Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1015

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: 33021
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:1083 original size:1 final size:1

Alignment explanation

Indices: 1073--1170 Score: 88 Period size: 1 Copynumber: 98.0 Consensus size: 1 1063 ATGGCAATGG * * * ** * * * * * 1073 AAAAAGAAAAAAACAAAACAAAAAAAAAGGAAAAAGAAAAAAGAAAAAACAAAACAAAAAAAAGA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA * * 1138 AAAAGAAAAAAAAAAAAAAAACAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1171 GTGAAGATTT Statistics Matches: 75, Mismatches: 22, Indels: 0 0.77 0.23 0.00 Matches are distributed among these distances: 1 75 1.00 ACGTcount: A:0.88, C:0.05, G:0.07, T:0.00 Consensus pattern (1 bp): A Found at i:1112 original size:36 final size:34 Alignment explanation

Indices: 1072--1168 Score: 153 Period size: 36 Copynumber: 2.8 Consensus size: 34 1062 CATGGCAATG 1072 GAAAAAGAAAAAAACAAAACAAAAAAAAAGGAAAAA 1 GAAAAA-AAAAAAACAAAACAAAAAAAAA-GAAAAA 1108 GAAAAAAGAAAAAACAAAAC-AAAAAAAAGAAAAA 1 GAAAAAA-AAAAAACAAAACAAAAAAAAAGAAAAA 1142 GAAAAAAAAAAAA-AAAACAAAAAAAAA 1 GAAAAAAAAAAAACAAAACAAAAAAAAA 1169 AAGTGAAGAT Statistics Matches: 59, Mismatches: 0, Indels: 7 0.89 0.00 0.11 Matches are distributed among these distances: 32 5 0.08 33 14 0.24 34 13 0.22 35 9 0.15 36 18 0.31 ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00 Consensus pattern (34 bp): GAAAAAAAAAAAACAAAACAAAAAAAAAGAAAAA Found at i:1169 original size:37 final size:35 Alignment explanation

Indices: 1072--1171 Score: 139 Period size: 34 Copynumber: 2.8 Consensus size: 35 1062 CATGGCAATG * 1072 GAAAAAGAAAAAAACAAAACAAAAAAAAAGGAAAAA 1 GAAAAAAAAAAAAACAAAA-AAAAAAAAAGGAAAAA * * 1108 GAAAAAAGAAAAAACAAAACAAAAAAAA-GAAAAA 1 GAAAAAAAAAAAAACAAAAAAAAAAAAAGGAAAAA * 1142 GAAAAAAAAAAAAAAAACAAAAAAAAAAAG 1 GAAAAAAAAAAAAACAA-AAAAAAAAAAAG 1172 TGAAGATTTG Statistics Matches: 56, Mismatches: 6, Indels: 4 0.85 0.09 0.06 Matches are distributed among these distances: 34 21 0.38 35 18 0.32 36 17 0.30 ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00 Consensus pattern (35 bp): GAAAAAAAAAAAAACAAAAAAAAAAAAAGGAAAAA Found at i:5468 original size:16 final size:19 Alignment explanation

Indices: 5441--5478 Score: 55 Period size: 17 Copynumber: 2.2 Consensus size: 19 5431 TATTAGGTAG 5441 ATTTTGAATATT-TA-TAT 1 ATTTTGAATATTATATTAT 5458 ATTTT-AATATTATATTAT 1 ATTTTGAATATTATATTAT 5476 ATT 1 ATT 5479 ATTTTTTATG Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 16 6 0.32 17 7 0.37 18 6 0.32 ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61 Consensus pattern (19 bp): ATTTTGAATATTATATTAT Found at i:6508 original size:13 final size:13 Alignment explanation

Indices: 6490--6628 Score: 55 Period size: 13 Copynumber: 10.8 Consensus size: 13 6480 ATTTGATAAT 6490 TTATATATTTATA 1 TTATATATTTATA * 6503 TTATAT-TTAATA 1 TTATATATTTATA * * 6515 TTTTTTAATGTTATA 1 TTATAT-AT-TTATA * * 6530 TTATAT-TTGAAAA 1 TTATATATT-TATA 6543 TTA-ATATTTATAA 1 TTATATATTTAT-A ** 6556 TTA-ATAAATATA 1 TTATATATTTATA * 6568 TT-TAATATTCATA 1 TTAT-ATATTTATA 6581 TTTATATATTTATA 1 -TTATATATTTATA 6595 --ATA-ATTTACATA 1 TTATATATTT--ATA * 6607 TTACATATTTATA 1 TTATATATTTATA 6620 -TATAT-TTTA 1 TTATATATTTA 6629 ATATATTTAA Statistics Matches: 93, Mismatches: 18, Indels: 32 0.65 0.13 0.22 Matches are distributed among these distances: 10 4 0.04 11 7 0.08 12 23 0.25 13 33 0.35 14 13 0.14 15 13 0.14 ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55 Consensus pattern (13 bp): TTATATATTTATA Found at i:6510 original size:27 final size:27 Alignment explanation

