among these distances: 3 61 0.91 4 6 0.09 ACGTcount: A:0.21, C:0.32, G:0.33, T:0.14 Consensus pattern (3 bp): AGC Left flanking sequence: Indices 1250 -- 1749 GGGCAANGCAGCTACGGNAAGCTGCTNTCTGCAGCTTTTAGGAGAGGCAGGNCAGCACCTTGCTC GAAGCAGCTGAAGCAGTAGCCCTCAGCAGCAGCAGCAGCAGCAGCAGCAGCAACAGNCAGCAGCA GGGGAGAGACACTCTATGGCGTCCCCNACTGAGGGGGNTCCGCTGCGCTGCTGCTGCATTTTATT GCTTCTTCTTGCAACCCCTGGTGCTTGCTGAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAG CAGCAGAGAAGGCTGCAACGCGGCGTTNGAGAAGCTACGAAGCTCACAGTGGGGCGAGACTGTGT CTGCTCTTGCTGCAGCTGCTGCAGCAGCCGCAGCAGCAAAGGGAACTGCAGCAGCGGTGTCACTT NCTTCCCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGAGCTGTGCCGGAGACGCTGC ATGCAGTGCTACGACCGTTCGTGCTGCTGCTTGATGAGAGTTAGA Right flanking sequence: Indices 1841 -- 2340 TAATTCTTAGCGTTTTATTATTGGGGTGTATGTACAGCTCGGAACCGCCCCTAGTACAATTTGCT GGTGGCTGTTNAATCCAAATCCTCGCAGCAAACCCNNTAAACCCTAAACCCTAAANCCCTGCGAC ACTNAAGAACGCGCTGGTCTGAGAAGCAAGAGAGCCAATTTAAAAATTNCGAGCAGCAGACGCAC TGCAGCAGCNAAAATGGTGCTGCTGTTGCTGCNTGCTGCTGCTCCTGGAAANGCACCTTGCTGCG GCTGCTGCTGCTGCTGCTACGAGTGCTNGTGCTGCAGCAGCAGCAGCAGCAGCAGNCGCGGGGCT TCCGCCNTGTACGGCACAGCAGGGAAGCCAACGAGGCCGCATTTGAAAACAGCATATTTCCTTCT TTGGTCTCCAAACTGCTCCAGCCTGAAAGCAAACAAACAAGTGATCTGCTGCTGCTGCTGCTGCT GCTGCTGCACGGCAGTCGTAGCAGCAGCAGCAGCAGCAGCAGCAG Found at i:1772 original size:13 final size:13 Alignment explanation

Indices: 1746--1795 Score: 65 Period size: 13 Copynumber: 3.9 Consensus size: 13 1736 TGATGAGAGT * * 1746 TAGAAGCAGTAGC 1 TAGCAGCAGCAGC 1759 TAGCAGCAGCAGC 1 TAGCAGCAGCAGC * 1772 TAGCCGCAGCAGC 1 TAGCAGCAGCAGC * 1785 -AGCAGCGGCAG 1 TAGCAGCAGCAG 1796 TCGCTGCTGC Statistics Matches: 32, Mismatches: 5, Indels: 1 0.84 0.13 0.03 Matches are distributed among these distances: 12 9 0.28 13 23 0.72 ACGTcount: A:0.30, C:0.28, G:0.34, T:0.08 Consensus pattern (13 bp): TAGCAGCAGCAGC Left flanking sequence: Indices 1246 -- 1745 AGCAGGGCAANGCAGCTACGGNAAGCTGCTNTCTGCAGCTTTTAGGAGAGGCAGGNCAGCACCTT GCTCGAAGCAGCTGAAGCAGTAGCCCTCAGCAGCAGCAGCAGCAGCAGCAGCAGCAACAGNCAGC AGCAGGGGAGAGACACTCTATGGCGTCCCCNACTGAGGGGGNTCCGCTGCGCTGCTGCTGCATTT TATTGCTTCTTCTTGCAACCCCTGGTGCTTGCTGAGCAGCAGCAGCAGCAGCAACAGCAGCAGCA GCAGCAGCAGAGAAGGCTGCAACGCGGCGTTNGAGAAGCTACGAAGCTCACAGTGGGGCGAGACT GTGTCTGCTCTTGCTGCAGCTGCTGCAGCAGCCGCAGCAGCAAAGGGAACTGCAGCAGCGGTGTC ACTTNCTTCCCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGAGCTGTGCCGGAGACG CTGCATGCAGTGCTACGACCGTTCGTGCTGCTGCTTGATGAGAGT Right flanking sequence: Indices 1796 -- 2295 