Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold567

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 41828
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.31

Warning! 1830 characters in sequence are not A, C, G, or T


Found at i:1845 original size:25 final size:25

Alignment explanation

Indices: 1817--1871 Score: 74 Period size: 25 Copynumber: 2.2 Consensus size: 25 1807 AACTGTCATT * * 1817 GATAGTATATCCTGAAACTGCTATA 1 GATAGTATATACTGAAACTACTATA * * 1842 GATAGTATATACTGAGACTATTATA 1 GATAGTATATACTGAAACTACTATA 1867 GATAG 1 GATAG 1872 ACTATATTGA Statistics Matches: 26, Mismatches: 4, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 25 26 1.00 ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33 Consensus pattern (25 bp): GATAGTATATACTGAAACTACTATA Found at i:7190 original size:153 final size:154 Alignment explanation

Indices: 7004--7308 Score: 603 Period size: 153 Copynumber: 2.0 Consensus size: 154 6994 TCAGTTTGTG 7004 TTTATTTATTATCAATCGAGGTTTATTAAAAAGTTATTACCTTCAAAACCTTATTGTTAAAGAAA 1 TTTATTTATTATCAATCGAGGTTTATTAAAAAGTTATTACCTTCAAAACCTTATTGTTAAAGAAA 7069 GCTTAATTTAAAGCAAATGATCTACGAGAATGTGATATTTAAAAATTGAGGTGCAGAAACGTAAT 66 GCTTAATTTAAAGCAAATGATCTACGAGAATGTGATATTTAAAAATTGAGGTGCAGAAACGTAAT 7134 GTTAGAAAATAGTTATTGTTTTTA 131 GTTAGAAAATAGTTATTGTTTTTA 7158 TTTATTTA-TATCAATCGAGGTTTATTAAAAAGTTATTACCTTCAAAACCTTATTGTTAAAGAAA 1 TTTATTTATTATCAATCGAGGTTTATTAAAAAGTTATTACCTTCAAAACCTTATTGTTAAAGAAA 7222 GCTTAATTTAAAGCAAATGATCTACGAGAATGTGATATTTAAAAATTGAGGTGCAGAAACGTAAT 66 GCTTAATTTAAAGCAAATGATCTACGAGAATGTGATATTTAAAAATTGAGGTGCAGAAACGTAAT 7287 GTTAGAAAATAGTTATTGTTTT 131 GTTAGAAAATAGTTATTGTTTT 7309 GGAAAACCGT Statistics Matches: 151, Mismatches: 0, Indels: 1 0.99 0.00 0.01 Matches are distributed among these distances: 153 143 0.95 154 8 0.05 ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37 Consensus pattern (154 bp): TTTATTTATTATCAATCGAGGTTTATTAAAAAGTTATTACCTTCAAAACCTTATTGTTAAAGAAA GCTTAATTTAAAGCAAATGATCTACGAGAATGTGATATTTAAAAATTGAGGTGCAGAAACGTAAT GTTAGAAAATAGTTATTGTTTTTA Found at i:7865 original size:22 final size:21 Alignment explanation

Indices: 7802--7870 Score: 57 Period size: 22 Copynumber: 3.1 Consensus size: 21 7792 CAGCAAAGCT * 7802 GCTAGTAATCAGAATGGCTAAGA 1 GCTA-TAAACAGAATGGCTAA-A ** * * 7825 GCCGTAAACAGGATAGCTATAA 1 GCTATAAACAGAATGGCTA-AA 7847 GCTATAAACAGAATGGCTACAA 1 GCTATAAACAGAATGGCTA-AA 7869 GC 1 GC 7871 CATACATATA Statistics Matches: 35, Mismatches: 10, Indels: 3 0.73 0.21 0.06 Matches are distributed among these distances: 22 32 0.91 23 3 0.09 ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19 Consensus pattern (21 bp): GCTATAAACAGAATGGCTAAA Found at i:7922 original size:32 final size:32 Alignment explanation