Indices: 6480--6554 Score: 84 Period size: 27 Copynumber: 2.9 Consensus size: 27 6470 TTTTAAGTAG 6480 ATTTGATAATTTATATATTTATATTAT 1 ATTTGATAATTTATATATTTATATTAT * * * 6507 ATTTAATATTTTTTA-ATGTTATATTAT 1 ATTTGATAATTTATATAT-TTATATTAT * 6534 ATTTGA-AAATTA-ATATTTATA 1 ATTTGATAATTTATATATTTATA 6555 ATTAATAAAT Statistics Matches: 39, Mismatches: 7, Indels: 6 0.75 0.13 0.12 Matches are distributed among these distances: 25 6 0.15 26 7 0.18 27 26 0.67 ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57 Consensus pattern (27 bp): ATTTGATAATTTATATATTTATATTAT Found at i:6591 original size:8 final size:8 Alignment explanation

Indices: 6578--6647 Score: 52 Period size: 8 Copynumber: 8.1 Consensus size: 8 6568 TTTAATATTC 6578 ATATTTAT 1 ATATTTAT 6586 ATATTTAT 1 ATATTTAT * 6594 AATAATTTAC 1 -AT-ATTTAT * 6604 ATA-TTAC 1 ATATTTAT 6611 ATATTTATAT 1 ATA-TT-TAT 6621 ATATTTTAAT 1 ATA-TTT-AT * 6631 ATATTTAA 1 ATATTTAT 6639 ATATTTAT 1 ATATTTAT 6647 A 1 A 6648 ACATATAAAT Statistics Matches: 52, Mismatches: 4, Indels: 12 0.76 0.06 0.18 Matches are distributed among these distances: 7 7 0.13 8 18 0.35 9 9 0.17 10 18 0.35 ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54 Consensus pattern (8 bp): ATATTTAT Found at i:6637 original size:35 final size:32 Alignment explanation

Indices: 6488--6643 Score: 146 Period size: 32 Copynumber: 4.9 Consensus size: 32 6478 AGATTTGATA * 6488 ATTTATATATTTATATTATATTTAATATT--T 1 ATTTATATATTTATAATATATTTAATATTCAT * * * * 6518 -TTTA-AT-GTTATATTATATTTGAAAATTAAT 1 ATTTATATATTTATAATATATTT-AATATTCAT * 6548 ATTTATA-ATTAATAAATATATTTAATATTCAT 1 ATTTATATATTTAT-AATATATTTAATATTCAT 6580 ATTTATATATTTATAATA-ATTTACATATTACAT 1 ATTTATATATTTATAATATATTTA-ATATT-CAT * 6613 ATTTATATATATTTTAATATATTTAAATATT 1 ATTTATATAT-TTATAATATATTT-AATATT 6644 TATAACATAT Statistics Matches: 104, Mismatches: 9, Indels: 21 0.78 0.07 0.16 Matches are distributed among these distances: 27 13 0.12 28 7 0.07 29 4 0.04 30 1 0.01 31 9 0.09 32 27 0.26 33 26 0.25 34 7 0.07 35 9 0.09 36 1 0.01 ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55 Consensus pattern (32 bp): ATTTATATATTTATAATATATTTAATATTCAT Found at i:7784 original size:46 final size:47 Alignment explanation

Indices: 7722--7816 Score: 133 Period size: 47 Copynumber: 2.0 Consensus size: 47 7712 TGGGTTTCTA * 7722 TATTATTATTAGTA-TTTA-GTTCAAGGGTATTGAAAGGGAACCAT-CT 1 TATTATTATTAGTATTTTATGTTCAA-GGCATTGAAAGGG-ACCATACT * 7768 TATTATTATTATTATTTTATGTTCAAGGCATTGAAAGGGACCATACT 1 TATTATTATTAGTATTTTATGTTCAAGGCATTGAAAGGGACCATACT 7815 TA 1 TA 7817 AAAGTTCAAA Statistics Matches: 44, Mismatches: 2, Indels: 5 0.86 0.04 0.10 Matches are distributed among these distances: 46 18 0.41 47 20 0.45 48 6 0.14 ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41 Consensus pattern (47 bp): TATTATTATTAGTATTTTATGTTCAAGGCATTGAAAGGGACCATACT Found at i:13933 original size:49 final size:49 Alignment explanation