TCGCTGCTGCAGCTGCTGTAGCTGCTGCTGCTGCAGCAGCACCAGTAATTCTTAGCGTTTTATTA TTGGGGTGTATGTACAGCTCGGAACCGCCCCTAGTACAATTTGCTGGTGGCTGTTNAATCCAAAT CCTCGCAGCAAACCCNNTAAACCCTAAACCCTAAANCCCTGCGACACTNAAGAACGCGCTGGTCT GAGAAGCAAGAGAGCCAATTTAAAAATTNCGAGCAGCAGACGCACTGCAGCAGCNAAAATGGTGC TGCTGTTGCTGCNTGCTGCTGCTCCTGGAAANGCACCTTGCTGCGGCTGCTGCTGCTGCTGCTAC GAGTGCTNGTGCTGCAGCAGCAGCAGCAGCAGCAGNCGCGGGGCTTCCGCCNTGTACGGCACAGC AGGGAAGCCAACGAGGCCGCATTTGAAAACAGCATATTTCCTTCTTTGGTCTCCAAACTGCTCCA GCCTGAAAGCAAACAAACAAGTGATCTGCTGCTGCTGCTGCTGCT Found at i:1795 original size:9 final size:9 Alignment explanation

Indices: 1760--1835 Score: 66 Period size: 9 Copynumber: 8.3 Consensus size: 9 1750 AGCAGTAGCT * 1760 AGCAGCAGC 1 AGCTGCAGC * 1769 AGCTAGCCGC 1 AGCT-GCAGC * 1779 AGCAGCAGC 1 AGCTGCAGC * * 1788 AGCGGCAGT 1 AGCTGCAGC * * 1797 CGCTGCTGC 1 AGCTGCAGC * * 1806 AGCTGCTGT 1 AGCTGCAGC * 1815 AGCTGCTGC 1 AGCTGCAGC * 1824 TGCTGCAGC 1 AGCTGCAGC 1833 AGC 1 AGC 1836 ACCAGTAATT Statistics Matches: 50, Mismatches: 16, Indels: 2 0.74 0.24 0.03 Matches are distributed among these distances: 9 43 0.86 10 7 0.14 ACGTcount: A:0.18, C:0.33, G:0.34, T:0.14 Consensus pattern (9 bp): AGCTGCAGC Left flanking sequence: Indices 1260 -- 1759 GCTACGGNAAGCTGCTNTCTGCAGCTTTTAGGAGAGGCAGGNCAGCACCTTGCTCGAAGCAGCTG AAGCAGTAGCCCTCAGCAGCAGCAGCAGCAGCAGCAGCAGCAACAGNCAGCAGCAGGGGAGAGAC ACTCTATGGCGTCCCCNACTGAGGGGGNTCCGCTGCGCTGCTGCTGCATTTTATTGCTTCTTCTT GCAACCCCTGGTGCTTGCTGAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGAGAA GGCTGCAACGCGGCGTTNGAGAAGCTACGAAGCTCACAGTGGGGCGAGACTGTGTCTGCTCTTGC TGCAGCTGCTGCAGCAGCCGCAGCAGCAAAGGGAACTGCAGCAGCGGTGTCACTTNCTTCCCAGC AGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGAGCTGTGCCGGAGACGCTGCATGCAGTGCT ACGACCGTTCGTGCTGCTGCTTGATGAGAGTTAGAAGCAGTAGCT Right flanking sequence: Indices 1836 -- 2335 ACCAGTAATTCTTAGCGTTTTATTATTGGGGTGTATGTACAGCTCGGAACCGCCCCTAGTACAAT TTGCTGGTGGCTGTTNAATCCAAATCCTCGCAGCAAACCCNNTAAACCCTAAACCCTAAANCCCT GCGACACTNAAGAACGCGCTGGTCTGAGAAGCAAGAGAGCCAATTTAAAAATTNCGAGCAGCAGA CGCACTGCAGCAGCNAAAATGGTGCTGCTGTTGCTGCNTGCTGCTGCTCCTGGAAANGCACCTTG CTGCGGCTGCTGCTGCTGCTGCTACGAGTGCTNGTGCTGCAGCAGCAGCAGCAGCAGCAGNCGCG GGGCTTCCGCCNTGTACGGCACAGCAGGGAAGCCAACGAGGCCGCATTTGAAAACAGCATATTTC CTTCTTTGGTCTCCAAACTGCTCCAGCCTGAAAGCAAACAAACAAGTGATCTGCTGCTGCTGCTG CTGCTGCTGCTGCACGGCAGTCGTAGCAGCAGCAGCAGCAGCAGC Found at i:1955 original size:7 final size:7 Alignment explanation

