Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2093
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: 76832
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2818 original size:11 final size:11
Alignment explanation
Indices: 2802--2841 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
2792 GTAGTTTCTC
2802 AAAAAAATCAA
1 AAAAAAATCAA
2813 AAAAAAAT-AA
1 AAAAAAATCAA
*
2823 AAAAAATTCAA
1 AAAAAAATCAA
2834 AAAAAAAT
1 AAAAAAAT
2842 TTAGTTTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.12
Consensus pattern (11 bp):
AAAAAAATCAA
Found at i:2828 original size:21 final size:21
Alignment explanation
Indices: 2802--2841 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2792 GTAGTTTCTC
2802 AAAAAAATCAAAAAAAAATAA
1 AAAAAAATCAAAAAAAAATAA
*
2823 AAAAAATTCAAAAAAAAAT
1 AAAAAAATCAAAAAAAAAT
2842 TTAGTTTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.12
Consensus pattern (21 bp):
AAAAAAATCAAAAAAAAATAA
Found at i:2897 original size:15 final size:15
Alignment explanation
Indices: 2879--2930 Score: 83
Period size: 15 Copynumber: 3.7 Consensus size: 15
2869 TGGATATCAA
2879 GTGAAAAAAAAATTC
1 GTGAAAAAAAAATTC
2894 GTGAAAAAAAAATTC
1 GTGAAAAAAAAATTC
2909 --GAAAAAAAAATT-
1 GTGAAAAAAAAATTC
2921 GTGAAAAAAA
1 GTGAAAAAAA
2931 GAAGAGCTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
13 12 0.34
14 8 0.23
15 15 0.43
ACGTcount: A:0.65, C:0.04, G:0.13, T:0.17
Consensus pattern (15 bp):
GTGAAAAAAAAATTC
Found at i:2902 original size:14 final size:14
Alignment explanation
Indices: 2883--2930 Score: 64
Period size: 13 Copynumber: 3.5 Consensus size: 14
2873 TATCAAGTGA
2883 AAAAAAAATTCGTG
1 AAAAAAAATTCGTG
*
2897 AAAAAAAAATTCG-A
1 -AAAAAAAATTCGTG
2911 AAAAAAAATT-GTG
1 AAAAAAAATTCGTG
2924 AAAAAAA
1 AAAAAAA
2931 GAAGAGCTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 1 0.03
13 17 0.57
15 12 0.40
ACGTcount: A:0.69, C:0.04, G:0.10, T:0.17
Consensus pattern (14 bp):
AAAAAAAATTCGTG
Found at i:15804 original size:56 final size:55
Alignment explanation
Indices: 15688--15805 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
15678 TGCATGCTTT
* * * *
15688 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
15742 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
15798 CATTAAAT
1 CATTAAAT
15806 CAACAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:16443 original size:20 final size:20
Alignment explanation
Indices: 16412--16483 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
16402 AGCTAATAAC
* *
16412 GAGCTC-AATGAGTTAAATT
1 GAGCTCGAATGAGCTAACTT
* *
16431 GAGCTTGAATGAGCTGACTT
1 GAGCTCGAATGAGCTAACTT
16451 GAGCTCGAATGAGCTAACTT
1 GAGCTCGAATGAGCTAACTT
16471 GAGCTCGAATGAG
1 GAGCTCGAATGAG
16484 TTGAACCACA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 5 0.11
20 41 0.89
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (20 bp):
GAGCTCGAATGAGCTAACTT
Found at i:20325 original size:21 final size:21
Alignment explanation
Indices: 20299--20361 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
20289 TTGGTATTTG
20299 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
20320 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
20341 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
20362 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:21455 original size:10 final size:10
Alignment explanation
Indices: 21440--21481 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
21430 TTTGCAAGTT
21440 TTGAGCTAAA
1 TTGAGCTAAA
* *
21450 TTGAGCTGAT
1 TTGAGCTAAA
*
21460 TTGAGCT-CA
1 TTGAGCTAAA
21469 TTGAGCTAAA
1 TTGAGCTAAA
21479 TTG
1 TTG
21482 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:48089 original size:20 final size:20
Alignment explanation
Indices: 48043--48089 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
48033 AGCTCGTTTC
*
48043 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
48063 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
48083 CAGCTCA
1 CAGCTCA
48090 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:61548 original size:39 final size:40
Alignment explanation
Indices: 61440--61656 Score: 208
Period size: 40 Copynumber: 5.7 Consensus size: 40
61430 TTGAATGATG
* * *
61440 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* * *
61479 ATCCGGACTAAGAT-CCAAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
61520 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
61559 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA-
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
61598 -------TAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
61630 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
61657 AACGAGGAGC
Statistics
Matches: 149, Mismatches: 14, Indels: 28
0.78 0.07 0.15
Matches are distributed among these distances:
31 1 0.01
32 30 0.20
39 33 0.22
40 75 0.50
41 10 0.07
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:61607 original size:32 final size:32
Alignment explanation
Indices: 61566--61628 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
61556 AAATCCGGGT
61566 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
61598 TAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTA
61629 TAACCGGGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (32 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:69457 original size:38 final size:38
Alignment explanation
Indices: 69368--69577 Score: 156
Period size: 38 Copynumber: 5.6 Consensus size: 38
69358 ATGATGTCCG
* *
69368 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCT--ATCC
1 GGCTAAG-CCCGAAGGCATTTGTGC-GAGTTA-CTAAATCC
* * * *
69406 GACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTCC
1 GGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCC
*
69445 GGGCTAAG-CCGAAGGCATTGGTGCGAGTTACTAAATCC
1 -GGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCC
*
69483 GGTTAAGTCCCGAAGGCATTTGCTGC-AGTTACTAAA---
1 GGCTAAG-CCCGAAGGCATTTG-TGCGAGTTACTAAATCC
69519 ---TAAGTCCCGAAGGCATTTGTGCGAGTTACTTAAA-CC
1 GGCTAAG-CCCGAAGGCATTTGTGCGAGTTAC-TAAATCC
*
69555 GGGCTATGTCCCGAAGGCATTTG
1 -GGCTAAG-CCCGAAGGCATTTG
69578 AACGAGGAGC
Statistics
Matches: 143, Mismatches: 14, Indels: 28
0.77 0.08 0.15
Matches are distributed among these distances:
32 3 0.02
33 25 0.17
34 4 0.03
37 8 0.06
38 44 0.31
39 32 0.22
40 27 0.19
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (38 bp):
GGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCC
Found at i:69528 original size:33 final size:33
Alignment explanation
Indices: 69453--69548 Score: 113
Period size: 33 Copynumber: 2.7 Consensus size: 33
69443 CCGGGCTAAG
*
69453 CCGAAGGCATTGGTGCGAGTTACTAAATCCGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAA------TAAGTC
69492 CCGAAGGCATTTGCTGC-AGTTACTAAATAAGTC
1 CCGAAGGCATTTG-TGCGAGTTACTAAATAAGTC
69525 CCGAAGGCATTTGTGCGAGTTACT
1 CCGAAGGCATTTGTGCGAGTTACT
69549 TAAACCGGGC
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
32 3 0.06
33 26 0.48
39 22 0.41
40 3 0.06
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (33 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATAAGTC
Done.