Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold968
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: 55104
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:4908 original size:15 final size:15
Alignment explanation
Indices: 4888--4942 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
4878 ACTCTCCTCA
*
4888 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
4903 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
4918 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
4932 TTCTTTT-TCTC
1 TTCTTTTCTCTC
4943 GCTCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:7047 original size:13 final size:12
Alignment explanation
Indices: 7029--7067 Score: 60
Period size: 13 Copynumber: 3.1 Consensus size: 12
7019 AACTTTTTTT
7029 TTTTTTTTTCGAA
1 TTTTTTTTTC-AA
7042 TTTTTTTTTCAA
1 TTTTTTTTTCAA
7054 TTTTTTTTTACAA
1 TTTTTTTTT-CAA
7067 T
1 T
7068 CTCGTAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.72
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:12164 original size:12 final size:11
Alignment explanation
Indices: 12117--12156 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
12107 AGTTGTAAAG
*
12117 TTTTATTTTTAT
1 TTTTATTTAT-T
12129 TTTTATTTATT
1 TTTTATTTATT
12140 TATTTATTTATT
1 T-TTTATTTATT
12152 TTTTA
1 TTTTA
12157 CTTAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 6 0.23
12 20 0.77
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTATTTATT
Found at i:12164 original size:16 final size:15
Alignment explanation
Indices: 12118--12173 Score: 55
Period size: 16 Copynumber: 3.8 Consensus size: 15
12108 GTTGTAAAGT
12118 TTTA-TTTTTATT--
1 TTTATTTTTTATTAA
*
12130 TTTATTTATTTATTTA
1 TTTATTT-TTTATTAA
12146 TTTATTTTTTACTTAA
1 TTTATTTTTTA-TTAA
*
12162 TTTAATTTTTAT
1 TTTATTTTTTAT
12174 GTAAATATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
12 4 0.11
13 2 0.05
14 6 0.16
15 5 0.14
16 20 0.54
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTATTTTTTATTAA
Found at i:21004 original size:20 final size:20
Alignment explanation
Indices: 20981--21034 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
20971 AGTTTTTCCC
*
20981 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
21001 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
21021 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
21035 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:21016 original size:30 final size:30
Alignment explanation
Indices: 20981--21054 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
20971 AGTTTTTCCC
20981 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
21011 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
21041 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
21055 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:21044 original size:20 final size:20
Alignment explanation
Indices: 20981--21045 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
20971 AGTTTTTCCC
* * * *
20981 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
21001 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
21020 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
21041 AGCTC
1 AGCTC
21046 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:22667 original size:18 final size:18
Alignment explanation
Indices: 22646--22680 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
22636 AGAAAAGAAA
22646 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
22664 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
22681 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:25885 original size:18 final size:18
Alignment explanation
Indices: 25864--25898 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25854 AGAAAAGAAA
25864 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
25882 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
25899 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:33569 original size:18 final size:18
Alignment explanation
Indices: 33548--33582 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
33538 AGAAAAGAAA
33548 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
33566 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
33583 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:41258 original size:18 final size:18
Alignment explanation
Indices: 41237--41271 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41227 AGAAAAGAAA
41237 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