Indices: 1943--1965 Score: 37 Period size: 7 Copynumber: 3.1 Consensus size: 7 1933 GCAAACCCNN 1943 TAAACCC 1 TAAACCC 1950 TAAACCC 1 TAAACCC 1957 TAAANCCC 1 TAAA-CCC 1965 T 1 T 1966 GCGACACTNA Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 7 11 0.73 8 4 0.27 ACGTcount: A:0.39, C:0.39, G:0.00, T:0.17 Consensus pattern (7 bp): TAAACCC Left flanking sequence: Indices 1443 -- 1942 TTGCTTCTTCTTGCAACCCCTGGTGCTTGCTGAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGC AGCAGCAGAGAAGGCTGCAACGCGGCGTTNGAGAAGCTACGAAGCTCACAGTGGGGCGAGACTGT GTCTGCTCTTGCTGCAGCTGCTGCAGCAGCCGCAGCAGCAAAGGGAACTGCAGCAGCGGTGTCAC TTNCTTCCCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGAGCTGTGCCGGAGACGCT GCATGCAGTGCTACGACCGTTCGTGCTGCTGCTTGATGAGAGTTAGAAGCAGTAGCTAGCAGCAG CAGCTAGCCGCAGCAGCAGCAGCGGCAGTCGCTGCTGCAGCTGCTGTAGCTGCTGCTGCTGCAGC AGCACCAGTAATTCTTAGCGTTTTATTATTGGGGTGTATGTACAGCTCGGAACCGCCCCTAGTAC AATTTGCTGGTGGCTGTTNAATCCAAATCCTCGCAGCAAACCCNN Right flanking sequence: Indices 1966 -- 2395 GCGACACTNAAGAACGCGCTGGTCTGAGAAGCAAGAGAGCCAATTTAAAAATTNCGAGCAGCAGA CGCACTGCAGCAGCNAAAATGGTGCTGCTGTTGCTGCNTGCTGCTGCTCCTGGAAANGCACCTTG CTGCGGCTGCTGCTGCTGCTGCTACGAGTGCTNGTGCTGCAGCAGCAGCAGCAGCAGCAGNCGCG GGGCTTCCGCCNTGTACGGCACAGCAGGGAAGCCAACGAGGCCGCATTTGAAAACAGCATATTTC CTTCTTTGGTCTCCAAACTGCTCCAGCCTGAAAGCAAACAAACAAGTGATCTGCTGCTGCTGCTG CTGCTGCTGCTGCACGGCAGTCGTAGCAGCAGCAGCAGCAGCAGCAGCAGGGGGGTGGCGAGGAG CAGCAGCAGCAGCAGCAGCAGCAGCATCATGCTGCTGCAG Found at i:2142 original size:3 final size:3 Alignment explanation

Indices: 2134--2155 Score: 44 Period size: 3 Copynumber: 7.3 Consensus size: 3 2124 TGCTNGTGCT 2134 GCA GCA GCA GCA GCA GCA GCA G 1 GCA GCA GCA GCA GCA GCA GCA G 2156 NCGCGGGGCT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 19 1.00 ACGTcount: A:0.32, C:0.32, G:0.36, T:0.00 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 1634 -- 2133 TCACTTNCTTCCCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGAGCTGTGCCGGAGA CGCTGCATGCAGTGCTACGACCGTTCGTGCTGCTGCTTGATGAGAGTTAGAAGCAGTAGCTAGCA GCAGCAGCTAGCCGCAGCAGCAGCAGCGGCAGTCGCTGCTGCAGCTGCTGTAGCTGCTGCTGCTG CAGCAGCACCAGTAATTCTTAGCGTTTTATTATTGGGGTGTATGTACAGCTCGGAACCGCCCCTA GTACAATTTGCTGGTGGCTGTTNAATCCAAATCCTCGCAGCAAACCCNNTAAACCCTAAACCCTA AANCCCTGCGACACTNAAGAACGCGCTGGTCTGAGAAGCAAGAGAGCCAATTTAAAAATTNCGAG CAGCAGACGCACTGCAGCAGCNAAAATGGTGCTGCTGTTGCTGCNTGCTGCTGCTCCTGGAAANG CACCTTGCTGCGGCTGCTGCTGCTGCTGCTACGAGTGCTNGTGCT Right flanking sequence: Indices 2156 -- 2395 NCGCGGGGCTTCCGCCNTGTACGGCACAGCAGGGAAGCCAACGAGGCCGCATTTGAAAACAGCAT ATTTCCTTCTTTGGTCTCCAAACTGCTCCAGCCTGAAAGCAAACAAACAAGTGATCTGCTGCTGC TGCTGCTGCTGCTGCTGCACGGCAGTCGTAGCAGCAGCAGCAGCAGCAGCAGCAGGGGGGTGGCG AGGAGCAGCAGCAGCAGCAGCAGCAGCAGCATCATGCTGCTGCAG Found at i:2284 original size:3 final size:3 Alignment explanation

