Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold672
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: 58529
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1589 original size:13 final size:13
Alignment explanation
Indices: 1571--1607 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
1561 ATATGTATTT
1571 CTCGAAAAAAAAA
1 CTCGAAAAAAAAA
1584 CTCG-AAAAAAAA
1 CTCGAAAAAAAAA
*
1596 TTC-AAAAAAAAA
1 CTCGAAAAAAAAA
1608 AATTCAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.70, C:0.14, G:0.05, T:0.11
Consensus pattern (13 bp):
CTCGAAAAAAAAA
Found at i:1605 original size:14 final size:14
Alignment explanation
Indices: 1588--1619 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1578 AAAAAACTCG
1588 AAAAAAAATTCAAA
1 AAAAAAAATTCAAA
1602 AAAAAAAATTCAAA
1 AAAAAAAATTCAAA
1616 AAAA
1 AAAA
1620 CACTAGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAAAAATTCAAA
Found at i:1607 original size:12 final size:12
Alignment explanation
Indices: 1575--1619 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
1565 GTATTTCTCG
*
1575 AAAAAAAAACTC
1 AAAAAAAAATTC
*
1587 GAAAAAAAATTC
1 AAAAAAAAATTC
1599 AAAAAAAAAAATTC
1 --AAAAAAAAATTC
1613 AAAAAAA
1 AAAAAAA
1620 CACTAGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 17 0.61
14 11 0.39
ACGTcount: A:0.78, C:0.09, G:0.02, T:0.11
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:1685 original size:14 final size:13
Alignment explanation
Indices: 1661--1724 Score: 76
Period size: 13 Copynumber: 4.9 Consensus size: 13
1651 AGTAATCAAG
1661 TTGTG-AAAAAAA
1 TTGTGAAAAAAAA
*
1673 TTTTGAAAAAAAA
1 TTGTGAAAAAAAA
1686 TTGTGAAAAAAAAA
1 TTGTG-AAAAAAAA
**
1700 TTGTGAAAAAATT
1 TTGTGAAAAAAAA
*
1713 TTTTGAAAAAAA
1 TTGTGAAAAAAA
1725 GAGAGCTAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
12 4 0.09
13 27 0.61
14 13 0.30
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:1689 original size:25 final size:25
Alignment explanation
Indices: 1661--1724 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 25
1651 AGTAATCAAG
*
1661 TTGTGAAAAAAATTTTGAAAAAAAA
1 TTGTGAAAAAAATTGTGAAAAAAAA
**
1686 TTGTGAAAAAAAAATTGTGAAAAAATT
1 TTGTG--AAAAAAATTGTGAAAAAAAA
*
1713 TTTTGAAAAAAA
1 TTGTGAAAAAAA
1725 GAGAGCTAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 12 0.36
27 21 0.64
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (25 bp):
TTGTGAAAAAAATTGTGAAAAAAAA
Found at i:6684 original size:13 final size:12
Alignment explanation
Indices: 6666--6720 Score: 83
Period size: 12 Copynumber: 4.5 Consensus size: 12
6656 CCGTATGCAA
6666 TTTTTTTCAAATT
1 TTTTTTTC-AATT
6679 TTTTTTTCAATT
1 TTTTTTTCAATT
*
6691 TTTTTTTCGATT
1 TTTTTTTCAATT
*
6703 TTTTTTTCGATT
1 TTTTTTTCAATT
6715 TTTTTT
1 TTTTTT
6721 GATTACATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
12 33 0.80
13 8 0.20
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (12 bp):
TTTTTTTCAATT
Found at i:11690 original size:13 final size:13
Alignment explanation
Indices: 11672--11728 Score: 80
Period size: 13 Copynumber: 4.5 Consensus size: 13
11662 TTGTAGATTC
11672 AAAAAAAATCGAA
1 AAAAAAAATCGAA
11685 AAAAAAAATCG-A
1 AAAAAAAATCGAA
*
11697 AAAAAAAATTGAA
1 AAAAAAAATCGAA
* *
11710 AAAAAAATTTGAA
1 AAAAAAAATCGAA
11723 AAAAAA
1 AAAAAA
11729 TTGCATACGG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
12 11 0.27
13 30 0.73
ACGTcount: A:0.77, C:0.04, G:0.07, T:0.12
Consensus pattern (13 bp):
AAAAAAAATCGAA
Found at i:11731 original size:24 final size:25
Alignment explanation
Indices: 11672--11728 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
11662 TTGTAGATTC
*
11672 AAAAAAAATCGAAAAAAAAAATCGA
1 AAAAAAAATTGAAAAAAAAAATCGA
* *
11697 AAAAAAAATTGAAAAAAAAATTTGA
1 AAAAAAAATTGAAAAAAAAAATCGA
11722 AAAAAAA
1 AAAAAAA
11729 TTGCATACGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.77, C:0.04, G:0.07, T:0.12
Consensus pattern (25 bp):
AAAAAAAATTGAAAAAAAAAATCGA
Found at i:16734 original size:14 final size:14
Alignment explanation
Indices: 16715--16776 Score: 106
Period size: 14 Copynumber: 4.4 Consensus size: 14
16705 ACTAGCTCTC
16715 TTTTTTTCAAAATT
1 TTTTTTTCAAAATT
*
16729 TTTTTTTCACAATT
1 TTTTTTTCAAAATT
*
16743 TTTTTTTCACAATT
1 TTTTTTTCAAAATT
