Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3001
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: 61027
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:1657 original size:41 final size:40
Alignment explanation
Indices: 1559--1657 Score: 90
Period size: 41 Copynumber: 2.4 Consensus size: 40
1549 ATTTTGATTG
* * *
1559 AAAAAAAAAATTCAAAAAAAAGTGAAAAAAAAATCGAGCA
1 AAAAAAAAAAATGAAAAAAAAGTGAAAAAAAAATCAAGCA
* * ** **
1599 AAAAAAAAGAAAAGAAAAAAAGGTGAGCAAAAAATCAAGTTT
1 AAAAAAAA-AAATGAAAAAAAAGTGAAAAAAAAATCAAG-CA
*
1641 AAAAAAAAAAGTGAAAA
1 AAAAAAAAAAATGAAAA
1658 GTCTTGCGAG
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
40 8 0.17
41 30 0.65
42 8 0.17
ACGTcount: A:0.72, C:0.05, G:0.13, T:0.10
Consensus pattern (40 bp):
AAAAAAAAAAATGAAAAAAAAGTGAAAAAAAAATCAAGCA
Found at i:2521 original size:13 final size:13
Alignment explanation
Indices: 2505--2559 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
2495 AAAGTGAGAG
2505 AAAAAGAAAATGA
1 AAAAAGAAAATGA
*
2518 AAAAAGAAATTG-
1 AAAAAGAAAATGA
*
2530 AAAAAGAAAAAGCGA
1 AAAAAG-AAAA-TGA
*
2545 AAAAAGAAATTGA
1 AAAAAGAAAATGA
2558 AA
1 AA
2560 GAGAGCTTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 6 0.18
13 18 0.53
14 4 0.12
15 6 0.18
ACGTcount: A:0.73, C:0.02, G:0.16, T:0.09
Consensus pattern (13 bp):
AAAAAGAAAATGA
Found at i:2554 original size:27 final size:25
Alignment explanation
Indices: 2504--2559 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 25
2494 AAAAGTGAGA
*
2504 GAAAAAGAAAATGAAAAAAGAAATT
1 GAAAAAGAAAACGAAAAAAGAAATT
2529 GAAAAAGAAAAAGCGAAAAAAGAAATT
1 GAAAAAG-AAAA-CGAAAAAAGAAATT
2556 GAAA
1 GAAA
2560 GAGAGCTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 7 0.25
26 4 0.14
27 17 0.61
ACGTcount: A:0.71, C:0.02, G:0.18, T:0.09
Consensus pattern (25 bp):
GAAAAAGAAAACGAAAAAAGAAATT
Found at i:2593 original size:33 final size:33
Alignment explanation
Indices: 2556--2618 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
2546 AAAAGAAATT
2556 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
2589 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
2619 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:4425 original size:20 final size:20
Alignment explanation
Indices: 4400--4445 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
4390 CCCAGCTCGA
*
4400 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
4420 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
4440 TTAGCT
1 TTAGCT
4446 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:4436 original size:30 final size:30
Alignment explanation
Indices: 4393--4465 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
4383 AGTTTTTCCC
*
4393 AGCTCGATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCGTTTGAGCTCA-ATTGAGCTTAATTT
* *
4422 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
4452 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
4466 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 9 0.23
30 30 0.77
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:6686 original size:18 final size:18
Alignment explanation
Indices: 6665--6749 Score: 55
Period size: 18 Copynumber: 4.6 Consensus size: 18
6655 GTAACAAGAA
6665 ATTGAAAAAGAGAGTGAG
1 ATTGAAAAAGAGAGTGAG
*
6683 ATTGAAGAAAGA-AATGAG
1 ATTGAA-AAAGAGAGTGAG
* * **
6701 AGTGTAAAAGAAACGAGTGTC
1 ATTG-AAAA-AGA-GAGTGAG
* * *
6722 ATGGAAAAAGAAATTGAG
1 ATTGAAAAAGAGAGTGAG
6740 ATTGAAAAAG
1 ATTGAAAAAG
6750 GATGTGAAAA
Statistics
Matches: 48, Mismatches: 14, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
18 28 0.58
19 11 0.23
20 4 0.08
21 5 0.10
ACGTcount: A:0.52, C:0.02, G:0.28, T:0.18
Consensus pattern (18 bp):
ATTGAAAAAGAGAGTGAG
Found at i:6804 original size:48 final size:47
Alignment explanation
Indices: 6725--6830 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
6715 GAGTGTCATG
*
6725 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