Indices: 7896--8005 Score: 159 Period size: 32 Copynumber: 3.4 Consensus size: 32 7886 ATGATTGGCC * 7896 CAAAGCCATCAGTAGCAGTGATATGATCGGTA 1 CAAAGCCATCAGTAACAGTGATATGATCGGTA * * * 7928 CACAGCCATCAGTAACAATAATATGATCGG-A 1 CAAAGCCATCAGTAACAGTGATATGATCGGTA 7959 TCAAAGCCATCAGTAACAGTGATATGATCGGTA 1 -CAAAGCCATCAGTAACAGTGATATGATCGGTA * 7992 CACAGCCATCAGTA 1 CAAAGCCATCAGTA 8006 GTATCGCAGC Statistics Matches: 68, Mismatches: 8, Indels: 4 0.85 0.10 0.05 Matches are distributed among these distances: 31 1 0.01 32 66 0.97 33 1 0.01 ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21 Consensus pattern (32 bp): CAAAGCCATCAGTAACAGTGATATGATCGGTA Found at i:8242 original size:24 final size:24 Alignment explanation

Indices: 8176--8262 Score: 77 Period size: 24 Copynumber: 3.6 Consensus size: 24 8166 GCCATGCTCA ** * * 8176 AAATCAGTCATACAATTCACAGAAA 1 AAATCAGTCATTTAAATCACAG-AC 8201 AAAT-AGTCATTTAAATCACAGAC 1 AAATCAGTCATTTAAATCACAGAC ** ** 8224 AAATCAGTCATTTTCATCATGGAC 1 AAATCAGTCATTTAAATCACAGAC * 8248 AAATCAATCATTTAA 1 AAATCAGTCATTTAA 8263 CCTCAAGGGG Statistics Matches: 50, Mismatches: 11, Indels: 3 0.78 0.17 0.05 Matches are distributed among these distances: 23 5 0.10 24 41 0.82 25 4 0.08 ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28 Consensus pattern (24 bp): AAATCAGTCATTTAAATCACAGAC Found at i:10466 original size:16 final size:17 Alignment explanation

Indices: 10445--10478 Score: 52 Period size: 18 Copynumber: 2.0 Consensus size: 17 10435 TCACATTGAA 10445 ATGTTTT-TTAAAAACC 1 ATGTTTTATTAAAAACC 10461 ATGTTTTCATTAAAAACC 1 ATGTTTT-ATTAAAAACC 10479 CTTCTTGAAA Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 16 7 0.44 18 9 0.56 ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41 Consensus pattern (17 bp): ATGTTTTATTAAAAACC Found at i:11232 original size:22 final size:22 Alignment explanation

Indices: 11189--11254 Score: 62 Period size: 22 Copynumber: 3.0 Consensus size: 22 11179 TGCTAGTAAT * * 11189 CAGAATGGCTA-AGAGCCGTAAA 1 CAGAATAGCTACA-AGCCATAAA * * * 11211 CAGGATAGCTATAAGCTATAAA 1 CAGAATAGCTACAAGCCATAAA * 11233 CAGAATGGCTACAAGCCATAAA 1 CAGAATAGCTACAAGCCATAAA 11255 TATAGCAATA Statistics Matches: 35, Mismatches: 8, Indels: 2 0.78 0.18 0.04 Matches are distributed among these distances: 22 34 0.97 23 1 0.03 ACGTcount: A:0.44, C:0.18, G:0.21, T:0.17 Consensus pattern (22 bp): CAGAATAGCTACAAGCCATAAA Found at i:11381 original size:32 final size:31 Alignment explanation

