Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold907
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: 58825
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:7228 original size:40 final size:40
Alignment explanation
Indices: 7135--7358 Score: 224
Period size: 40 Copynumber: 5.7 Consensus size: 40
7125 GCTCCTCGTT
* * * *
7135 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
7175 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
7214 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
7254 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
7294 CAAATGCCTTC-GGATCTT-AGTCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
7334 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
7359 CAGCATTCAA
Statistics
Matches: 153, Mismatches: 24, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
38 2 0.01
39 51 0.33
40 97 0.63
41 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:10600 original size:27 final size:27
Alignment explanation
Indices: 10570--10747 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
10560 ATATTGAGTC
* * * *
10570 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
10597 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
10624 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
10652 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
10679 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
10706 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
10733 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
10748 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:10709 original size:82 final size:81
Alignment explanation
Indices: 10591--10746 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
10581 TGCTATATAA
* *
10591 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
10656 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
10673 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
10737 CACTTAGTGC
65 CACTTAGTGC
10747 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:15022 original size:188 final size:187
Alignment explanation
Indices: 14705--15083 Score: 704
Period size: 188 Copynumber: 2.0 Consensus size: 187
14695 AAATTATCCT
14705 AAAAATGCAGATGTATTCACTTAATTTCAAATAATTAATTCCATCTAGATGCCTTAAATATAACT
1 AAAAATGCAGATGTATTCACTTAATTTCAAATAATTAATTCCATCTAGATGCCTTAAATATAACT
* *
14770 CTTTTCAAAAGTTATCACAATGCTATCACTAAGTGGGGAAAGGAAACCCTAACTTTCTGACCATT
66 CTTTTCAAAAGTTATCACAAGGCTATCACTAAGTGGGGAAAGAAAACCCTAACTTTCTGACCATT
14835 AATGCACTACTTAATATTATGGTGGATCCAAGTCTCGAAGGACACCTGTTTCTTCTGC
131 AATGCACTACTTAATATTATGGTGGATCCAAGTCTCGAAGGACACC-GTTTCTTCTGC
*
14893 AAAAATGCAGATGTATTCACTTAATTTCAAATAATTAATTCCATCTATATGCCTTAAATATAACT
1 AAAAATGCAGATGTATTCACTTAATTTCAAATAATTAATTCCATCTAGATGCCTTAAATATAACT
*
14958 CTTTTCAAAAGTTATCACAAGGCTATCACTGAGTGGGGAAAGAAAACCCTAACTTTCTGACCATT
66 CTTTTCAAAAGTTATCACAAGGCTATCACTAAGTGGGGAAAGAAAACCCTAACTTTCTGACCATT
*
15023 AATGCACTACTTAATATTATGGTGGATCCAAGTCTCGATGGACACCGTTTCTTCTGC
131 AATGCACTACTTAATATTATGGTGGATCCAAGTCTCGAAGGACACCGTTTCTTCTGC
15080 AAAA
1 AAAA
15084 TAGCATATAG
Statistics
Matches: 186, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
187 15 0.08
188 171 0.92
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.32
Consensus pattern (187 bp):
AAAAATGCAGATGTATTCACTTAATTTCAAATAATTAATTCCATCTAGATGCCTTAAATATAACT
CTTTTCAAAAGTTATCACAAGGCTATCACTAAGTGGGGAAAGAAAACCCTAACTTTCTGACCATT
AATGCACTACTTAATATTATGGTGGATCCAAGTCTCGAAGGACACCGTTTCTTCTGC
Found at i:19436 original size:16 final size:17
Alignment explanation
Indices: 19415--19449 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
19405 AATTGAATAA
*
19415 TTGTTAA-AAGCTAAAT
1 TTGTTAATAAACTAAAT
19431 TTGTTAATAAACTAAAT
1 TTGTTAATAAACTAAAT
19448 TT
1 TT
19450 AGAAATGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (17 bp):
TTGTTAATAAACTAAAT
Found at i:21338 original size:24 final size:22
Alignment explanation