6773 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
6821 GAAAAAGAAA
1 GAAAAAGAAA
6831 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:8542 original size:20 final size:20
Alignment explanation
Indices: 8496--8542 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
8486 AGCTTGTTTC
*
8496 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
8516 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
8536 CAGCTCA
1 CAGCTCA
8543 ATCTTAACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:10809 original size:21 final size:21
Alignment explanation
Indices: 10785--10852 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
10775 GATTTTGAAT
10785 GAAATCGAGAGAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
***** *
10806 GAAAAT-GAGAGAATCTTGAAT
1 G-AAATCGAGAGAAGAAACAAA
*
10827 GAAATCGAGAAAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
10848 GAAAT
1 GAAAT
10853 GAAAGAAAAA
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 4 0.12
21 24 0.75
22 4 0.12
ACGTcount: A:0.59, C:0.07, G:0.22, T:0.12
Consensus pattern (21 bp):
GAAATCGAGAGAAGAAACAAA
Found at i:10825 original size:42 final size:42
Alignment explanation
Indices: 10763--10859 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
10753 AGATTATGAG
* * *
10763 AGAAAATGAGAGGATTTTGAATGAAATCGAGAGAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
10805 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
*
10847 AG-AAATGAAAGAA
1 AGAAAATGAGAGAA
10860 AAAGAAAAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 10 0.20
42 41 0.80
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (42 bp):
AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
Found at i:10886 original size:18 final size:18
Alignment explanation
Indices: 10863--10912 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
10853 GAAAGAAAAA
*
10863 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
10881 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
10899 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
10913 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:10889 original size:24 final size:24
Alignment explanation
Indices: 10856--10937 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
10846 AAGAAATGAA
10856 AGAAAAAGAAAAAGAGATTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
* * * *
10880 TGAAAAAGAAAATGAGATTGAAAA
1 AGAAAAAGAAAAAGAGATTGAGAG
* * *
10904 AGAGAATGAAAAAGAGTTTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
10928 AGAAAAAGAA
1 AGAAAAAGAA
10938 TGTGAACAAG
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (24 bp):
AGAAAAAGAAAAAGAGATTGAGAG
Found at i:12784 original size:30 final size:30
Alignment explanation
Indices: 12750--12846 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
12740 TAAACTAAAA
*
12750 TGAGCTAAACTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
12780 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
12810 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
12840 TGAGCTA
1 TGAGCTA
12847 GGAGTAAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.86
31 5 0.10
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:18282 original size:20 final size:20
Alignment explanation
Indices: 18235--18283 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
18225 AAATGAGCTC
18235 AAATGAGCTGAGTTGAGCTGG
1 AAATGAGCTGAG-TGAGCTGG
*
18256 ACA-GAGCTCGAG-GAGCTGG
1 AAATGAGCT-GAGTGAGCTGG
18275 AAATGAGCT
1 AAATGAGCT
18284 AGGATCAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 9 0.38
20 10 0.42
21 5 0.21
ACGTcount: A:0.31, C:0.14, G:0.37, T:0.18
Consensus pattern (20 bp):
AAATGAGCTGAGTGAGCTGG
Found at i:19146 original size:22 final size:21
Alignment explanation
Indices: 19113--19154 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
19103 TCAAACCTAC
19113 ACAAGCATGCAAAATTTACACA
1 ACAAGCATGCAAAA-TTACACA
*
19135 ACAAGGCA-GCAACATTACAC
1 ACAA-GCATGCAAAATTACAC
19155 TACCATCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.33
