Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold633
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: 41496
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1126 original size:19 final size:20
Alignment explanation
Indices: 1102--1159 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 20
1092 GAAGAAAAAC
1102 AAAAAAGATGAGTGAT-AAA
1 AAAAAAGATGAGTGATCAAA
1121 AAAAAAGA-GAGTGATTCAAA
1 AAAAAAGATGAGTGA-TCAAA
1141 AGAAAAAGAAATGAGTGAT
1 A-AAAAAG--ATGAGTGAT
1160 GAGATTGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 6 0.18
19 9 0.27
20 4 0.12
21 6 0.18
23 2 0.06
24 6 0.18
ACGTcount: A:0.60, C:0.02, G:0.22, T:0.16
Consensus pattern (20 bp):
AAAAAAGATGAGTGATCAAA
Found at i:4162 original size:12 final size:12
Alignment explanation
Indices: 4145--4169 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4135 AATTTTAGAC
4145 GCATTTAAATAA
1 GCATTTAAATAA
4157 GCATTTAAATAA
1 GCATTTAAATAA
4169 G
1 G
4170 TTTCATTACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (12 bp):
GCATTTAAATAA
Found at i:5648 original size:20 final size:19
Alignment explanation
Indices: 5622--5673 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
5612 ATAAACGCAA
5622 ATGAGCTTAAAATGAGCT-G
1 ATGAGC-TAAAATGAGCTCG
*
5641 ATTGAGCTAAGAGTGAGCTCG
1 A-TGAGCTAA-AATGAGCTCG
5662 ATGAGCTAAAAT
1 ATGAGCTAAAAT
5674 TGAGTTGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 6 0.21
20 20 0.71
21 2 0.07
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.25
Consensus pattern (19 bp):
ATGAGCTAAAATGAGCTCG
Found at i:5685 original size:20 final size:19
Alignment explanation
Indices: 5621--5685 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
5611 TATAAACGCA
*
5621 AATGAGCTTAAAATGAGCTG
1 AATGAGC-TAAAATGAGTTG
* * *
5641 ATTGAGCTAAGAGTGAGCTCG
1 AATGAGCTAA-AATGAG-TTG
5662 -ATGAGCTAAAATTGAGTTG
1 AATGAGCTAAAA-TGAGTTG
5681 AATGA
1 AATGA
5686 ACTTGAAGTA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
19 6 0.18
20 27 0.79
21 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.28, T:0.26
Consensus pattern (19 bp):
AATGAGCTAAAATGAGTTG
Found at i:10156 original size:13 final size:12
Alignment explanation
Indices: 10137--10171 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
10127 ATATACTTCG
10137 ATTTTTTTTTGA
1 ATTTTTTTTTGA
10149 ATTTTTTTTTGA
1 ATTTTTTTTTGA
10161 ATTTTCTTTTT
1 ATTTT-TTTTT
10172 CAAATTTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (12 bp):
ATTTTTTTTTGA
Found at i:11695 original size:20 final size:20
Alignment explanation
Indices: 11672--11718 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
11662 GGGTTAAGAT
*
11672 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
11692 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
11712 TGAGCTG
1 TGAGCTG
11719 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:12216 original size:12 final size:12
Alignment explanation
Indices: 12199--12275 Score: 70
Period size: 12 Copynumber: 6.4 Consensus size: 12
12189 CGAAAGAAAA
12199 GAAAAAGAGATT
1 GAAAAAGAGATT
*
12211 GAAAAAGAAATT
1 GAAAAAGAGATT
12223 GAAAAAGA-A--
1 GAAAAAGAGATT
12232 GAAAAAGAAAGATT
1 GAAAAAG--AGATT
*
12246 GGAAAAAGAAATT
1 -GAAAAAGAGATT
* *
12259 GAAAGAGAGCTT
1 GAAAAAGAGATT
12271 GAAAA
1 GAAAA
12276 GAAATCGAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
9 7 0.13
11 2 0.04
12 33 0.62
13 4 0.08
15 7 0.13
ACGTcount: A:0.62, C:0.01, G:0.23, T:0.13
Consensus pattern (12 bp):
GAAAAAGAGATT
Found at i:18312 original size:31 final size:31
Alignment explanation
Indices: 18247--18312 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
18237 TTTAACTTGA
*
18247 TTTTTTTTGCTCAACTTTTTTTTTCTTTTCT
1 TTTTTTTTGCTCAACTTTTTTTTACTTTTCT
*
18278 TTTTTTTTGCTCGA-TTTCTTTTTCACTTTT-T
1 TTTTTTTTGCTCAACTTT-TTTTT-ACTTTTCT
18309 TTTT
1 TTTT
18313 CATTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 3 0.10
31 23 0.74
32 5 0.16
ACGTcount: A:0.06, C:0.15, G:0.05, T:0.74
Consensus pattern (31 bp):
TTTTTTTTGCTCAACTTTTTTTTACTTTTCT
Found at i:18313 original size:12 final size:11
Alignment explanation
Indices: 18266--18356 Score: 58
Period size: 11 Copynumber: 7.6 Consensus size: 11
18256 CTCAACTTTT
*
18266 TTTTTCTTTTCT
1 TTTTT-TTTTCA
18278 TTTTTTTTGCTCGA
1 TTTTTTTT--TC-A
*
18292 TTTCTTTTTCA
1 TTTTTTTTTCA
18303 CTTTTTTTTTCA
1 -TTTTTTTTTCA
18315 TTTTTTTTCAATCA
1 TTTTTTTT---TCA
* *
18329 ATTTTTTTTGA
1 TTTTTTTTTCA
*
18340 -TTTTTTTTGA
1 TTTTTTTTTCA
