Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1512
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: 23241
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:2622 original size:86 final size:86
Alignment explanation
Indices: 2470--2654 Score: 264
Period size: 86 Copynumber: 2.2 Consensus size: 86
2460 AAGGCTGATA
* * * *
2470 TTTCC-CCTAATTCAACTCAAACTAAATCAACTCAACCGAATTAAGCTTGAACACCCAAACATTT
1 TTTCCTCC-AATTCAACTCAAACTAAATCAACTCAACCAAACTAAACTTGAACACCCAAACAGTT
2534 GGAAGTGACTAAATCAATCCTT
65 GGAAGTGACTAAATCAATCCTT
* * * * **
2556 TTTCCTCCAATTCAACTCAAGCTCAATCCACTCAACTAAACTAAACTTGAACACCCAAGTAGTTG
1 TTTCCTCCAATTCAACTCAAACTAAATCAACTCAACCAAACTAAACTTGAACACCCAAACAGTTG
2621 GAAGTGACTAAATCAATCCTT
66 GAAGTGACTAAATCAATCCTT
2642 TTTCCTCCAATTC
1 TTTCCTCCAATTC
2655 GAACACCCAA
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
86 86 0.98
87 2 0.02
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (86 bp):
TTTCCTCCAATTCAACTCAAACTAAATCAACTCAACCAAACTAAACTTGAACACCCAAACAGTTG
GAAGTGACTAAATCAATCCTT
Found at i:2662 original size:51 final size:51
Alignment explanation
Indices: 2604--2705 Score: 168
Period size: 51 Copynumber: 2.0 Consensus size: 51
2594 AACTAAACTT
* *
2604 GAACACCCAAGTAGTTGGAAGTGACTAAATCAATCCTTTTTCCTCCAATTC
1 GAACACCCAAGTAGTTAGAAGTGACTAAATCAATCCTTTTTCCCCCAATTC
* *
2655 GAACACCCAAGTAGTTAGAAGTGACTACATCAGTCCTTTTTCCCCCAATTC
1 GAACACCCAAGTAGTTAGAAGTGACTAAATCAATCCTTTTTCCCCCAATTC
2706 AACTCAAAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.28
Consensus pattern (51 bp):
GAACACCCAAGTAGTTAGAAGTGACTAAATCAATCCTTTTTCCCCCAATTC
Found at i:3520 original size:3 final size:3
Alignment explanation
Indices: 3512--3555 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
3502 AGCGATCACC
3512 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -AA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
3556 ACGCCGGTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3895 original size:30 final size:31
Alignment explanation
Indices: 3859--3960 Score: 111
Period size: 30 Copynumber: 3.4 Consensus size: 31
3849 ATTAATAATT
3859 AATAAATTTTTAATTTTTAAATTT-TATTTA
1 AATAAATTTTTAATTTTTAAATTTATATTTA
* * *
3889 AATAAATTATTGATATTT-AATTTATATTTA
1 AATAAATTTTTAATTTTTAAATTTATATTTA
* * * *
3919 TATAAA-TTTAAAATTTAAAATTTATATTTA
1 AATAAATTTTTAATTTTTAAATTTATATTTA
3949 AATAAATATTTT
1 AATAAAT-TTTT
3961 TTATATAATA
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
29 10 0.18
30 43 0.77
32 3 0.05
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (31 bp):
AATAAATTTTTAATTTTTAAATTTATATTTA
Found at i:3975 original size:20 final size:21
Alignment explanation
Indices: 3939--3995 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
3929 AAATTTAAAA
*
3939 TTTATATTTAAATAAATAT-TT
1 TTTATA-TAAAATAAATATATT
*
3960 TTTATATAATATAAATATATT
1 TTTATATAAAATAAATATATT
*
3981 TTTATTTAAAATAAA
1 TTTATATAAAATAAA
3996 ATTAATAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTATATAAAATAAATATATT
Found at i:4002 original size:26 final size:26
Alignment explanation
Indices: 3973--4067 Score: 69
Period size: 26 Copynumber: 3.8 Consensus size: 26
3963 ATATAATATA
*
3973 AATATATTTTTATTTAAAATAAAATT
1 AATATATATTTATTTAAAATAAAATT
* * *
3999 AATA-ATAATTTATTT-AAGTATAATA
1 AATATAT-ATTTATTTAAAATAAAATT
*
4024 AATATACAATTTATTTAAAA-AATAATT
1 AATATA-TATTTATTTAAAATAA-AATT
4051 --TA-ATATTT-TTTAAAATA
1 AATATATATTTATTTAAAATA
