Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1697
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: 44940
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:2624 original size:17 final size:18
Alignment explanation
Indices: 2599--2636 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2589 TTTCTTCAAC
* *
2599 TTCTTTTTCA-ATTTCTT
1 TTCTGTTTCACATTCCTT
2616 TTCTGTTTCACATTCCTT
1 TTCTGTTTCACATTCCTT
2634 TTC
1 TTC
2637 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.24, G:0.03, T:0.63
Consensus pattern (18 bp):
TTCTGTTTCACATTCCTT
Found at i:6792 original size:23 final size:22
Alignment explanation
Indices: 6741--6792 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
6731 CCTCGTCTTT
*
6741 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
6763 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
6786 TTCTTTT
1 TTCTTTT
6793 TCAATTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:6801 original size:12 final size:13
Alignment explanation
Indices: 6772--6805 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
6762 CTCATTTTCT
6772 CTTCTTTCTTCAA
1 CTTCTTTCTTCAA
6785 CTTCTTT-TTCAA
1 CTTCTTTCTTCAA
*
6797 TTTCTTTCT
1 CTTCTTTCT
6806 GTTTCACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62
Consensus pattern (13 bp):
CTTCTTTCTTCAA
Found at i:12947 original size:20 final size:20
Alignment explanation
Indices: 12924--12970 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
12914 GGGTTAAGAT
*
12924 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
12944 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
12964 TGAGCTG
1 TGAGCTG
12971 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:14695 original size:48 final size:48
Alignment explanation
Indices: 14640--14745 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
14630 TTGTCTTTTC
*
14640 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
14688 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
14736 TTTCTTTTTC
1 TTTCTTTTTC
14746 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:14742 original size:18 final size:18
Alignment explanation
Indices: 14721--14804 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 18
14711 TTTTCACATC
*
14721 CTTTTTCAATCTCAATTT
1 CTTTTTCAATCTCACTTT
* * *
14739 CTTTTTCCATGACACTCTTT
1 CTTTTTCAAT--CTCACTTT
* * *
14759 CTTTTACACTCTC-GTTT
1 CTTTTTCAATCTCACTTT
*
14776 CTTTCTTCAATCTCACTCT
1 CTTT-TTCAATCTCACTTT
14795 CTTTTTCAAT
1 CTTTTTCAAT
14805 TTCTTGTTCC
Statistics
Matches: 49, Mismatches: 13, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
17 7 0.14
18 24 0.49
19 6 0.12
20 12 0.24
ACGTcount: A:0.17, C:0.29, G:0.02, T:0.52
Consensus pattern (18 bp):
CTTTTTCAATCTCACTTT
Found at i:17396 original size:20 final size:20
Alignment explanation
Indices: 17373--17419 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
17363 GGGTTAAGAT
*
17373 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
17393 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
17413 TGAGCTG
1 TGAGCTG
17420 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:18402 original size:18 final size:17
Alignment explanation
Indices: 18381--18425 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
18371 GAATGACGAG
18381 AGAAAAAGAAACTGAAAA
1 AGAAAAA-AAACTGAAAA
*
18399 AGAAACAAAAATTGAAAA
1 AGAAA-AAAAACTGAAAA
18417 AGAGAAAAA
1 AGA-AAAAA
18426 GATTGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (17 bp):
AGAAAAAAAACTGAAAA
Found at i:18430 original size:18 final size:18
Alignment explanation
Indices: 18379--18430 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
18369 AAGAATGACG
*
18379 AGAGAAAAAGAAACTGAAAA
1 AGAGAAAAAG--ATTGAAAA
*
18399 AGA-AACAAAAATTGAAAA
1 AGAGAA-AAAGATTGAAAA
18417 AGAGAAAAAGATTG
1 AGAGAAAAAGATTG
18431 GAGAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 17 0.63
19 4 0.15
20 6 0.22
ACGTcount: A:0.67, C:0.04, G:0.19, T:0.10
Consensus pattern (18 bp):
AGAGAAAAAGATTGAAAA
Found at i:19940 original size:23 final size:21
Alignment explanation
Indices: 19909--19952 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
19899 AAGGGCATAA
*
19909 AATGCTCTTTAAAGACTCCTTTT
1 AATGATCTTT-AAG-CTCCTTTT
19932 AATGATCTTTAAGCTCCTTTT
1 AATGATCTTTAAGCTCCTTTT
19953 TTTTAACAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 3 0.15
23 9 0.45
ACGTcount: A:0.25, C:0.20, G:0.09, T:0.45
Consensus pattern (21 bp):
AATGATCTTTAAGCTCCTTTT
Found at i:20104 original size:21 final size:23
Alignment explanation
Indices: 20059--20105 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
20049 TCACCTGCAA
* *
20059 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
20082 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
20103 TAA
1 TAA
20106 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:22862 original size:11 final size:10
Alignment explanation