18350 TTTTTTT
1 TTTTTTT
18357 GTTACTCCAA
Statistics
Matches: 66, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
10 10 0.15
11 20 0.30
12 17 0.26
13 2 0.03
14 17 0.26
ACGTcount: A:0.10, C:0.11, G:0.04, T:0.75
Consensus pattern (11 bp):
TTTTTTTTTCA
Found at i:18337 original size:37 final size:36
Alignment explanation
Indices: 18246--18356 Score: 94
Period size: 37 Copynumber: 3.2 Consensus size: 36
18236 TTTTAACTTG
*
18246 ATTTTTTTTGCTCAA---CTTTTT--TTTTCTTTTC
1 ATTTTTTTTGCTCAATTTCTTTTTCATTTTTTTTTC
* *
18277 TTTTTTTTTGCTCGATTTCTTTTTCACTTTTTTTTTC
1 ATTTTTTTTGCTCAATTTCTTTTTCA-TTTTTTTTTC
* *
18314 ATTTTTTTT-CAATCAATTT-TTTTTGA-TTTTTTTTG
1 ATTTTTTTTGC--TCAATTTCTTTTTCATTTTTTTTTC
18349 ATTTTTTT
1 ATTTTTTT
18357 GTTACTCCAA
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
31 13 0.20
34 6 0.09
35 16 0.25
36 1 0.02
37 23 0.35
38 6 0.09
ACGTcount: A:0.11, C:0.12, G:0.05, T:0.73
Consensus pattern (36 bp):
ATTTTTTTTGCTCAATTTCTTTTTCATTTTTTTTTC
Found at i:18357 original size:9 final size:10
Alignment explanation
Indices: 18329--18356 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
18319 TTTTCAATCA
18329 ATTTTTTTTG
1 ATTTTTTTTG
18339 ATTTTTTTTG
1 ATTTTTTTTG
18349 ATTTTTTT
1 ATTTTTTT
18357 GTTACTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.07, T:0.82
Consensus pattern (10 bp):
ATTTTTTTTG
Found at i:24925 original size:15 final size:15
Alignment explanation
Indices: 24905--24945 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
24895 ACTAGCTTAT
24905 TTTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
24920 TTTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
24935 TTTTTTTTTCA
1 TTTTTTTTTCA
24946 ACTTGATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.66
Consensus pattern (15 bp):
TTTTTTTTTCACGAA
Found at i:24996 original size:14 final size:14
Alignment explanation
Indices: 24977--25013 Score: 60
Period size: 12 Copynumber: 2.8 Consensus size: 14
24967 GTTTGAATGG
24977 GAATTTTTTTTTTT
1 GAATTTTTTTTTTT
24991 GAA--TTTTTTTTT
1 GAATTTTTTTTTTT
25003 GAATTTTTTTT
1 GAATTTTTTTT
25014 AAAAAAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 12 0.57
14 9 0.43
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (14 bp):
GAATTTTTTTTTTT
Found at i:24999 original size:12 final size:12
Alignment explanation
Indices: 24982--25013 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
24972 AATGGGAATT
24982 TTTTTTTTTGAA
1 TTTTTTTTTGAA
24994 TTTTTTTTTGAA
1 TTTTTTTTTGAA
25006 TTTTTTTT
1 TTTTTTTT
25014 AAAAAAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:26053 original size:21 final size:23
Alignment explanation
Indices: 26008--26054 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
25998 TCACCTGCAA
* *
26008 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
26031 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
26052 TAA
1 TAA
26055 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:29631 original size:11 final size:11
Alignment explanation
Indices: 29615--29668 Score: 72
Period size: 11 Copynumber: 4.7 Consensus size: 11
29605 AGTTTCTTTG
29615 AAAAAATTCAAA
1 AAAAAATTC-AA
*
29627 AAAAAATTTGAA
1 AAAAAA-TTCAA
29639 AAAAAATTCAA
1 AAAAAATTCAA
*
29650 AAAAAATTCGA
1 AAAAAATTCAA
29661 AAAAAATT
1 AAAAAATT
29669 TAGTTTCTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
11 22 0.58
12 14 0.37
13 2 0.05
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (11 bp):
AAAAAATTCAA
Found at i:29632 original size:12 final size:12
Alignment explanation
Indices: 29615--29666 Score: 70
Period size: 12 Copynumber: 4.3 Consensus size: 12
29605 AGTTTCTTTG
29615 AAAAAATTCAAA
1 AAAAAATTCAAA
**
29627 AAAAAATTTGAA
1 AAAAAATTCAAA
29639 AAAAAATTC-AA
1 AAAAAATTCAAA
29650 AAAAAATTCGAAA
1 AAAAAATTC-AAA
29663 AAAA
1 AAAA
29667 TTTAGTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
11 11 0.31
12 18 0.51
13 6 0.17
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.17
Consensus pattern (12 bp):
AAAAAATTCAAA
Found at i:29647 original size:24 final size:23
Alignment explanation
Indices: 29615--29666 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 23
29605 AGTTTCTTTG
*
29615 AAAAAATTCAAAAAAAAATTTGAA
1 AAAAAATTC-AAAAAAAATTCGAA
29639 AAAAAATTCAAAAAAAATTCGAA
1 AAAAAATTCAAAAAAAATTCGAA
29662 AAAAA
1 AAAAA
29667 TTTAGTTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.17
Consensus pattern (23 bp):
AAAAAATTCAAAAAAAATTCGAA
Done.