Indices: 11277--11382 Score: 126 Period size: 32 Copynumber: 3.4 Consensus size: 31 11267 ATTGGCCCAA * 11277 AGCCATCAGT-AGAGTGATATGATCGGCACAC 1 AGCCATCAGTAACAGTGATATGATCGG-ACAC * * * 11308 AGCCATCAGGTAACAAT-AAATGATCGGATCAA 1 AGCCATCA-GTAACAGTGATATGATCGGA-CAC 11340 AGCCATCAGTAACAGTGATATGATCGGTACAC 1 AGCCATCAGTAACAGTGATATGATCGG-ACAC 11372 AGCCATCAGTA 1 AGCCATCAGTA 11383 GTATCACAGC Statistics Matches: 63, Mismatches: 7, Indels: 9 0.80 0.09 0.11 Matches are distributed among these distances: 31 16 0.25 32 43 0.68 33 4 0.06 ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20 Consensus pattern (31 bp): AGCCATCAGTAACAGTGATATGATCGGACAC Found at i:11596 original size:24 final size:24 Alignment explanation

Indices: 11551--11639 Score: 72 Period size: 24 Copynumber: 3.7 Consensus size: 24 11541 ATGTCATGCT ** * 11551 CAAAATTAGTCATACAATTCACAGA 1 CAAAA-TAGTCATTTAAATCACAGA 11576 CAAAATAGTCATTTAAATCACAGA 1 CAAAATAGTCATTTAAATCACAGA * ** * 11600 -TAAATCAGTCATTTTCATCACGGA 1 CAAAAT-AGTCATTTAAATCACAGA * * 11624 CAAATTAATCATTTAA 1 CAAAATAGTCATTTAA 11640 CCTCGAGGGG Statistics Matches: 50, Mismatches: 12, Indels: 5 0.75 0.18 0.07 Matches are distributed among these distances: 23 4 0.08 24 38 0.76 25 8 0.16 ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29 Consensus pattern (24 bp): CAAAATAGTCATTTAAATCACAGA Found at i:11756 original size:27 final size:27 Alignment explanation

Indices: 11713--11774 Score: 67 Period size: 27 Copynumber: 2.3 Consensus size: 27 11703 TATTTTGGTT 11713 ATTTTACCCTAAGAGGGT-ATCTC-GATC 1 ATTTTACCCTAAGAGGGTAAT-TCAG-TC * 11740 ATTTTACCCTTCA-AGGGTAATTCAGTC 1 ATTTTACCC-TAAGAGGGTAATTCAGTC 11767 ATTTTACC 1 ATTTTACC 11775 ACGTATCGCA Statistics Matches: 31, Mismatches: 1, Indels: 6 0.82 0.03 0.16 Matches are distributed among these distances: 27 26 0.84 28 5 0.16 ACGTcount: A:0.26, C:0.23, G:0.15, T:0.37 Consensus pattern (27 bp): ATTTTACCCTAAGAGGGTAATTCAGTC Found at i:20131 original size:15 final size:15 Alignment explanation

Indices: 20108--20139 Score: 55 Period size: 15 Copynumber: 2.1 Consensus size: 15 20098 TTTATTTGGT * 20108 TTTAGATCAAGTTAA 1 TTTAAATCAAGTTAA 20123 TTTAAATCAAGTTAA 1 TTTAAATCAAGTTAA 20138 TT 1 TT 20140 AAGATTTTAA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44 Consensus pattern (15 bp): TTTAAATCAAGTTAA Found at i:20348 original size:15 final size:15 Alignment explanation

Indices: 20328--20368 Score: 55 Period size: 15 Copynumber: 2.7 Consensus size: 15 20318 CTCTAATCAT * * 20328 TTTAAATTTAGATTA 1 TTTAAAATTAAATTA 20343 TTTAAAATTAAATTA 1 TTTAAAATTAAATTA 20358 TTTCAAAATTA 1 TTT-AAAATTA 20369 TTTTAAATTC Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 15 16 0.70 16 7 0.30 ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49 Consensus pattern (15 bp): TTTAAAATTAAATTA Found at i:22436 original size:15 final size:16 Alignment explanation

