Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold948
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: 50182
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Found at i:5454 original size:27 final size:27
Alignment explanation
Indices: 5391--5565 Score: 160
Period size: 27 Copynumber: 6.5 Consensus size: 27
5381 AAATTGTACA
*
5391 GCACTAAGTGTGCGATTTGACTA-GTT
1 GCACTAAGTGTGCGATTTGACTATGAT
** *
5417 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGATTTGACTATGAT
* * **
5444 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGAT
*
5471 GCACTAAGTGTGCGAGTTTGACTATTA-
1 GCACTAAGTGTGCGA-TTTGACTATGAT
* *
5498 GCACTAAGTGTGCGATTTGATTACG-T
1 GCACTAAGTGTGCGATTTGACTATGAT
* *
5524 AGCACTAAGTGTGCGACGTTGATTAT-AT
1 -GCACTAAGTGTGCGA-TTTGACTATGAT
*
5552 AGCACTGAGTGTGC
1 -GCACTAAGTGTGC
5566 AGACTCAATT
Statistics
Matches: 124, Mismatches: 19, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
26 27 0.22
27 69 0.56
28 28 0.23
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGAT
Found at i:5502 original size:81 final size:80
Alignment explanation
Indices: 5391--5539 Score: 221
Period size: 81 Copynumber: 1.9 Consensus size: 80
5381 AAATTGTACA
*
5391 GCACTAAGTGTGCGATTTGACTAGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTAGTTGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTGT
5455 GCGAATTGACCATGCG
65 GCGAATTGACCATGCG
** *
5471 GCACTAAGTGTGCGAGTTTGACTA-TTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTAGTT-GCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
5535 TGCGA
64 TGCGA
5540 CGTTGATTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
80 17 0.27
81 44 0.71
82 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (80 bp):
GCACTAAGTGTGCGATTTGACTAGTTGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGTG
CGAATTGACCATGCG
Found at i:9527 original size:43 final size:43
Alignment explanation
Indices: 9479--9644 Score: 176
Period size: 43 Copynumber: 3.9 Consensus size: 43
9469 GTTACCGAGA
*
9479 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
**
9522 TGTGATTATGTGTAAGACCATGTCTGGGACATTGGCATCGTTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCG-TAT
*** * * * *
9566 T-TGATTTTGTTTAAGACCCTGTATGGGACAGTGGCATCG-AT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* * *
9607 ATGTGATAACATGTAAGACCATATCTGGGATA-TGGCAT
1 -TGTGATTACATGTAAGACCATGTCTGGGACATTGGCAT
9645 TGTACAAGCT
Statistics
Matches: 103, Mismatches: 17, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
41 2 0.02
42 7 0.07
43 90 0.87
44 4 0.04
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
Found at i:12236 original size:20 final size:20
Alignment explanation
Indices: 12211--12266 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
12201 TAATATTTCA
12211 CACATTT-ACCACATAATTTT
1 CACATTTCA-CACATAATTTT
12231 CACATTTCACACATAATTTT
1 CACATTTCACACATAATTTT
*
12251 CACATTTCACAAATAA
1 CACATTTCACACATAA
12267 ATCCCTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 33 0.97
21 1 0.03
ACGTcount: A:0.39, C:0.25, G:0.00, T:0.36
Consensus pattern (20 bp):
CACATTTCACACATAATTTT
Found at i:14351 original size:28 final size:26
Alignment explanation
Indices: 14300--14418 Score: 84
Period size: 24 Copynumber: 4.6 Consensus size: 26
14290 GACATTACCG
* *
14300 TAAATGTGAAAGTCCGTCAAGACTATCA
1 TAAATGTGGAAGT-C-TCAGGACTATCA
**
14328 TAAATGTGGAAGTCTATCAGGACTATTG
1 TAAATGTGGAAGTC--TCAGGACTATCA
* *
14356 TATACGTGGAAG--TCAGGACTATCA
1 TAAATGTGGAAGTCTCAGGACTATCA
* *
14380 TATATGTGGAAG--TCAGGACTATCG