4068 TTTTAATTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
22 7 0.13
23 5 0.09
24 1 0.02
25 15 0.28
26 21 0.39
27 5 0.09
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (26 bp):
AATATATATTTATTTAAAATAAAATT
Found at i:4083 original size:20 final size:20
Alignment explanation
Indices: 4042--4083 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
4032 ATTTATTTAA
*
4042 AAAATAATTTAATATTTTTT
1 AAAATAATTTAATATTTATT
*
4062 AAAATATTTTAAT-TTTAATT
1 AAAATAATTTAATATTT-ATT
4082 AA
1 AA
4084 TTAAGAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AAAATAATTTAATATTTATT
Found at i:5847 original size:2 final size:2
Alignment explanation
Indices: 5840--5870 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5830 AGATTATAAA
5840 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5871 AACATTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9512 original size:21 final size:21
Alignment explanation
Indices: 9488--9531 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
9478 GAATATTAAA
9488 AGTATGTTGATGACTCTTGTT
1 AGTATGTTGATGACTCTTGTT
9509 AGTATGTTGATGACTCTTGTT
1 AGTATGTTGATGACTCTTGTT
9530 AG
1 AG
9532 CGTGCTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.09, G:0.25, T:0.45
Consensus pattern (21 bp):
AGTATGTTGATGACTCTTGTT
Found at i:12152 original size:25 final size:25
Alignment explanation
Indices: 12123--12170 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
12113 CTAAATTTTG
12123 TAGGAGTGTGTTTATTTTTTAAATA
1 TAGGAGTGTGTTTATTTTTTAAATA
12148 TAGGAGTGTGTTTATTTTTTAAA
1 TAGGAGTGTGTTTATTTTTTAAA
12171 ATTAGATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (25 bp):
TAGGAGTGTGTTTATTTTTTAAATA
Found at i:12448 original size:2 final size:2
Alignment explanation
Indices: 12441--12468 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12431 GATATGATCT
12441 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12469 ATAATAGCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14119 original size:2 final size:2
Alignment explanation
Indices: 14112--14161 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
14102 ACATGAACGC
14112 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
14154 TG TA TA TA
1 TA TA TA TA
14162 AATTCTTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15952 original size:2 final size:2
Alignment explanation
Indices: 15945--15971 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15935 AAATTTGTGG
15945 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
15972 AGGCTTATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18642 original size:2 final size:2
Alignment explanation
Indices: 18635--18661 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18625 TGAGCGTAGG
18635 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
18662 TTACACATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23145 original size:8 final size:8
Alignment explanation
Indices: 23105--23164 Score: 68
Period size: 8 Copynumber: 7.6 Consensus size: 8
23095 GGTGCAGCCG
*
23105 AAAAAGAG
1 AAAAAGAA
*
23113 AGAAAGAA
1 AAAAAGAA
*
23121 AAAAA-AG
1 AAAAAGAA
*
23128 AAAGAGAA
1 AAAAAGAA
23136 AAAAAGAA
1 AAAAAGAA
23144 AAAAAGAA
1 AAAAAGAA
*
23152 AGAAAGAA
1 AAAAAGAA
23160 AAAAA
1 AAAAA
23165 TTTATCTATA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
7 5 0.12
8 37 0.88
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Done.