22 9 0.50
23 3 0.17
ACGTcount: A:0.48, C:0.26, G:0.12, T:0.14
Consensus pattern (21 bp):
ACAAGCATGCAAAATTACACA
Found at i:19838 original size:10 final size:10
Alignment explanation
Indices: 19823--19849 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
19813 TACTCCTTCA
19823 AGCTCAAATC
1 AGCTCAAATC
19833 AGCTCAAATC
1 AGCTCAAATC
19843 AGCTCAA
1 AGCTCAA
19850 CTTCAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:33548 original size:15 final size:16
Alignment explanation
Indices: 33485--33604 Score: 50
Period size: 16 Copynumber: 7.1 Consensus size: 16
33475 TCTATTGAGC
33485 AAATAAGAGAAAAAGAA
1 AAATAA-AGAAAAAGAA
* ***
33502 AAAGAAAGTTGTAA-AA
1 AAATAAAG-AAAAAGAA
* *
33518 AAATAAAGGAAGAGAA
1 AAATAAAGAAAAAGAA
33534 AAAT-AAGAAAAAGAA
1 AAATAAAGAAAAAGAA
*
33549 AACAAAAGAGAGTAACAAGAA
1 AA-ATAA-AGA--AA-AAGAA
33570 AAATATCCAAGAAAAAGAA
1 AAATA---AAGAAAAAGAA
*
33589 GAA-AAAG-AAAAGAA
1 AAATAAAGAAAAAGAA
33603 AA
1 AA
33605 TCGAGAAAAT
Statistics
Matches: 77, Mismatches: 15, Indels: 25
0.66 0.13 0.21
Matches are distributed among these distances:
14 8 0.10
15 15 0.19
16 18 0.23
17 8 0.10
18 4 0.05
19 7 0.09
20 6 0.08
21 7 0.09
22 3 0.04
23 1 0.01
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.07
Consensus pattern (16 bp):
AAATAAAGAAAAAGAA
Found at i:36068 original size:12 final size:13
Alignment explanation
Indices: 36051--36083 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
36041 TTAAACTAAG
36051 TAAATAAATAA-A
1 TAAATAAATAATA
36063 TAAATAAATAATA
1 TAAATAAATAATA
*
36076 AAAATAAA
1 TAAATAAA
36084 ACTTTACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAATAATA
Found at i:37482 original size:23 final size:22
Alignment explanation
Indices: 37430--37482 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
37420 TCCACGTCTT
*
37430 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
37452 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
37475 TTTCTTTT
1 TTTCTTTT
37483 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:45438 original size:20 final size:20
Alignment explanation
Indices: 45392--45438 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
45382 AGCTCGTTTC
*
45392 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
45412 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
45432 CAGCTCA
1 CAGCTCA
45439 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:47828 original size:30 final size:31
Alignment explanation
Indices: 47794--47890 Score: 94
Period size: 30 Copynumber: 3.2 Consensus size: 31
47784 AGCTCACTCC
*
47794 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * *
47824 TAGCTCAAC-TTCAGCTTA-GAAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACG-AGCTAAACCT
* *
47854 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
47884 TAGCTCA
1 TAGCTCA
47891 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
29 1 0.02
30 45 0.88
31 5 0.10
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:60547 original size:24 final size:22
Alignment explanation
Indices: 60494--60552 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 22
60484 CCACAGTCTT
60494 TTTCTTTTGTT-TCTTTTTCTAA
1 TTTCTTTT-TTCTCTTTTTCTAA
*
60516 -TTCATTTTTCTCTTCTTTCTCAA
1 TTTCTTTTTTCTCTT-TTTCT-AA
*
60539 TTTCTTTTTACTCT
1 TTTCTTTTTTCTCT
60553 CAATCTCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 2 0.07
21 10 0.33
22 5 0.17
23 2 0.07
24 11 0.37
ACGTcount: A:0.10, C:0.20, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTCTTTTTTCTCTTTTTCTAA
Found at i:60553 original size:17 final size:17
Alignment explanation
Indices: 60533--60569 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
60523 TTCTCTTCTT
*
60533 TCTCAATTTCTTTTTAC
1 TCTCAATCTCTTTTTAC
*
60550 TCTCAATCTCTTTTTGC
1 TCTCAATCTCTTTTTAC
60567 TCT
1 TCT
60570 GATACCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.27, G:0.03, T:0.57
Consensus pattern (17 bp):
TCTCAATCTCTTTTTAC
Done.