Indices: 21261--21333 Score: 76
Period size: 24 Copynumber: 3.1 Consensus size: 22
21251 TCAATATGTT
21261 TTTTAATAAAAAATTTTAAAAAAA
1 TTTTAATAAAAAA--TTAAAAAAA
* *
21285 TTTTAATAAAAGAA-GATAAAAAG
1 TTTTAATAAAA-AATTA-AAAAAA
21308 TTCTTAATAAAAAATTAAAAAAA
1 TT-TTAATAAAAAATTAAAAAAA
21331 TTT
1 TTT
21334 ATTAAGTTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 2 0.05
23 16 0.39
24 21 0.51
25 2 0.05
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (22 bp):
TTTTAATAAAAAATTAAAAAAA
Found at i:21824 original size:28 final size:28
Alignment explanation
Indices: 21766--21829 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
21756 TTAGTTTTTG
** *
21766 AAATATTTTTATTTTTATTTTGATAATTA
1 AAATA-TTTTATTTAAATTTTGATAACTA
* *
21795 AATTATTTTATTTAAATTTTGATACCTA
1 AAATATTTTATTTAAATTTTGATAACTA
21823 AAATATT
1 AAATATT
21830 CATTCTTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (28 bp):
AAATATTTTATTTAAATTTTGATAACTA
Found at i:22557 original size:16 final size:16
Alignment explanation
Indices: 22536--22569 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
22526 CACTTTAACA
*
22536 CCCATTTCCCTTTTCC
1 CCCATTTCCCGTTTCC
22552 CCCATTTCCCGTTTCC
1 CCCATTTCCCGTTTCC
22568 CC
1 CC
22570 TCTTCCCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.53, G:0.03, T:0.38
Consensus pattern (16 bp):
CCCATTTCCCGTTTCC
Found at i:22669 original size:17 final size:17
Alignment explanation
Indices: 22647--22686 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 17
22637 AATCAACCTT
22647 CACCTCCGGCACCAATC
1 CACCTCCGGCACCAATC
*
22664 CACCT-C--CACCGATC
1 CACCTCCGGCACCAATC
22678 CACCTCCGG
1 CACCTCCGG
22687 TCTTCCACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 6
0.73 0.04 0.23
Matches are distributed among these distances:
14 12 0.63
15 1 0.05
16 1 0.05
17 5 0.26
ACGTcount: A:0.20, C:0.55, G:0.12, T:0.12
Consensus pattern (17 bp):
CACCTCCGGCACCAATC
Found at i:24570 original size:16 final size:16
Alignment explanation
Indices: 24549--24589 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
24539 TAATTTGATA
*
24549 TAATTTTAGTAACAAT
1 TAATTTTAATAACAAT
24565 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
24581 TAGTTTTAA
1 TAATTTTAA
24590 GCATAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:27847 original size:20 final size:19
Alignment explanation
Indices: 27803--27848 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
27793 TATCCAAACA
27803 TTAGAAAAGTAAATCATTT
1 TTAGAAAAGTAAATCATTT
* *
27822 TCAGAAAAGTAAATTATTTT
1 TTAGAAAAGTAAATCA-TTT
27842 TTAGAAA
1 TTAGAAA
27849 TTATTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.37
Consensus pattern (19 bp):
TTAGAAAAGTAAATCATTT
Found at i:27851 original size:14 final size:15
Alignment explanation
Indices: 27832--27860 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
27822 TCAGAAAAGT
27832 AAATTATTTT-TTAG
1 AAATTATTTTATTAG
27846 AAATTATTTTATTAG
1 AAATTATTTTATTAG
27861 CAAACAAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (15 bp):
AAATTATTTTATTAG
Found at i:28961 original size:157 final size:157
Alignment explanation
Indices: 28675--28989 Score: 549
Period size: 157 Copynumber: 2.0 Consensus size: 157
28665 TCTTAAAATG
* *
28675 TCCTTAGTCAAGTATTATTGTGCGTTTGAACAATGATAATGCATTGAGGCTAATGTCTAGTTGAT
1 TCCTTAGTCAAGTATTATTGTGCGCTTGAACAATGATAATGCATTGAGACTAATGTCTAGTTGAT
*
28740 TGATGACAAAGTGTTTTCATTGACATAGGGATGTCAAAATCGATTCATGAGTATGTATTAGAGAA
66 TGATGACAAAGTGTTTTCATTGACATAGGGATGTCAAAATCGATACATGAGTATGTATTAGAGAA
28805 CAACATACTGGACTAACTCACTATGAT
131 CAACATACTGGACTAACTCACTATGAT
* *
28832 TCCTTAGTCAAGTATTATTGTGGGCTTGAACAATGATAATGCATTGAGACTAATGTGTAGTTGAT
1 TCCTTAGTCAAGTATTATTGTGCGCTTGAACAATGATAATGCATTGAGACTAATGTCTAGTTGAT
* * * *
28897 TGATGGCAAAGTGTTTTTATTGACATAGGGATGTCAAAATTGATACATGAGTATGTGTTAGAGAA
66 TGATGACAAAGTGTTTTCATTGACATAGGGATGTCAAAATCGATACATGAGTATGTATTAGAGAA
28962 CAACATACTGGACTAACTCACTATGAT