16757 TTTTTTTCAAAATT
1 TTTTTTTCAAAATT
16771 TTTTTT
1 TTTTTT
16777 CACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 46 1.00
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTTTTCAAAATT
Found at i:16836 original size:12 final size:12
Alignment explanation
Indices: 16819--16863 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
16809 TGGAAACTAG
16819 TTTTTTTTTGAA
1 TTTTTTTTTGAA
16831 TTTTTTTTTGAA
1 TTTTTTTTTGAA
* *
16843 TTTTTTTTCGAG
1 TTTTTTTTTGAA
16855 TTTTTTTTT
1 TTTTTTTTT
16864 CGAGAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.11, C:0.02, G:0.09, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:20305 original size:23 final size:23
Alignment explanation
Indices: 20275--20363 Score: 151
Period size: 23 Copynumber: 3.9 Consensus size: 23
20265 CTTTTTGAAC
*
20275 CATTTCCATTTCGAACCAAATTA
1 CATTTCCATTTCGTACCAAATTA
20298 CATTTCCATTTCGTACCAAATTA
1 CATTTCCATTTCGTACCAAATTA
20321 CATTTCCATTTCGTACCAAATTA
1 CATTTCCATTTCGTACCAAATTA
* *
20344 TATTACCATTTCGTACCAAA
1 CATTTCCATTTCGTACCAAA
20364 CCCAAACCCA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (23 bp):
CATTTCCATTTCGTACCAAATTA
Found at i:27552 original size:6 final size:6
Alignment explanation
Indices: 27541--27566 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
27531 ATAAATAAAT
27541 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
27567 CTTTACAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:28114 original size:20 final size:21
Alignment explanation
Indices: 28071--28114 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
28061 CAATCCGTGC
* *
28071 GCTCTACTTCAAGCTCACTCA
1 GCTCAACTTCAAGCTCAATCA
*
28092 GCTCAACTTC-AGCTCAATGA
1 GCTCAACTTCAAGCTCAATCA
28112 GCT
1 GCT
28115 TGATGCGACC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.25, C:0.34, G:0.14, T:0.27
Consensus pattern (21 bp):
GCTCAACTTCAAGCTCAATCA
Found at i:29408 original size:55 final size:55
Alignment explanation
Indices: 29293--29409 Score: 148
Period size: 55 Copynumber: 2.1 Consensus size: 55
29283 TGCATGTTTT
* * *
29293 CATT-AATGCCGTCCATGCATGGGAACATCTCATTAAATCCATGTCTTTGCTTCC
1 CATTAAATGCCGTCCATGCATGGGAACATCTCATTAAATCCATGGCTTTGCTGCA
* * * *
29347 CTTTAAATGCCGTTCCATGCATGGGAACATCTCCTT-AATTCGTGGCTTTGCTGCA
1 CATTAAATGCCG-TCCATGCATGGGAACATCTCATTAAATCCATGGCTTTGCTGCA
29402 CATTAAAT
1 CATTAAAT
29410 CAGCAAGCAG
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
54 3 0.06
55 28 0.53
56 22 0.42
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (55 bp):
CATTAAATGCCGTCCATGCATGGGAACATCTCATTAAATCCATGGCTTTGCTGCA
Found at i:29705 original size:23 final size:22
Alignment explanation
Indices: 29671--29735 Score: 103
Period size: 23 Copynumber: 2.9 Consensus size: 22
29661 GAACACCTTT
*
29671 AAAACATGCATTAAATTCGGCC
1 AAAACATACATTAAATTCGGCC
29693 AGAAACATACATTAAATTCGGCC
1 A-AAACATACATTAAATTCGGCC
29716 AAAGACATACATTAAATTCG
1 AAA-ACATACATTAAATTCG
29736 TCTGGAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
22 3 0.08
23 37 0.93
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.23
Consensus pattern (22 bp):
AAAACATACATTAAATTCGGCC
Found at i:29973 original size:13 final size:13
Alignment explanation
Indices: 29957--29991 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
29947 TTTAAACAAA
*
29957 TTAATTAACTTAT
1 TTAATTAACTAAT
29970 TTAATTAACTAAT
1 TTAATTAACTAAT
*
29983 TTAACTAAC
1 TTAATTAAC
29992 AGCAACTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATTAACTAAT
Found at i:36649 original size:12 final size:12
Alignment explanation
Indices: 36606--36659 Score: 72
Period size: 12 Copynumber: 4.5 Consensus size: 12
36596 CCGTATGCAA
*
36606 TTTTTTTTCAAA
1 TTTTTTTTCAAT
36618 TTTTTTTTCAAT
1 TTTTTTTTCAAT
*
36630 TTTTTTTTCGAT
1 TTTTTTTTCAAT
**
36642 TTTTTTTTTGAT
1 TTTTTTTTCAAT
36654 TTTTTT
1 TTTTTT
36660 GAATCTACAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.13, C:0.06, G:0.04, T:0.78
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:36656 original size:11 final size:11
Alignment explanation
Indices: 36617--36659 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
36607 TTTTTTTCAA
**
36617 ATTTTTTTTCA
1 ATTTTTTTTTG
36628 ATTTTTTTTTCG
1 ATTTTTTTTT-G