41255 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
41272 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:49621 original size:20 final size:19
Alignment explanation
Indices: 49598--49662 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
49588 AAGCTCAAAC
49598 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
49618 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
49638 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
49658 GAGCT
1 GAGCT
49663 GGGAAAACTA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:51506 original size:6 final size:6
Alignment explanation
Indices: 51497--51620 Score: 51
Period size: 6 Copynumber: 20.3 Consensus size: 6
51487 TCTCTTTCAA
* * ** * *
51497 TTTCTT TTTCTC TTTCTTT TCTTCTC TTTCAA TTTCTT TTTC-A TCTCTT
1 TTTCTT TTTCTT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT
** * *
51546 TTTC-T TTTCAC TCTCTT TTT-TT TTTTTT TTTCACATT TTTCTT TTTC--
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT--C-TT TTTCTT TTTCTT
*
51593 TTTCTT TCATTTTT TTTCTT TTTCTT TT
1 TTTCTT T--TTCTT TTTCTT TTTCTT TT
51621 CTCGCTCAAT
Statistics
Matches: 87, Mismatches: 19, Indels: 24
0.67 0.15 0.18
Matches are distributed among these distances:
4 4 0.05
5 13 0.15
6 52 0.60
7 5 0.06
8 8 0.09
9 5 0.06
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTCTT
Found at i:51527 original size:32 final size:32
Alignment explanation
Indices: 51487--51551 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
51477 CTTTTCAAGC
*
51487 TCTCTTTCAATTTCTTTTTC-TCTTTCTTTTCT
1 TCTCTTTCAATTTCTTTTTCATCTCT-TTTTCT
51519 TCTCTTTCAATTTCTTTTTCATCTCTTTTTCT
1 TCTCTTTCAATTTCTTTTTCATCTCTTTTTCT
51551 T
1 T
51552 TTCACTCTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 27 0.87
33 4 0.13
ACGTcount: A:0.08, C:0.25, G:0.00, T:0.68
Consensus pattern (32 bp):
TCTCTTTCAATTTCTTTTTCATCTCTTTTTCT
Found at i:51555 original size:16 final size:17
Alignment explanation
Indices: 51529--51569 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
51519 TCTCTTTCAA
51529 TTTCTTTTTCA-TCTCTT
1 TTTC-TTTTCACTCTCTT
51546 TTTCTTTTCACTCTCTT
1 TTTCTTTTCACTCTCTT
51563 TTT-TTTT
1 TTTCTTTT
51570 TTTTTTTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTCTTTTCACTCTCTT
Found at i:51570 original size:23 final size:21
Alignment explanation
Indices: 51544--51621 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 21
51534 TTTTCATCTC
51544 TTTTTCTTTTCACTCTCTTTTTT
1 TTTTTCTTTTCACT-T-TTTTTT
*
51567 TTTTTTTTTTCACATTTTTCTTT
1 TTTTTCTTTTCAC-TTTTT-TTT
51590 TTCTTTC-TTTCA-TTTTTTTT
1 TT-TTTCTTTTCACTTTTTTTT
51610 CTTTTTCTTTTC
1 -TTTTTCTTTTC
51622 TCGCTCAATC
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
20 7 0.15
21 11 0.23
22 3 0.06
23 23 0.48
24 4 0.08
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTTCTTTTCACTTTTTTTT
Found at i:51606 original size:38 final size:37
Alignment explanation
Indices: 51509--51616 Score: 96
Period size: 36 Copynumber: 2.9 Consensus size: 37
51499 TCTTTTTCTC
* * ** *
51509 TTTC-TTTTCTTCTCTTTCAATTTCTTTTTCATCTCTT
1 TTTCTTTTTCTT-TCTTTCATTTTTTTTTTTTTCACTT
* *
51546 TTTCTTTTCACTCTCTTT--TTTTTTTTTTTTTCACATT
1 TTTCTTTT-TCTTTCTTTCATTTTTTTTTTTTTCAC-TT
51583 TTTCTTTTTCTTTCTTTCATTTTTTTTCTTTTTC
1 TTTCTTTTTCTTTCTTTCATTTTTTTT-TTTTTC
51617 TTTTCTCGCT
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
36 18 0.32
37 14 0.25
38 16 0.29
39 8 0.14
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.73
Consensus pattern (37 bp):
TTTCTTTTTCTTTCTTTCATTTTTTTTTTTTTCACTT
Found at i:52699 original size:11 final size:11
Alignment explanation
Indices: 52673--52713 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
52663 TTTTGCTCGA
*
52673 TTTTTTTTCACT
1 TTTTTTTTGA-T
52685 TTTTTTTTGAAT
1 TTTTTTTTG-AT
52697 TTTTTTTTGAT
1 TTTTTTTTGAT
52708 TTTTTT
1 TTTTTT
52714 GTTACTCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 8 0.30
12 18 0.67
13 1 0.04
ACGTcount: A:0.10, C:0.05, G:0.05, T:0.80
Consensus pattern (11 bp):
TTTTTTTTGAT
Found at i:54330 original size:20 final size:19
Alignment explanation
Indices: 54307--54371 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
54297 AAGCTCAAAC
54307 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
54327 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
54347 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
54367 GAGCT
1 GAGCT
54372 GGGAAAACTA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Done.