131 CAACATACTGGACTAACTCACTATGAT
28989 T
1 T
28990 ATGTTTCTTG
Statistics
Matches: 149, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
157 149 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.34
Consensus pattern (157 bp):
TCCTTAGTCAAGTATTATTGTGCGCTTGAACAATGATAATGCATTGAGACTAATGTCTAGTTGAT
TGATGACAAAGTGTTTTCATTGACATAGGGATGTCAAAATCGATACATGAGTATGTATTAGAGAA
CAACATACTGGACTAACTCACTATGAT
Found at i:34853 original size:12 final size:12
Alignment explanation
Indices: 34836--34863 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
34826 TTGAACATAG
34836 TTGAAACGGTCT
1 TTGAAACGGTCT
34848 TTGAAACGGTCT
1 TTGAAACGGTCT
34860 TTGA
1 TTGA
34864 TCATGTGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (12 bp):
TTGAAACGGTCT
Found at i:37915 original size:65 final size:65
Alignment explanation
Indices: 37840--37974 Score: 254
Period size: 65 Copynumber: 2.1 Consensus size: 65
37830 TGTTCCATGC
*
37840 AAAG-AGATTAAATGTAGGATGAGATAGATGAATATAAATATTTCTATGTCAAAAGTTTCAGTTA
1 AAAGAAGATTAAATGTAGGATGAGATAGACGAATATAAATATTTCTATGTCAAAAGTTTCAGTTA
37904 AAAGAAGATTAAATGTAGGATGAGATAGACGAATATAAATATTTCTATGTCAAAAGTTTCAGTTA
1 AAAGAAGATTAAATGTAGGATGAGATAGACGAATATAAATATTTCTATGTCAAAAGTTTCAGTTA
37969 AAAGAA
1 AAAGAA
37975 AATGTAGCTT
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
64 4 0.06
65 65 0.94
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.30
Consensus pattern (65 bp):
AAAGAAGATTAAATGTAGGATGAGATAGACGAATATAAATATTTCTATGTCAAAAGTTTCAGTTA
Found at i:42099 original size:11 final size:11
Alignment explanation
Indices: 42083--42112 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
42073 CCTTACTACT
42083 TTTCTCTTGTA
1 TTTCTCTTGTA
*
42094 TTTCTCTTGTG
1 TTTCTCTTGTA
42105 TTTCTCTT
1 TTTCTCTT
42113 CTCATCATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.03, C:0.20, G:0.10, T:0.67
Consensus pattern (11 bp):
TTTCTCTTGTA
Found at i:45871 original size:28 final size:27
Alignment explanation
Indices: 45823--45881 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 27
45813 CGGTATCAAA
45823 TATTTTAATATATGTGTAGAAATCATAT
1 TATTTTAATATATGTGTAG-AATCATAT
*
45851 TATTTTAA-ATATCG-GTGAGAATGATAT
1 TATTTTAATATAT-GTGT-AGAATCATAT
45878 TATT
1 TATT
45882 AAGCATTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (27 bp):
TATTTTAATATATGTGTAGAATCATAT
Found at i:56889 original size:79 final size:80
Alignment explanation
Indices: 56778--56961 Score: 207
Period size: 79 Copynumber: 2.3 Consensus size: 80
56768 GCTACTCGTT
* * *
56778 CAAATGCCTTCAGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTC-GGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC--GATCTTAACCC
* *
56841 GGATTTAGTAAC-TCGCA
63 GGATATAGTAACTTAGCA
* **
56858 CAAATGCCTTCGGGCTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGATCTTAGTCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGATCTTAACCCGGA
* *
56922 TATGGTCACTTAGCA
66 TATAGTAACTTAGCA
56937 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
56962 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.02
78 24 0.27
79 52 0.58
80 12 0.13
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGATCTTAACCCGGA
TATAGTAACTTAGCA
Found at i:56961 original size:40 final size:40
Alignment explanation
Indices: 56759--56961 Score: 220
Period size: 40 Copynumber: 5.1 Consensus size: 40
56749 CGGAATTTAA
** * *
56759 CCGGATATAGCT-ACTCGTTCAAATGCCTTCAGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
56799 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
56839 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
56878 CCGGA-ATTAGTATCTCGCACAAATGCCTTC--GATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
56917 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
56957 CCGGA
1 CCGGA
56962 CATCATTCAA
Statistics
Matches: 138, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
37 1 0.01
39 53 0.38
40 82 0.59
41 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.