Indices: 2276--2303 Score: 56 Period size: 3 Copynumber: 9.3 Consensus size: 3 2266 AACAAGTGAT 2276 CTG CTG CTG CTG CTG CTG CTG CTG CTG C 1 CTG CTG CTG CTG CTG CTG CTG CTG CTG C 2304 ACGGCAGTCG Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 25 1.00 ACGTcount: A:0.00, C:0.36, G:0.32, T:0.32 Consensus pattern (3 bp): CTG Left flanking sequence: Indices 1776 -- 2275 CGCAGCAGCAGCAGCGGCAGTCGCTGCTGCAGCTGCTGTAGCTGCTGCTGCTGCAGCAGCACCAG TAATTCTTAGCGTTTTATTATTGGGGTGTATGTACAGCTCGGAACCGCCCCTAGTACAATTTGCT GGTGGCTGTTNAATCCAAATCCTCGCAGCAAACCCNNTAAACCCTAAACCCTAAANCCCTGCGAC ACTNAAGAACGCGCTGGTCTGAGAAGCAAGAGAGCCAATTTAAAAATTNCGAGCAGCAGACGCAC TGCAGCAGCNAAAATGGTGCTGCTGTTGCTGCNTGCTGCTGCTCCTGGAAANGCACCTTGCTGCG GCTGCTGCTGCTGCTGCTACGAGTGCTNGTGCTGCAGCAGCAGCAGCAGCAGCAGNCGCGGGGCT TCCGCCNTGTACGGCACAGCAGGGAAGCCAACGAGGCCGCATTTGAAAACAGCATATTTCCTTCT TTGGTCTCCAAACTGCTCCAGCCTGAAAGCAAACAAACAAGTGAT Right flanking sequence: Indices 2304 -- 2395 ACGGCAGTCGTAGCAGCAGCAGCAGCAGCAGCAGCAGGGGGGTGGCGAGGAGCAGCAGCAGCAGC AGCAGCAGCAGCATCATGCTGCTGCAG Found at i:2321 original size:3 final size:3 Alignment explanation

Indices: 2315--2381 Score: 76 Period size: 3 Copynumber: 22.3 Consensus size: 3 2305 CGGCAGTCGT * * * * * * 2315 AGC AGC AGC AGC AGC AGC AGC AGC AG- GGG GGT GGC GAGG AGC AGC 1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC -AGC AGC AGC 2360 AGC AGC AGC AGC AGC AGC AGC A 1 AGC AGC AGC AGC AGC AGC AGC A 2382 TCATGCTGCT Statistics Matches: 56, Mismatches: 6, Indels: 4 0.85 0.09 0.06 Matches are distributed among these distances: 2 1 0.02 3 54 0.96 4 1 0.02 ACGTcount: A:0.30, C:0.27, G:0.42, T:0.01 Consensus pattern (3 bp): AGC Left flanking sequence: Indices 1815 -- 2314 AGCTGCTGCTGCTGCAGCAGCACCAGTAATTCTTAGCGTTTTATTATTGGGGTGTATGTACAGCT CGGAACCGCCCCTAGTACAATTTGCTGGTGGCTGTTNAATCCAAATCCTCGCAGCAAACCCNNTA AACCCTAAACCCTAAANCCCTGCGACACTNAAGAACGCGCTGGTCTGAGAAGCAAGAGAGCCAAT TTAAAAATTNCGAGCAGCAGACGCACTGCAGCAGCNAAAATGGTGCTGCTGTTGCTGCNTGCTGC TGCTCCTGGAAANGCACCTTGCTGCGGCTGCTGCTGCTGCTGCTACGAGTGCTNGTGCTGCAGCA GCAGCAGCAGCAGCAGNCGCGGGGCTTCCGCCNTGTACGGCACAGCAGGGAAGCCAACGAGGCCG CATTTGAAAACAGCATATTTCCTTCTTTGGTCTCCAAACTGCTCCAGCCTGAAAGCAAACAAACA AGTGATCTGCTGCTGCTGCTGCTGCTGCTGCTGCACGGCAGTCGT Right flanking sequence: Indices 2382 -- 2395 TCATGCTGCTGCAG