1 TAAATGTGGAAGTCTCAGGACTATCA
* *
14404 TATATATGGAAGTCT
1 TAAATGTGGAAGTCT
14419 GTTATGACTA
Statistics
Matches: 76, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
24 43 0.57
26 1 0.01
27 1 0.01
28 31 0.41
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (26 bp):
TAAATGTGGAAGTCTCAGGACTATCA
Found at i:14376 original size:24 final size:24
Alignment explanation
Indices: 14344--14417 Score: 112
Period size: 24 Copynumber: 3.1 Consensus size: 24
14334 TGGAAGTCTA
* *
14344 TCAGGACTATTGTATACGTGGAAG
1 TCAGGACTATCGTATATGTGGAAG
*
14368 TCAGGACTATCATATATGTGGAAG
1 TCAGGACTATCGTATATGTGGAAG
*
14392 TCAGGACTATCGTATATATGGAAG
1 TCAGGACTATCGTATATGTGGAAG
14416 TC
1 TC
14418 TGTTATGACT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.30
Consensus pattern (24 bp):
TCAGGACTATCGTATATGTGGAAG
Found at i:14415 original size:48 final size:49
Alignment explanation
Indices: 14315--14417 Score: 127
Period size: 48 Copynumber: 2.1 Consensus size: 49
14305 GTGAAAGTCC
* *
14315 GTCAAGACTATCATAAATGTGGAAGTCTATCAGGACTATTGTATACGTGGAA
1 GTCAAGACTATCATAAATGTGGAAG--T-TCAGGACTATCGTATACATGGAA
* * *
14367 GTCAGGACTATCATATATGTGGAAG-TCAGGACTATCGTATATATGGAA
1 GTCAAGACTATCATAAATGTGGAAGTTCAGGACTATCGTATACATGGAA
14415 GTC
1 GTC
14418 TGTTATGACT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
48 23 0.50
52 23 0.50
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (49 bp):
GTCAAGACTATCATAAATGTGGAAGTTCAGGACTATCGTATACATGGAA
Found at i:21555 original size:13 final size:13
Alignment explanation
Indices: 21537--21561 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21527 GTAAGTGATT
21537 TTGATGATTTTTC
1 TTGATGATTTTTC
21550 TTGATGATTTTT
1 TTGATGATTTTT
21562 GCACTTTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (13 bp):
TTGATGATTTTTC
Found at i:22337 original size:47 final size:44
Alignment explanation
Indices: 22270--22392 Score: 140
Period size: 47 Copynumber: 2.7 Consensus size: 44
22260 TTTGTATACT
* * *
22270 AGTGTAAGACGTGTCTGGGACATGCATTGACCATATTATG-AGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGA-CAT-TGA-GAAGAGCC
*
22316 AGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGACAAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGACATTGAG--AAGAGCC
22364 AGTGTAAGACATGTCTGGGACATGCATCG
1 AGTGTAAGACATGTCTGGGACATGCATCG
22393 GCTACAAGAT
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
45 1 0.01
46 17 0.25
47 30 0.44
48 20 0.29
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACATTGAGAAGAGCC
Found at i:23511 original size:42 final size:43
Alignment explanation
Indices: 23441--23521 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 43
23431 AGACACGAGC
* *
23441 GTGTCATGGCCGTGTGAGGGACATGGGCCAT-AGACACGGGTGT
1 GTGTCATGGCCGTGTGAGGCACACGGGCCATCAG-CACGGGTGT
* *
23484 GTGTCA-GGCCGTGTGTGTCACACGGGCCATCAGCACGG
1 GTGTCATGGCCGTGTGAGGCACACGGGCCATCAGCACGG
23522 CCATGTCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
42 25 0.76
43 8 0.24
ACGTcount: A:0.17, C:0.23, G:0.40, T:0.20
Consensus pattern (43 bp):
GTGTCATGGCCGTGTGAGGCACACGGGCCATCAGCACGGGTGT
Found at i:23575 original size:20 final size:21
Alignment explanation
Indices: 23537--23575 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
23527 TCATTATGAA
23537 CACACGGGCGTGTTGCCCTTC
1 CACACGGGCGTGTTGCCCTTC
23558 CACACGGGCGTG-TGCCCT
1 CACACGGGCGTGTTGCCCT
23576 GTTTCAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.10, C:0.38, G:0.31, T:0.21
Consensus pattern (21 bp):
CACACGGGCGTGTTGCCCTTC