Indices: 22401--22442 Score: 50 Period size: 15 Copynumber: 2.6 Consensus size: 16 22391 TAATTGATTT * * 22401 AATAAAATAACAGGTA 1 AATAAAATAAAAGGGA 22417 AATAAAA-AAAAGGGA 1 AATAAAATAAAAGGGA 22432 AATAATAATAA 1 AATAA-AATAA 22443 TAATGATGTT Statistics Matches: 22, Mismatches: 2, Indels: 3 0.81 0.07 0.11 Matches are distributed among these distances: 15 11 0.50 16 9 0.41 17 2 0.09 ACGTcount: A:0.69, C:0.02, G:0.12, T:0.17 Consensus pattern (16 bp): AATAAAATAAAAGGGA Found at i:23063 original size:7 final size:6 Alignment explanation

Indices: 23047--23076 Score: 51 Period size: 6 Copynumber: 4.8 Consensus size: 6 23037 CAAGGATAAG 23047 TTTTTC TTTTTC TTTTTTC TTTTTC TTTTT 1 TTTTTC TTTTTC -TTTTTC TTTTTC TTTTT 23077 ATATATTTTT Statistics Matches: 23, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 6 17 0.74 7 6 0.26 ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87 Consensus pattern (6 bp): TTTTTC Found at i:23065 original size:13 final size:13 Alignment explanation

Indices: 23047--23076 Score: 60 Period size: 13 Copynumber: 2.3 Consensus size: 13 23037 CAAGGATAAG 23047 TTTTTCTTTTTCT 1 TTTTTCTTTTTCT 23060 TTTTTCTTTTTCT 1 TTTTTCTTTTTCT 23073 TTTT 1 TTTT 23077 ATATATTTTT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 17 1.00 ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87 Consensus pattern (13 bp): TTTTTCTTTTTCT Found at i:23225 original size:22 final size:21 Alignment explanation

Indices: 23190--23234 Score: 63 Period size: 22 Copynumber: 2.1 Consensus size: 21 23180 ATCTACTCAC * 23190 TTTTTTATGTTTGAATCTCTTT 1 TTTTTTATGCTTGAATC-CTTT * 23212 TTTTTTTTGCTTGAATCCTTT 1 TTTTTTATGCTTGAATCCTTT 23233 TT 1 TT 23235 ATTTCATTGA Statistics Matches: 21, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 21 6 0.29 22 15 0.71 ACGTcount: A:0.11, C:0.11, G:0.09, T:0.69 Consensus pattern (21 bp): TTTTTTATGCTTGAATCCTTT Found at i:23630 original size:23 final size:23 Alignment explanation

Indices: 23600--23644 Score: 81 Period size: 23 Copynumber: 2.0 Consensus size: 23 23590 GTATAAATAG 23600 AGGCTACATTGTTCATTTTAATC 1 AGGCTACATTGTTCATTTTAATC * 23623 AGGCTACATTTTTCATTTTAAT 1 AGGCTACATTGTTCATTTTAAT 23645 GATCAATTCA Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 23 21 1.00 ACGTcount: A:0.27, C:0.16, G:0.11, T:0.47 Consensus pattern (23 bp): AGGCTACATTGTTCATTTTAATC Found at i:23702 original size:21 final size:21 Alignment explanation

Indices: 23676--23715 Score: 55 Period size: 21 Copynumber: 1.9 Consensus size: 21 23666 TTCAATTAAG * 23676 TCTTTCATT-AAGTGTTTTTTT 1 TCTTTC-TTCAAGTATTTTTTT 23697 TCTTTCTTCAAGTATTTTT 1 TCTTTCTTCAAGTATTTTT 23716 CATCTAGTTC Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 20 2 0.12 21 15 0.88 ACGTcount: A:0.15, C:0.12, G:0.07, T:0.65 Consensus pattern (21 bp): TCTTTCTTCAAGTATTTTTTT Found at i:29690 original size:12 final size:12 Alignment explanation