Indices: 13860--13958 Score: 180 Period size: 49 Copynumber: 2.0 Consensus size: 49 13850 AATTTTAAGT * * 13860 ATGGTTCCCTTTCAATGCCTTTGAACATAAAATAATAATAATAATAAAG 1 ATGGTTCCCTTTCAATACCCTTGAACATAAAATAATAATAATAATAAAG 13909 ATGGTTCCCTTTCAATACCCTTGAACATAAAATAATAATAATAATAAAG 1 ATGGTTCCCTTTCAATACCCTTGAACATAAAATAATAATAATAATAAAG 13958 A 1 A 13959 AACCCAAAAA Statistics Matches: 48, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 49 48 1.00 ACGTcount: A:0.44, C:0.15, G:0.09, T:0.31 Consensus pattern (49 bp): ATGGTTCCCTTTCAATACCCTTGAACATAAAATAATAATAATAATAAAG Found at i:15082 original size:27 final size:27 Alignment explanation

Indices: 15040--15117 Score: 75 Period size: 34 Copynumber: 2.6 Consensus size: 27 15030 ATTAATATGT * 15040 TATAAATATTTAAATATATTATAAATTA 1 TATAAATATGT-AATATATTATAAATTA 15068 TATAAATATGTAATATTTAATATATTATAAATTA 1 TATAAATATG-------TAATATATTATAAATTA 15102 TATAAATATGTAATAT 1 TATAAATATGTAATAT 15118 TTAAATATAT Statistics Matches: 42, Mismatches: 1, Indels: 15 0.72 0.02 0.26 Matches are distributed among these distances: 27 6 0.14 28 9 0.21 34 26 0.62 35 1 0.02 ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46 Consensus pattern (27 bp): TATAAATATGTAATATATTATAAATTA Found at i:15094 original size:34 final size:35 Alignment explanation

Indices: 15044--15168 Score: 209 Period size: 35 Copynumber: 3.6 Consensus size: 35 15034 ATATGTTATA 15044 AATATTTAAATATATTATAAATTATATAAATATGT 1 AATATTTAAATATATTATAAATTATATAAATATGT 15079 AATATTT-AATATATTATAAATTATATAAATATGT 1 AATATTTAAATATATTATAAATTATATAAATATGT 15113 AATATTTAAATATATTATAAATTATATAAATA-GAT 1 AATATTTAAATATATTATAAATTATATAAATATG-T * 15148 AATTTTTAAATATAATTATAA 1 AATATTTAAATAT-ATTATAA 15169 CATAAAAAAT Statistics Matches: 86, Mismatches: 1, Indels: 5 0.93 0.01 0.05 Matches are distributed among these distances: 34 35 0.41 35 44 0.51 36 7 0.08 ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46 Consensus pattern (35 bp): AATATTTAAATATATTATAAATTATATAAATATGT Found at i:15124 original size:15 final size:15 Alignment explanation

Indices: 15070--15125 Score: 58 Period size: 15 Copynumber: 3.5 Consensus size: 15 15060 ATAAATTATA 15070 TAAATATGTAATATT 1 TAAATATGTAATATT * * 15085 TAATATATTATAAATTATA 1 TAA-ATA-TGT-AA-TATT 15104 TAAATATGTAATATT 1 TAAATATGTAATATT 15119 TAAATAT 1 TAAATAT 15126 ATTATAAATT Statistics Matches: 33, Mismatches: 4, Indels: 8 0.73 0.09 0.18 Matches are distributed among these distances: 15 13 0.39 16 5 0.15 17 4 0.12 18 5 0.15 19 6 0.18 ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46 Consensus pattern (15 bp): TAAATATGTAATATT Found at i:15179 original size:35 final size:35 Alignment explanation

