Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2951
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: 31463
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:637 original size:13 final size:14
Alignment explanation
Indices: 619--672 Score: 74
Period size: 13 Copynumber: 3.7 Consensus size: 14
609 GATATCAAGT
619 TGAAAAAAAATT-G
1 TGAAAAAAAATTCG
632 TGAAAAAAAATTCG
1 TGAAAAAAAATTCG
646 TGAAAAAAAAAATTTCG
1 TG--AAAAAAAA-TTCG
663 TGAAAAAAAA
1 TGAAAAAAAA
673 GAAGAAGCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.32
14 3 0.08
15 8 0.22
16 8 0.22
17 6 0.16
ACGTcount: A:0.63, C:0.04, G:0.13, T:0.20
Consensus pattern (14 bp):
TGAAAAAAAATTCG
Found at i:640 original size:14 final size:15
Alignment explanation
Indices: 621--672 Score: 72
Period size: 16 Copynumber: 3.5 Consensus size: 15
611 TATCAAGTTG
621 AAAAAAAATT-GTG-
1 AAAAAAAATTCGTGA
634 AAAAAAAATTCGTGAA
1 AAAAAAAATTCGTG-A
650 AAAAAAAATTTCGTGA
1 AAAAAAAA-TTCGTGA
666 AAAAAAA
1 AAAAAAA
673 GAAGAAGCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.29
14 3 0.09
16 16 0.46
17 6 0.17
ACGTcount: A:0.65, C:0.04, G:0.12, T:0.19
Consensus pattern (15 bp):
AAAAAAAATTCGTGA
Found at i:654 original size:17 final size:17
Alignment explanation
Indices: 634--672 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
624 AAAAATTGTG
634 AAAAAAAATTCGTGAAA
1 AAAAAAAATTCGTGAAA
*
651 AAAAAAATTTCGTGAAA
1 AAAAAAAATTCGTGAAA
668 AAAAA
1 AAAAA
673 GAAGAAGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.18
Consensus pattern (17 bp):
AAAAAAAATTCGTGAAA
Found at i:3681 original size:23 final size:22
Alignment explanation
Indices: 3629--3681 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
3619 TCCACGTCTT
*
3629 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
3651 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
3674 TTTCTTTT
1 TTTCTTTT
3682 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:7415 original size:20 final size:20
Alignment explanation
Indices: 7392--7438 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
7382 GGGTTAAGAT
*
7392 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
7412 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
7432 TGAGCTG
1 TGAGCTG
7439 GAAACGAGCT
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:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:13972 original size:48 final size:48
Alignment explanation
Indices: 13917--14022 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
13907 TTGTCTTTTC
*
13917 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
13965 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
14013 TTTCTTTTTC
1 TTTCTTTTTC
14023 CATGACACTC
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:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:15107 original size:27 final size:28
Alignment explanation
Indices: 15039--15111 Score: 78
Period size: 30 Copynumber: 2.6 Consensus size: 28
15029 CTCGCAAGAC
* **
15039 TTTTCACTTTTTTTTCTTTCTTCTTTTT
1 TTTTCACTTTTTTTTGTCACTTCTTTTT
15067 TTTT-ACTCGATTTTTTTGTCACTTCTTTTT
1 TTTTCACT---TTTTTTTGTCACTTCTTTTT
15097 TTTTC-CTTTTTTTTG
1 TTTTCACTTTTTTTTG
15112 AAATTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
27 11 0.29
28 4 0.11
30 23 0.61
ACGTcount: A:0.05, C:0.16, G:0.04, T:0.74
Consensus pattern (28 bp):
TTTTCACTTTTTTTTGTCACTTCTTTTT
Found at i:15219 original size:11 final size:11
Alignment explanation
Indices: 15205--15233 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
15195 TCCAACTCAA
15205 TTTTTTTTGA-
1 TTTTTTTTGAC
15215 TTTTTTTTGAC
1 TTTTTTTTGAC
15226 TTTTTTTT
1 TTTTTTTT
15234 ACGTTACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAC
Found at i:16652 original size:20 final size:20
Alignment explanation
Indices: 16629--16675 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
16619 GGGTTAAGAT
*
16629 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
16649 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
16669 TGAGCTG
1 TGAGCTG
16676 GAAACGAGCT
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:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:21586 original size:13 final size:13
Alignment explanation
Indices: 21568--21607 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
21558 GTAGTTTCTC
21568 GAAAAAAAAATTT
1 GAAAAAAAAATTT
*
21581 GAAAAAAAAATTC
1 GAAAAAAAAATTT
*
21594 AAAAAAAAAATTT
1 GAAAAAAAAATTT
21607 G
1 G
21608 GTTTCCATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (13 bp):
GAAAAAAAAATTT
Found at i:21587 original size:12 final size:12
Alignment explanation
Indices: 21569--21602 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
21559 TAGTTTCTCG
*
21569 AAAAAAAAATTTG
1 AAAAAAAAA-TTC
21582 AAAAAAAAATTC
1 AAAAAAAAATTC
21594 AAAAAAAAA
1 AAAAAAAAA
21603 ATTTGGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:21666 original size:15 final size:16
Alignment explanation
Indices: 21643--21684 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
21633 GATATCAAGT
21643 TGAAAAAAAAAATTCG
1 TGAAAAAAAAAATTCG
21659 TGAAAAAAAAAATTCG
1 TGAAAAAAAAAATTCG
21675 TGAAAAAAAA
1 TGAAAAAAAA
21685 GAAGCTAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.67, C:0.05, G:0.12, T:0.17
Consensus pattern (16 bp):
TGAAAAAAAAAATTCG
Found at i:25143 original size:17 final size:17
Alignment explanation
Indices: 25121--25155 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
25111 CAACTAGCCA
25121 AGGACAACTCAAGAGTC
1 AGGACAACTCAAGAGTC
25138 AGGACAACTCAAGAGTC
1 AGGACAACTCAAGAGTC
25155 A
1 A
25156 TTTTCTAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (17 bp):
AGGACAACTCAAGAGTC
Found at i:26014 original size:21 final size:21
Alignment explanation
Indices: 25988--26050 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
25978 TTGGTATTTG
25988 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
26009 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
26030 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
26051 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:26420 original size:17 final size:17
Alignment explanation
Indices: 26398--26431 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
26388 AAGTTAGCCG
26398 AATGGTCTCTTTCAATC
1 AATGGTCTCTTTCAATC
26415 AATGGTCTCTTTCAATC
1 AATGGTCTCTTTCAATC
26432 CTTAAGGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (17 bp):
AATGGTCTCTTTCAATC
Found at i:28361 original size:23 final size:22
Alignment explanation
Indices: 28309--28362 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
28299 TCCACGTCTT
*
28309 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
28331 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
28354 TTTCTTTTC
1 TTTCTTTTC
28363 CTCACTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 3 0.11
22 5 0.19
23 13 0.48
24 6 0.22
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Done.