Indices: 22841--22897 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
22831 ATAAAAAAAA
*
22841 TGAGCTGAAT
1 TGAGCTAAAT
22851 TGTAGCTAAAT
1 TG-AGCTAAAT
**
22862 TGAGCTTGAT
1 TGAGCTAAAT
22872 TGAGCTGAAA-
1 TGAGCT-AAAT
*
22882 TGAGCTCAAT
1 TGAGCTAAAT
22892 TGAGCT
1 TGAGCT
22898 GGTCGGAGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 26 0.68
11 10 0.26
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (10 bp):
TGAGCTAAAT
Found at i:22877 original size:20 final size:20
Alignment explanation
Indices: 22838--22898 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
22828 CCAATAAAAA
*
22838 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
**
22858 AAATTGAGCTTGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
22879 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
22899 GTCGGAGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:29138 original size:23 final size:22
Alignment explanation
Indices: 29087--29138 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
29077 CCTCGTCTTT
*
29087 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
29109 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
29132 TTCTTTT
1 TTCTTTT
29139 TCAATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:32613 original size:17 final size:16
Alignment explanation
Indices: 32591--32647 Score: 98
Period size: 16 Copynumber: 3.6 Consensus size: 16
32581 CTTCTTCTTC
32591 TTTTTTT-ACGAAATTT
1 TTTTTTTCACG-AATTT
32607 TTTTTTTCACGAATTT
1 TTTTTTTCACGAATTT
32623 TTTTTTTCACGAATTT
1 TTTTTTTCACGAATTT
32639 TTTTTTTCA
1 TTTTTTTCA
32648 ACTTGATATC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 37 0.93
17 3 0.08
ACGTcount: A:0.19, C:0.11, G:0.05, T:0.65
Consensus pattern (16 bp):
TTTTTTTCACGAATTT
Found at i:32704 original size:11 final size:11
Alignment explanation
Indices: 32688--32739 Score: 70
Period size: 11 Copynumber: 4.7 Consensus size: 11
32678 GAAACCAAAT
32688 TTTTTTTTGAA
1 TTTTTTTTGAA
32699 TTTTTTTTGAA
1 TTTTTTTTGAA
**
32710 TTTTTTTTTTA
1 TTTTTTTTGAA
32721 -TTTTTTTGAAA
1 TTTTTTTTG-AA
32732 TTTTTTTT
1 TTTTTTTT
32740 TGAAGAAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
10 7 0.20
11 21 0.60
12 7 0.20
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:32715 original size:21 final size:22
Alignment explanation
Indices: 32689--32738 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
32679 AAACCAAATT
32689 TTTTTTTGAAT-TTTTTTTG-AA
1 TTTTTTT-AATATTTTTTTGAAA
**
32710 TTTTTTTTTTATTTTTTTGAAA
1 TTTTTTTAATATTTTTTTGAAA
32732 TTTTTTT
1 TTTTTTT
32739 TTGAAGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 15 0.60
22 9 0.36
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (22 bp):
TTTTTTTAATATTTTTTTGAAA
Found at i:32740 original size:22 final size:24
Alignment explanation
Indices: 32684--32743 Score: 90
Period size: 22 Copynumber: 2.6 Consensus size: 24
32674 AATGGAAACC
32684 AAATTTTTTTTTGAATTTTTTTTG
1 AAATTTTTTTTTGAATTTTTTTTG
*
32708 -AATTTTTTTTT-TA-TTTTTTTG
1 AAATTTTTTTTTGAATTTTTTTTG
32729 AAATTTTTTTTTGAA
1 AAATTTTTTTTTGAA
32744 GAAACTACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 8 0.25
22 12 0.38
23 12 0.38
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.72
Consensus pattern (24 bp):
AAATTTTTTTTTGAATTTTTTTTG
Found at i:33778 original size:21 final size:23
Alignment explanation
Indices: 33733--33779 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
33723 TCACCTGCAA
* *
33733 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
33756 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
33777 TAA
1 TAA
33780 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:39193 original size:12 final size:12
Alignment explanation
Indices: 39176--39219 Score: 81
Period size: 12 Copynumber: 3.8 Consensus size: 12
39166 AATGGAAACC
39176 AATTTTTTTTTG
1 AATTTTTTTTTG
39188 AATTTTTTTTTG
1 AATTTTTTTTTG
39200 AA-TTTTTTTTG
1 AATTTTTTTTTG
39211 AATTTTTTT
1 AATTTTTTT
39220 GAAGAAACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.35
12 20 0.65
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.75
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:39195 original size:11 final size:11
Alignment explanation
Indices: 39179--39219 Score: 73
Period size: 11 Copynumber: 3.6 Consensus size: 11
39169 GGAAACCAAT
39179 TTTTTTTTGAA
1 TTTTTTTTGAA
39190 TTTTTTTTTGAA
1 -TTTTTTTTGAA
39202 TTTTTTTTGAA
1 TTTTTTTTGAA
39213 TTTTTTT
1 TTTTTTT
39220 GAAGAAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:40256 original size:21 final size:23
Alignment explanation
Indices: 40211--40257 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
40201 TCACCTGCAA
* *
40211 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
40234 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
40255 TAA
1 TAA
40258 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Done.