Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold861
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: 47742
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Found at i:9533 original size:23 final size:22
Alignment explanation
Indices: 9481--9533 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
9471 TCCACGTCTT
*
9481 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
9503 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
9526 TTTCTTTT
1 TTTCTTTT
9534 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:19566 original size:30 final size:29
Alignment explanation
Indices: 19464--19566 Score: 89
Period size: 30 Copynumber: 3.4 Consensus size: 29
19454 CGAGTTTAAA
* *
19464 CTAAAATGAGCTAAGTTTTAGCTCGTGAG
1 CTAAATTGAGCTAAGGTTTAGCTCGTGAG
* * * * * * *
19493 CTAAAGTTAAGCTGAGGCTAAACTCCTAAG
1 CTAAA-TTGAGCTAAGGTTTAGCTCGTGAG
*
19523 CTGAAGTTGAGCTAAGGTTTAGCTCGTGAG
1 CT-AAATTGAGCTAAGGTTTAGCTCGTGAG
19553 CTAAATATGAGCTA
1 CTAAAT-TGAGCTA
19567 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 18, Indels: 5
0.70 0.24 0.07
Matches are distributed among these distances:
29 8 0.15
30 43 0.81
31 2 0.04
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (29 bp):
CTAAATTGAGCTAAGGTTTAGCTCGTGAG
Found at i:23860 original size:11 final size:11
Alignment explanation
Indices: 23840--23872 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
23830 GAATTGGTAC
23840 GAAATGGTATG
1 GAAATGGTATG
*
23851 GAATTGGTAT-
1 GAAATGGTATG
23861 GAAATGGTATG
1 GAAATGGTATG
23872 G
1 G
23873 TATTTGGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (11 bp):
GAAATGGTATG
Found at i:23887 original size:21 final size:21
Alignment explanation
Indices: 23829--23885 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
23819 TTGGTATTTG
23829 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
23850 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
23871 GGTATTTGGTACGAA
1 GG-AATTGGTACGAA
23886 TGTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 22 0.69
22 10 0.31
ACGTcount: A:0.32, C:0.04, G:0.33, T:0.32
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:28646 original size:24 final size:23
Alignment explanation
Indices: 28592--28647 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
28582 GATTAATTAA
**
28592 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
28615 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
28639 GAAATGGTA
1 GAAATGGTA
28648 ATGGTTCAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.23, C:0.04, G:0.32, T:0.41
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:32868 original size:15 final size:15
Alignment explanation
Indices: 32848--32902 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
32838 ACTCTCCTCA
*
32848 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
32863 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
32878 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
32892 TTCTTTT-TCTC
1 TTCTTTTCTCTC
32903 GCTCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:35510 original size:14 final size:13
Alignment explanation
Indices: 35503--35536 Score: 59
Period size: 14 Copynumber: 2.5 Consensus size: 13
35493 AAAAAACTTG
35503 AAAAAAAATTCAAA
1 AAAAAAAATTC-AA
35517 AAAAAAAATTCAA
1 AAAAAAAATTCAA
35530 AAAAAAA
1 AAAAAAA
35537 GTTTGTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:35609 original size:16 final size:13
Alignment explanation
Indices: 35578--35630 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
35568 ATTTAGTATT
*
35578 GAAGGAAAAAAAA
1 GAAGAAAAAAAAA
35591 GAAGAAAAAAAATTCA
1 GAAGAAAAAAAA---A
**
35607 GAATTAAAAAAAA
1 GAAGAAAAAAAAA
35620 GAAGAAAAAAA
1 GAAGAAAAAAA
35631 TCGAAATTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 21 0.66
16 11 0.34
ACGTcount: A:0.75, C:0.02, G:0.15, T:0.08
Consensus pattern (13 bp):
GAAGAAAAAAAAA
Found at i:35627 original size:27 final size:28
Alignment explanation
Indices: 35582--35651 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 28
35572 AGTATTGAAG
35582 GAAAAAAAAGAAGAAAAAAAATTC-AGAATT
1 GAAAAAAAAGAAG-AAAAAAA-TCGA-AATT
35612 -AAAAAAAAGAAGAAAAAAATCGAAATT
1 GAAAAAAAAGAAGAAAAAAATCGAAATT
35639 GAAAAAAAA-AAGA
1 GAAAAAAAAGAAGA
35652 GTGATTGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
27 10 0.26
28 16 0.42
29 12 0.32
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (28 bp):
GAAAAAAAAGAAGAAAAAAATCGAAATT
Found at i:37544 original size:29 final size:29
Alignment explanation
Indices: 37481--37548 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
37471 TAATCAACCA
37481 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
37510 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
37539 CGCACACTTA
1 CGCACACTTA
37549 CCTTTTTCCG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:37692 original size:29 final size:30
Alignment explanation
Indices: 37653--37731 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
37643 CTTAATAATC
37653 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
37683 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
37712 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
37732 ATCTCATGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:37724 original size:177 final size:173
Alignment explanation
Indices: 37379--37725 Score: 498
Period size: 177 Copynumber: 2.0 Consensus size: 173
37369 CTCAAGGACC
* * *
37379 TTTTCCGCTGTCCAAAATTGACTCGGTAAAGTTGCACCCTTCATGTAAATAATTTATAGAAATAT
1 TTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATAGAAATAT
* * *
37444 ATATAGGGTTGCACGCATAATGTTTAGTAATCAACCACGCACACTTAGTGCCATGCACTTTAAAC
66 ATATAGGGTTGCACACATAATGCTTAATAATCAACCACGCACACTTAGTGCCATGCACTTTAAAC
* ***
37509 TCACACACTTAGTGCCATGCATTTCAAGTTCGCACACTTACCT
131 TCACACACTTAGTGCCATACATTTCAAACCCGCACACTTACCT
37552 TTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATAGAAAATA
1 TTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATAG-AAATA
* * *
37617 TATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGTACTTT
65 TATATA--GGGTT-GCACACATAATGCTTAATAATCAACCACGCACACTTAGTGCCATGCACTTT
* **
37682 AAACTCGCACACTTAGTGCTGTACAATTT-AAACCCGCACACTTA
127 AAACTCACACACTTAGTGCCATAC-ATTTCAAACCCGCACACTTA
37726 GTGCCAATCT
Statistics
Matches: 153, Mismatches: 16, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
173 56 0.37
174 11 0.07
176 5 0.03
177 77 0.50
178 4 0.03
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (173 bp):
TTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATAGAAATAT
ATATAGGGTTGCACACATAATGCTTAATAATCAACCACGCACACTTAGTGCCATGCACTTTAAAC
TCACACACTTAGTGCCATACATTTCAAACCCGCACACTTACCT
Found at i:45835 original size:29 final size:29
Alignment explanation
Indices: 45772--45839 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
45762 TAATCAACCA
45772 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
45801 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
45830 CGCACACTTA
1 CGCACACTTA
45840 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:45981 original size:29 final size:30
Alignment explanation
Indices: 45942--46020 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
45932 CTTAATAATC
45942 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
45972 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
46001 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
46021 ATCTCATGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Done.