Indices: 15044--15208 Score: 171 Period size: 35 Copynumber: 4.7 Consensus size: 35 15034 ATATGTTATA * 15044 AATATTTAAATATATTATAAATTATATAAATATG-T 1 AATATTTAAATATATTATAAATTATAAAAATA-GAT * 15079 AATATTT-AATATATTATAAATTATATAAATATG-T 1 AATATTTAAATATATTATAAATTATAAAAATA-GAT * 15113 AATATTTAAATATATTATAAATTATATAAATAGAT 1 AATATTTAAATATATTATAAATTATAAAAATAGAT * * 15148 AATTTTTAAATATAATTATAACA-TA-AAAAATATAT 1 AATATTTAAATAT-ATTATAA-ATTATAAAAATAGAT * * 15183 AA-ATATAATATAAATATATAAATTAT 1 AATATTTAA-ATATAT-TATAAATTAT 15209 CAAATCTACT Statistics Matches: 116, Mismatches: 6, Indels: 15 0.85 0.04 0.11 Matches are distributed among these distances: 34 42 0.36 35 64 0.55 36 9 0.08 37 1 0.01 ACGTcount: A:0.55, C:0.01, G:0.02, T:0.43 Consensus pattern (35 bp): AATATTTAAATATATTATAAATTATAAAAATAGAT Found at i:16243 original size:11 final size:11 Alignment explanation

Indices: 16227--16251 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 16217 GACATAAAAA 16227 ATAATATAAAT 1 ATAATATAAAT 16238 ATAATATAAAT 1 ATAATATAAAT 16249 ATA 1 ATA 16252 TAAATATTTC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36 Consensus pattern (11 bp): ATAATATAAAT Found at i:17180 original size:20 final size:20 Alignment explanation

Indices: 17152--17226 Score: 87 Period size: 20 Copynumber: 3.8 Consensus size: 20 17142 TCATACCCTG 17152 ATGTATCGATACATTTTTCA 1 ATGTATCGATACATTTTTCA * * * * 17172 ATATATCGATACATGTATGA 1 ATGTATCGATACATTTTTCA * * * 17192 ATGTATCGATATATTCTACA 1 ATGTATCGATACATTTTTCA 17212 ATGTATCGATACATT 1 ATGTATCGATACATT 17227 ATGTGTTTTT Statistics Matches: 43, Mismatches: 12, Indels: 0 0.78 0.22 0.00 Matches are distributed among these distances: 20 43 1.00 ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40 Consensus pattern (20 bp): ATGTATCGATACATTTTTCA Found at i:17219 original size:40 final size:39 Alignment explanation

Indices: 17152--17229 Score: 111 Period size: 40 Copynumber: 2.0 Consensus size: 39 17142 TCATACCCTG * * 17152 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA 1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA * * 17192 ATGTATCGATATATTCTACAATGTATCGATACATTATG 1 ATGTATCGATACATTCTACAATATATCGATACATTATG 17230 TGTTTTTACC Statistics Matches: 34, Mismatches: 4, Indels: 1 0.87 0.10 0.03 Matches are distributed among these distances: 39 4 0.12 40 30 0.88 ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40 Consensus pattern (39 bp): ATGTATCGATACATTCTACAATATATCGATACATTATGA Found at i:20688 original size:1 final size:1 Alignment explanation

Indices: 20682--20779 Score: 79 Period size: 1 Copynumber: 98.0 Consensus size: 1 20672 AAATCTTCAC * * ** * * * * 20682 TTTTTTTTTTTGTTTTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTCTTTTTTTCTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT ** * * * 20747 TTTCCTTTTTTTTTGTTTTGTTTTTTTCTTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 20780 CCAATTGCCA Statistics Matches: 75, Mismatches: 22, Indels: 0 0.77 0.23 0.00 Matches are distributed among these distances: 1 75 1.00 ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87 Consensus pattern (1 bp): T Found at i:20721 original size:30 final size:31 Alignment explanation

Indices: 20684--20781 Score: 126 Period size: 30 Copynumber: 3.0 Consensus size: 31 20674 ATCTTCACTT 20684 TTTTTTTTTGTTTTTTTTTTTTTCTTTTTCC 1 TTTTTTTTTGTTTTTTTTTTTTTCTTTTTCC 20715 TTTTTTTTGTTTTGTTTTTTTCTTTTTTTCTTTTTCC 1 ---TTTTT-TTTTG-TTTTTT-TTTTTTTCTTTTTCC * 20752 TTTTTTTTTG-TTTTGTTTTTTTCTTTTTCC 1 TTTTTTTTTGTTTTTTTTTTTTTCTTTTTCC 20782 AATTGCCATG Statistics Matches: 60, Mismatches: 1, Indels: 10 0.85 0.01 0.14 Matches are distributed among these distances: 30 15 0.25 31 4 0.07 33 5 0.08 34 10 0.17 35 5 0.08 36 6 0.10 37 15 0.25 ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85 Consensus pattern (31 bp): TTTTTTTTTGTTTTTTTTTTTTTCTTTTTCC Found at i:20744 original size:37 final size:38 Alignment explanation