Found at i:28625 original size:47 final size:47
Alignment explanation
Indices: 28510--28720 Score: 278
Period size: 47 Copynumber: 4.7 Consensus size: 47
28500 GGAATGAAAA
* * *
28510 AACGTGGTGCTAAGTGGATATACCACGATTACACATATTGATACATGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT-T
* * *
28558 AACGTGGTGCTAAGTAGATATTCCATGGTTACATATATTGATTCATT
1 AACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCATT
*
28605 AACGTGGTGCTAAGTGGATATACCACGGTTA-A-ACA-TG------T
1 AACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCATT
*
28643 AACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATT
1 AACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCATT
28690 AACGTGGTGCTAAGTGGATATACCACGGTTA
1 AACGTGGTGCTAAGTGGATATACCACGGTTA
28721 AACATGTAAC
Statistics
Matches: 141, Mismatches: 13, Indels: 19
0.82 0.08 0.11
Matches are distributed among these distances:
38 31 0.22
39 1 0.01
40 2 0.01
41 2 0.01
44 2 0.01
45 2 0.01
46 1 0.01
47 60 0.43
48 40 0.28
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.31
Consensus pattern (47 bp):
AACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCATT
Found at i:28655 original size:38 final size:38
Alignment explanation
Indices: 28604--28765 Score: 198
Period size: 38 Copynumber: 4.0 Consensus size: 38
28594 ATTGATTCAT
28604 TAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
1 TAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
* *
28642 TAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTG
1 TAACGTGGTGCTAAGTGGATATACCACGGTTA-A-ACA-TG
28683 ATTCATTAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
1 ------TAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
* * *
28727 TAACTTGGTGCTAAGTGGATATGCCACGGTTATACATG
1 TAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
28765 T
1 T
28766 TAATTTGAAA
Statistics
Matches: 108, Mismatches: 7, Indels: 18
0.81 0.05 0.14
Matches are distributed among these distances:
38 67 0.62
39 1 0.01
40 2 0.02
41 2 0.02
44 2 0.02
45 2 0.02
46 1 0.01
47 31 0.29
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.30
Consensus pattern (38 bp):
TAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
Found at i:28695 original size:85 final size:85
Alignment explanation
Indices: 28552--28758 Score: 378
Period size: 85 Copynumber: 2.4 Consensus size: 85
28542 ACATATTGAT
* * *
28552 ACATGTAACGTGGTGCTAAGTAGATATTCCATGGTTACATATATTGATTCATTAACGTGGTGCTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
28617 AGTGGATATACCACGGTTAA
66 AGTGGATATACCACGGTTAA
28637 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
28702 AGTGGATATACCACGGTTAA
66 AGTGGATATACCACGGTTAA
*
28722 ACATGTAACTTGGTGCTAAGTGGATATGCCACGGTTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTA
28759 TACATGTTAA
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 118 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.31
Consensus pattern (85 bp):
ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
AGTGGATATACCACGGTTAA
Found at i:40482 original size:29 final size:29
Alignment explanation
Indices: 40449--40522 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
40439 GTTGTGAGAT
* *
40449 TGGCACTAGGTGTGCGAACTTGAAA-TGCA
1 TGGCACTAAGTGTGCG-ACTTGAAAGTACA
* *
40478 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGACTTGAAAGTACA
40507 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
40523 CGGTTGATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 6 0.15
29 34 0.85
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGACTTGAAAGTACA
Done.