Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold256
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: 46209
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:851 original size:50 final size:50
Alignment explanation
Indices: 727--975 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
717 GATAATAACA
* * ** * *
727 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
778 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
828 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
878 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
933 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
976 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:905 original size:100 final size:104
Alignment explanation
Indices: 726--975 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
716 TGATAATAAC
**
726 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
791 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
828 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
891 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
933 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
976 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:1092 original size:13 final size:13
Alignment explanation
Indices: 1071--1102 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1061 GCTTGGATCA
*
1071 TCATCAAATAAAT
1 TCATAAAATAAAT
1084 TCATAAAATAAAT
1 TCATAAAATAAAT
1097 TCATAA
1 TCATAA
1103 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:1349 original size:30 final size:30
Alignment explanation
Indices: 1314--1371 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1304 CCTCGACTCT
*
1314 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
1344 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
1372 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:2565 original size:10 final size:10
Alignment explanation
Indices: 2546--2610 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 10
2536 GCCATTGATG
*
2546 AAAATATAAA
1 AAAATTTAAA
2556 AAAATTTAAA
1 AAAATTTAAA
* *
2566 ATTATTTTAAA
1 A-AAATTTAAA
*
2577 AAAA-TAAAA
1 AAAATTTAAA
*
2586 AAAAATTAAA
1 AAAATTTAAA
**
2596 ATTATTTAAA
1 AAAATTTAAA
2606 AAAAT
1 AAAAT
2611 GAAATTGAGG
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
9 8 0.20
10 25 0.61
11 8 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:2589 original size:30 final size:30
Alignment explanation
Indices: 2546--2610 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
2536 GCCATTGATG
*
2546 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAAATTAAAATTA-TTTAAA
2577 AAAATA-AAAAAAAATTAAAATTATTTAAA
1 AAAATATAAAAAAAATTAAAATTATTTAAA
2606 AAAAT
1 AAAAT
2611 GAAATTGAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 11 0.33
30 16 0.48
31 6 0.18
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (30 bp):
AAAATATAAAAAAAATTAAAATTATTTAAA
Found at i:2666 original size:29 final size:29
Alignment explanation
Indices: 2634--2717 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 29
2624 AATTGAAATT
2634 AAATATGGATTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
* * **
2663 AAAT-T-GA---GAG-GAA-ATTGAAATT
1 AAATATGGATTTGAGAGAATTTTGGAAGG
*
2685 AAATATGGGTTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
2714 AAAT
1 AAAT
2718 TTAGAAGGAA
Statistics
Matches: 39, Mismatches: 9, Indels: 14
0.63 0.15 0.23
Matches are distributed among these distances:
22 9 0.23
23 4 0.10
24 4 0.10
27 5 0.13
28 4 0.10
29 13 0.33
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.30
Consensus pattern (29 bp):
AAATATGGATTTGAGAGAATTTTGGAAGG
Found at i:2666 original size:51 final size:51
Alignment explanation
Indices: 2611--2732 Score: 208
Period size: 51 Copynumber: 2.4 Consensus size: 51
2601 TTAAAAAAAT
*
2611 GAAATTGAGGGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
*
2662 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
*
2713 GAAATTTAGAAGGAAATTGA
1 GAAATTGAG-AGGAAATTGA
2733 GAGGATTAGA
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
51 57 0.85
52 10 0.15
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
Found at i:2982 original size:29 final size:28
Alignment explanation
Indices: 2932--2992 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
2922 CGATTTCTCG
*
2932 AAAAATAGACCATTCCGGTAAATAATAA
1 AAAAATAGACCATTCCAGTAAATAATAA
* * **
2960 AAAAATCGACCTATTTCAGTAAATTTTAA
1 AAAAATAGACC-ATTCCAGTAAATAATAA
2989 AAAA
1 AAAA
2993 GAACGACTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.26
Consensus pattern (28 bp):
AAAAATAGACCATTCCAGTAAATAATAA
Found at i:6921 original size:50 final size:50
Alignment explanation
Indices: 6846--6945 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
6836 TAATAAAGAA
6846 AAAAAATTTACCATTTGATTACAAATTACTGTTAAGATTAACGCTTGCTT
1 AAAAAATTTACCATTTGATTACAAATTACTGTTAAGATTAACGCTTGCTT
*
6896 AAAAAATTTACCTTTTGATTACAAATTACTGTTAAGATTAACGCTTGCTT
1 AAAAAATTTACCATTTGATTACAAATTACTGTTAAGATTAACGCTTGCTT
6946 TACCAATCTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (50 bp):
AAAAAATTTACCATTTGATTACAAATTACTGTTAAGATTAACGCTTGCTT
Found at i:10283 original size:21 final size:21
Alignment explanation
Indices: 10257--10297 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10247 ATCTGCTCAA
* *
10257 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
10278 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
10298 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:19261 original size:43 final size:42
Alignment explanation
Indices: 19214--19306 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 42
19204 CAACACAAAA
* *
19214 CAACCCCTTTCACAATCAAGGATACAGTAGAATCAGCACTTAG
1 CAACCCCTTTCACAATCAAGAATAC-GGAGAATCAGCACTTAG
* * * * * * *
19257 CAACCACTTTTAGAATCAATAATTCGGGGAATTAGCACTTAG
1 CAACCCCTTTCACAATCAAGAATACGGAGAATCAGCACTTAG
19299 CAACCCCT
1 CAACCCCT
19307 CGGGAAATCT
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
42 21 0.52
43 19 0.47
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (42 bp):
CAACCCCTTTCACAATCAAGAATACGGAGAATCAGCACTTAG
Found at i:25759 original size:19 final size:19
Alignment explanation
Indices: 25724--25762 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
25714 AATAGACTAA
*
25724 TTTATAAATTTGTCGAATT
1 TTTATAAATTTGACGAATT
25743 TTTATGAAATTT-ACGAATT
1 TTTAT-AAATTTGACGAATT
25762 T
1 T
25763 AGATTGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (19 bp):
TTTATAAATTTGACGAATT
Found at i:30378 original size:7 final size:7
Alignment explanation
Indices: 30368--30397 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
30358 AAATATAAAT
30368 AAAATTA
1 AAAATTA
30375 AAAATTA
1 AAAATTA
30382 AAAATT-
1 AAAATTA
30388 AAAATTA
1 AAAATTA
30395 AAA
1 AAA
30398 TATAGTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTA
Found at i:30383 original size:13 final size:14
Alignment explanation
Indices: 30368--30397 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
30358 AAATATAAAT
30368 AAAATTAAAAATTA
1 AAAATTAAAAATTA
30382 AAAATT-AAAATTA
1 AAAATTAAAAATTA
30395 AAA
1 AAA
30398 TATAGTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAATTAAAAATTA
Found at i:37466 original size:19 final size:19
Alignment explanation
Indices: 37444--37480 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
37434 AAAAAAAAAA
37444 AACA-AAATAAAATTACACT
1 AACATAAATAAAA-TACACT
37463 AACATAAATAAAATACAC
1 AACATAAATAAAATACAC
37481 AACTCCTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.65, C:0.16, G:0.00, T:0.19
Consensus pattern (19 bp):
AACATAAATAAAATACACT
Found at i:44613 original size:3 final size:3
Alignment explanation
Indices: 44605--44641 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
44595 AAGCTTATTT
44605 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
44642 ATATATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Done.