Indices: 29669--29793 Score: 54 Period size: 12 Copynumber: 9.8 Consensus size: 12 29659 AAAAACGAAA * 29669 TGATTAAAAACT 1 TGATGAAAAACT * * 29681 TGATGGAAAATT 1 TGATGAAAAACT * 29693 TTATGAAAAGACT 1 TGATGAAAA-ACT * 29706 TGATAAAAAACT 1 TGATGAAAAACT ** 29718 AT-AAAAAAAACT 1 -TGATGAAAAACT * * 29730 TGCTGCAAAACT 1 TGATGAAAAACT * 29742 TGATTAAAAAAACT 1 TGA-T-GAAAAACT * 29756 TGGTAATTAAAAACT 1 T-G--ATGAAAAACT * 29771 TGATAAAAGAACT 1 TGATGAAA-AACT * 29784 AGATGAAAAA 1 TGATGAAAAA 29794 TACTTGAAGA Statistics Matches: 84, Mismatches: 20, Indels: 18 0.69 0.16 0.15 Matches are distributed among these distances: 11 1 0.01 12 43 0.51 13 21 0.25 14 8 0.10 15 9 0.11 16 1 0.01 17 1 0.01 ACGTcount: A:0.53, C:0.08, G:0.13, T:0.26 Consensus pattern (12 bp): TGATGAAAAACT Found at i:29753 original size:14 final size:14 Alignment explanation

Indices: 29736--29800 Score: 53 Period size: 14 Copynumber: 4.6 Consensus size: 14 29726 AACTTGCTGC 29736 AAAACTTGATTAAA 1 AAAACTTGATTAAA * 29750 AAAACTTG-GTAATTA 1 AAAACTTGATTAA--A 29765 AAAACTTGA-TAAA 1 AAAACTTGATTAAA * * * 29778 AGAACTAGATGAAA 1 AAAACTTGATTAAA * 29792 AATACTTGA 1 AAAACTTGA 29801 AGAAAGAAAA Statistics Matches: 40, Mismatches: 7, Indels: 8 0.73 0.13 0.15 Matches are distributed among these distances: 13 11 0.28 14 17 0.43 15 12 0.30 ACGTcount: A:0.54, C:0.08, G:0.12, T:0.26 Consensus pattern (14 bp): AAAACTTGATTAAA Found at i:31689 original size:25 final size:26 Alignment explanation

Indices: 31648--31700 Score: 74 Period size: 25 Copynumber: 2.1 Consensus size: 26 31638 GCCCATTTTT * 31648 AAATAAACATTAAAAAATTATTTTAA 1 AAATAAACATTAAAAAAATATTTTAA 31674 AAATAAA-A-TAATAAAAATATTTTAA 1 AAATAAACATTAA-AAAAATATTTTAA 31699 AA 1 AA 31701 GTATTCAGGC Statistics Matches: 25, Mismatches: 1, Indels: 3 0.86 0.03 0.10 Matches are distributed among these distances: 24 3 0.12 25 15 0.60 26 7 0.28 ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32 Consensus pattern (26 bp): AAATAAACATTAAAAAAATATTTTAA Found at i:35914 original size:352 final size:353 Alignment explanation