36640 ATTTTTTTTTTG
1 A-TTTTTTTTTG
36652 ATTTTTTT
1 ATTTTTTT
36660 GAATCTACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 16 0.57
12 3 0.11
13 9 0.32
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.79
Consensus pattern (11 bp):
ATTTTTTTTTG
Found at i:41475 original size:10 final size:10
Alignment explanation
Indices: 41460--41497 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
41450 AAATTTGAAA
*
41460 AAAAAAATCG
1 AAAAAAATTG
41470 AAAAAAATTG
1 AAAAAAATTG
41480 AAAAAAAATTG
1 -AAAAAAATTG
41491 AAAAAAA
1 AAAAAAA
41498 ATTTCGAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.13
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:41475 original size:11 final size:11
Alignment explanation
Indices: 41459--41500 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
41449 GAAATTTGAA
*
41459 AAAAAAAATCG
1 AAAAAAAATTG
41470 -AAAAAAATTG
1 AAAAAAAATTG
41480 AAAAAAAATTG
1 AAAAAAAATTG
41491 AAAAAAAATT
1 AAAAAAAATT
41501 TCGAAGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:41492 original size:34 final size:35
Alignment explanation
Indices: 41417--41498 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 35
41407 AACATATTGT
* *
41417 AATTGAACAAAAAAATCAAAAAAAAAGAAGAGGAA
1 AATTGAAAAAAAAAATCAAAAAAAAAGAAGAGAAA
* **
41452 ATTTGAAAAAAAAAATCGAAAAAAATTGAA-A-AAA
1 AATTGAAAAAAAAAATC-AAAAAAAAAGAAGAGAAA
41486 AATTGAAAAAAAA
1 AATTGAAAAAAAA
41499 TTTCGAAGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
34 14 0.35
35 16 0.40
36 10 0.25
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (35 bp):
AATTGAAAAAAAAAATCAAAAAAAAAGAAGAGAAA
Found at i:57552 original size:40 final size:39
Alignment explanation
Indices: 57500--57683 Score: 165
Period size: 40 Copynumber: 4.6 Consensus size: 39
57490 TAACTCATTC
*
57500 AATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-TTTAAAACTCGCACA
*** *
57540 AATGCCTTCGGGACTTAACCCGGAATTGGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGG-ATTTAAAACTCGCACA
* *
57580 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAA-AACTCGCACA
* ** * ** *
57620 AATACCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-AAAC-TCGCACA
*
57661 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
57684 CAGCATTCAA
Statistics
Matches: 116, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
39 5 0.04
40 99 0.85
41 12 0.10
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAAAACTCGCACA
Found at i:57562 original size:79 final size:80
Alignment explanation
Indices: 57463--57683 Score: 193
Period size: 80 Copynumber: 2.8 Consensus size: 80
57453 CTCGTTCAAG
* * ** * *
57463 TGCCTTCGGGACATAGCCCGGTCA-TAGTAACTCATTC-AATGCCTTCGGGACTTAACCCGGATT
1 TGCCTTCGGGACATAACCCGG-AATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGA-A
*
57526 TTAA-AACTCGCACGAA
64 TTAATAACTCGCACAAA
* * * *
57542 TGCCTTCGGGACTTAACCCGGAATTGGTATCTCGCACAAAGGCCTTCGGGACTTAACCCGGAATT
1 TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
57607 AATAACTCGCACAAA
66 AATAACTCGCACAAA
* * ** * * *
57622 TACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGA-CATAACCCGGAAT-TAGTAACTCA-CACAAAGGCCTTCGGGACTTAACCCGGA
57684 CAGCATTCAA
Statistics
Matches: 116, Mismatches: 20, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
78 1 0.01
79 36 0.31
80 73 0.63
81 6 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
AATAACTCGCACAAA
Found at i:57643 original size:80 final size:80
Alignment explanation
Indices: 57503--57683 Score: 210
Period size: 80 Copynumber: 2.3 Consensus size: 80
57493 CTCATTCAAT
* * *
57503 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGACTTAACCCGGA-ATT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGGACTTAACCCGGATA-T
* *
57567 GGT-A-TCTCGCACAAA
65 AGTCACT-TAGCACAAA
**
57582 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTC-GGATCTTAGTCCGGAT
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGGA-CTTAACCCGGAT
57645 ATAGTCACTTAGCACAAA
63 ATAGTCACTTAGCACAAA
*
57663 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
57684 CAGCATTCAA
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
79 7 0.08
80 70 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGGACTTAACCCGGATATA
GTCACTTAGCACAAA
Done.