Indices: 20682--20779 Score: 168 Period size: 38 Copynumber: 2.7 Consensus size: 38 20672 AAATCTTCAC 20682 TTTTTTT-TTTTG-TTTTTT-TTTTTTTCTTTTTCC-T 1 TTTTTTTGTTTTGTTTTTTTCTTTTTTTCTTTTTCCTT 20716 TTTTTTTGTTTTGTTTTTTTCTTTTTTTCTTTTTCCTT 1 TTTTTTTGTTTTGTTTTTTTCTTTTTTTCTTTTTCCTT 20754 TTTTTTTGTTTTGTTTTTTTCTTTTT 1 TTTTTTTGTTTTGTTTTTTTCTTTTT 20780 CCAATTGCCA Statistics Matches: 60, Mismatches: 0, Indels: 4 0.94 0.00 0.06 Matches are distributed among these distances: 34 7 0.12 35 5 0.08 36 6 0.10 37 15 0.25 38 27 0.45 ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87 Consensus pattern (38 bp): TTTTTTTGTTTTGTTTTTTTCTTTTTTTCTTTTTCCTT Found at i:31392 original size:1 final size:1 Alignment explanation

Indices: 31382--31474 Score: 78 Period size: 1 Copynumber: 93.0 Consensus size: 1 31372 TGGCAATTGG * * * ** * * * * 31382 AAAAAGAAAAAAAACAAAACAAAAAAAAAGGAAAAAGAAAAAAAAAAAAACAAAACAAAAAAAAG 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA * * * 31447 GAAAAAGAAAAAAAAAACAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 31475 GTGAAGATTT Statistics Matches: 72, Mismatches: 20, Indels: 0 0.78 0.22 0.00 Matches are distributed among these distances: 1 72 1.00 ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00 Consensus pattern (1 bp): A Found at i:31442 original size:35 final size:36 Alignment explanation

Indices: 31381--31472 Score: 150 Period size: 35 Copynumber: 2.5 Consensus size: 36 31371 ATGGCAATTG 31381 GAAAAAGAAAAAAAACAAAACAAAAAAAAAGGAAAAA 1 GAAAAA-AAAAAAAACAAAACAAAAAAAAAGGAAAAA 31418 GAAAAAAAAAAAAACAAAAC-AAAAAAAAGGAAAAA 1 GAAAAAAAAAAAAACAAAACAAAAAAAAAGGAAAAA * 31453 GAAAAAAAAAACAAAAAAAA 1 GAAAAAAAAAA-AAACAAAA 31473 AAGTGAAGAT Statistics Matches: 53, Mismatches: 1, Indels: 3 0.93 0.02 0.05 Matches are distributed among these distances: 35 26 0.49 36 21 0.40 37 6 0.11 ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00 Consensus pattern (36 bp): GAAAAAAAAAAAAACAAAACAAAAAAAAAGGAAAAA Found at i:31481 original size:27 final size:27 Alignment explanation

Indices: 31382--31472 Score: 94 Period size: 28 Copynumber: 3.2 Consensus size: 27 31372 TGGCAATTGG * * 31382 AAAAAGAAAAAAAACAAAACAAAAAAAAA 1 AAAAAGAAAAAGAA-AAAAC-AAAACAAA * 31411 GGAAAAAGAAAAAAAAAAAAACAAAACAAA 1 --AAAAAG-AAAAAGAAAAAACAAAACAAA 31441 AAAAAGGAAAAAGAAAAAA-AAAACAAA 1 AAAAAG-AAAAAGAAAAAACAAAACAAA 31468 AAAAA 1 AAAAA 31473 AAGTGAAGAT Statistics Matches: 56, Mismatches: 3, Indels: 6 0.86 0.05 0.09 Matches are distributed among these distances: 27 13 0.23 28 17 0.30 30 7 0.12 31 11 0.20 32 8 0.14 ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00 Consensus pattern (27 bp): AAAAAGAAAAAGAAAAAACAAAACAAA Done.