Indices: 35258--35963 Score: 1405 Period size: 352 Copynumber: 2.0 Consensus size: 353 35248 TAGTCCTTTT 35258 CTAGCCCCAGACTTTCAGATATTCCTCTTATTATTTCTCTGGCTACTAGCCGGACTCTTTTGCTG 1 CTAGCCCCAGACTTTCAGATATTCCTCTTATTATTTCTCTGGCTACTAGCCGGACTCTTTTGCTG 35323 TATTCCAATGCAATTTCTCTGAAAAATTTAGGCAAATGCTGTTGTAATCTATGTTACGTACGCAT 66 TATTCCAATGCAATTTCTCTGAAAAATTTAGGCAAATGCTGTTGTAATCTATGTTACGTACGCAT 35388 ATTCGAAAATGAGAATAAGATAATGTAGTTTTAACTTTATAAAAGAGTTGTTTTTCAAAAATATT 131 ATTCGAAAATGAGAATAAGATAATGTAGTTTTAACTTTATAAAAGAGTTGTTTTTCAAAAATATT 35453 CGAATATATTGATATAGGATACATCCACTTACCCGACACTCTTACCGAATTGGAGAGGTCCCAAC 196 CGAATATATTGATATAGGATACATCCACTTACCCGACACTCTTACCGAATTGGAGAGGTCCCAAC 35518 AAATGTCAAATATTATGTTAGCTTGATTCTATTTCTTTTTTAATGAATTAGGATTTTGTTAATGT 261 AAATGTCAAATATTATGTTAGCTTGATTCTATTTCTTTTTTAATGAATTAGGATTTTGTTAATGT 35583 CTCCTTACACTGTTTATGAGTCGAAAGC 326 CTCCTTACACTGTTTATGAGTCGAAAGC 35611 CTAGCCCCAGA-TTTCAGATATTCCTCTTATTATTTCTCTGGCTACTAGCCGGACTCTTTTGCTG 1 CTAGCCCCAGACTTTCAGATATTCCTCTTATTATTTCTCTGGCTACTAGCCGGACTCTTTTGCTG 35675 TATTCCAATGCAATTTCTCTGAAAAATTTAGGCAAATGCTGTTGTAATCTATGTTACGTACGCAT 66 TATTCCAATGCAATTTCTCTGAAAAATTTAGGCAAATGCTGTTGTAATCTATGTTACGTACGCAT 35740 ATTCGAAAATGAGAATAAGATAATGTAGTTTTAACTTTATAAAAGAGTTGTTTTTCAAAAATATT 131 ATTCGAAAATGAGAATAAGATAATGTAGTTTTAACTTTATAAAAGAGTTGTTTTTCAAAAATATT 35805 CGAATATATTGATATAGGATACATCCACTTACCCGACACTCTTACCGAATTGGAGAGGTCCCAAC 196 CGAATATATTGATATAGGATACATCCACTTACCCGACACTCTTACCGAATTGGAGAGGTCCCAAC 35870 AAATGTCAAATATTATGTTAGCTTGATTCTATTTCTTTTTTAATGAATTAGGATTTTGTTAATGT 261 AAATGTCAAATATTATGTTAGCTTGATTCTATTTCTTTTTTAATGAATTAGGATTTTGTTAATGT 35935 CTCCTTACACTGTTTATGAGTCGAAAGC 326 CTCCTTACACTGTTTATGAGTCGAAAGC 35963 C 1 C 35964 CGTCTGAAAA Statistics Matches: 353, Mismatches: 0, Indels: 1 1.00 0.00 0.00 Matches are distributed among these distances: 352 342 0.97 353 11 0.03 ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37 Consensus pattern (353 bp): CTAGCCCCAGACTTTCAGATATTCCTCTTATTATTTCTCTGGCTACTAGCCGGACTCTTTTGCTG TATTCCAATGCAATTTCTCTGAAAAATTTAGGCAAATGCTGTTGTAATCTATGTTACGTACGCAT ATTCGAAAATGAGAATAAGATAATGTAGTTTTAACTTTATAAAAGAGTTGTTTTTCAAAAATATT CGAATATATTGATATAGGATACATCCACTTACCCGACACTCTTACCGAATTGGAGAGGTCCCAAC AAATGTCAAATATTATGTTAGCTTGATTCTATTTCTTTTTTAATGAATTAGGATTTTGTTAATGT CTCCTTACACTGTTTATGAGTCGAAAGC Done.