Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1393
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: 36433
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Found at i:6357 original size:27 final size:27
Alignment explanation
Indices: 6327--6481 Score: 152
Period size: 27 Copynumber: 5.7 Consensus size: 27
6317 ATATTAAGTC
* *
6327 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
6354 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
6382 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* ** *
6409 CGCACACTTAGTG-TCGCATGGTCAATT
1 CGCACACTTAGTGCT-ACATAATCAACT
** **
6436 CGCACACTTAGTGC-ATCATTTTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
*
6463 CGCACACTTAGTGCAACAT
1 CGCACACTTAGTGCTACAT
6482 GGTCAAATCG
Statistics
Matches: 111, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
26 1 0.01
27 84 0.76
28 26 0.23
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:6411 original size:55 final size:54
Alignment explanation
Indices: 6327--6481 Score: 168
Period size: 55 Copynumber: 2.9 Consensus size: 54
6317 ATATTAAGTC
* *
6327 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATC-AACT
* * * ** *
6382 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGTCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATCAACT
** ** *
6436 CGCACACTTAGTGC-ATCATTTTCATTTCGCACACTTAGTGCAACAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACAT
6482 GGTCAAATCG
Statistics
Matches: 84, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
53 1 0.01
54 40 0.48
55 43 0.51
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATCAACT
Found at i:6466 original size:54 final size:53
Alignment explanation
Indices: 6327--6492 Score: 181
Period size: 54 Copynumber: 3.1 Consensus size: 53
6317 ATATTAAGTC
* * * **
6327 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTG-CACATGGTCAAA-T
* *
6382 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGTCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTG-CACATGGTCAAAT
** **
6436 CGCACACTTAGTGC-ATCATTTTCATTTCGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTA-CATAGTCAACTCGCACACTTAGTGC-ACATGGTCAAAT
6490 CGC
1 CGC
6493 CAAATCGCAC
Statistics
Matches: 95, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
53 2 0.02
54 48 0.51
55 45 0.47
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (53 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCACATGGTCAAAT
Found at i:12612 original size:104 final size:104
Alignment explanation
Indices: 12432--12655 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
12422 TGTATATAAA
** * *
12432 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
12497 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
12536 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
12600 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
12640 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
12656 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:12707 original size:71 final size:72
Alignment explanation
Indices: 12574--12725 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
12564 TCATTGGTGG
* *
12574 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
12639 GAGGGGT
66 GAGGGGT
***
12646 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
12710 GAGGGGT
66 GAGGGGT
12717 TGCTAAGTG
1 TGCTAAGTG
12726 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:24603 original size:30 final size:30
Alignment explanation
Indices: 24569--24626 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
24559 TTTTCGAATA
* * *
24569 TAGGGGTAAAATGGTCATTTTGCCAAAGTT
1 TAGGGGCAAAATGGTAATTTTACCAAAGTT
24599 TAGGGGCAAAATGGTAATTTTACCAAAG
1 TAGGGGCAAAATGGTAATTTTACCAAAG
24627 CTGTGAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.29
Consensus pattern (30 bp):
TAGGGGCAAAATGGTAATTTTACCAAAGTT
Found at i:26497 original size:40 final size:40
Alignment explanation
Indices: 26452--26643 Score: 226
Period size: 40 Copynumber: 4.8 Consensus size: 40
26442 ATAACCACAA
* * *
26452 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
26492 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
26532 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* * * * *
26572 GCATAAATGCCTTCGGGACTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* *
26612 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
26644 CATTCAAATG
Statistics
Matches: 142, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 1 0.01
40 137 0.96
41 4 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:26536 original size:80 final size:80
Alignment explanation
Indices: 26423--26642 Score: 248
Period size: 80 Copynumber: 2.8 Consensus size: 80
26413 ACCCAAGTTT
* * * * * * * * *
26423 CTTCGGAATTTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGT-ATAG
1 CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAAG
*
26486 CAACTCGCACAAATGC
66 C-ACTAGCACAAATGC
* * *
26502 CTTCGGGTCTTAGCCCGGAT-ATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAA
1 CTTCGGGACTTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAA
* *
26566 TCACTAGCATAAATGC
65 GCACTAGCACAAATGC
* *
26582 CTTCGGGACTTAGCCCGGATAAAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGGATA
1 CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATA
26643 TCATTCAAAT
Statistics
Matches: 117, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
79 12 0.10
80 98 0.84
81 7 0.06
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAAG
CACTAGCACAAATGC
Found at i:33397 original size:13 final size:13
Alignment explanation
Indices: 33379--33403 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33369 CATATATGCA
33379 TCTATAATTTTTT
1 TCTATAATTTTTT
33392 TCTATAATTTTT
1 TCTATAATTTTT
33404 GGTTGGGCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TCTATAATTTTTT
Found at i:34637 original size:38 final size:38
Alignment explanation
Indices: 34542--34717 Score: 169
Period size: 38 Copynumber: 4.8 Consensus size: 38
34532 ATAACCACAA
* * *
34542 GCACAATTGCCTTCGGGTCTTAACCCGG-TATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAA--C
34581 GCACAAATGCCTTC-GGTCTTAGCCCGGATATATCAAC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAAC
34618 GCACAAATGCCTTCGGGTCTTAGCCCGGATA-ATC-AC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAAC
* * *
34654 TAGCA-TAATGCCTTC-GGACTTAGCCC--A-A-ATCTA-
1 --GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAAC
*
34687 GCA-AAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
34718 CATTCAAATG
Statistics
Matches: 121, Mismatches: 6, Indels: 23
0.81 0.04 0.15
Matches are distributed among these distances:
31 12 0.10
32 11 0.09
33 4 0.03
34 3 0.02
35 1 0.01
36 12 0.10
37 27 0.22
38 31 0.26
39 20 0.17
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.24
Consensus pattern (38 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAAC
Found at i:34645 original size:76 final size:69
Alignment explanation
Indices: 34539--34716 Score: 198
Period size: 76 Copynumber: 2.5 Consensus size: 69
34529 GATATAACCA
* * * *
34539 CAAGCACAATTGCCTTCGGGTCTTAACCCGG-TATAGCAACTCGCACAAATGCCTTCGGTCTTAG
1 CAAGCACAAATGCCTTCGGGTCTTAGCCCGGATA-AGC-ACTAGCA-AAATGCCTTCGGACTTAG
34603 CCCGGATATAT
63 CCC--A-A-AT
* *
34614 CAACGCACAAATGCCTTCGGGTCTTAGCCCGGATAATCACTAGCATAATGCCTTCGGACTTAGCC
1 CAA-GCACAAATGCCTTCGGGTCTTAGCCCGGATAAGCACTAGCAAAATGCCTTCGGACTTAGCC
34679 CAAAT
65 CAAAT
* *
34684 CTAGCA-AAATGCCTTCGGGACTTAGCCCGGATA
1 CAAGCACAAATGCCTTCGGGTCTTAGCCCGGATA
34717 TCATTCAAAT
Statistics
Matches: 93, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
68 26 0.28
69 3 0.03
70 4 0.04
71 1 0.01
72 1 0.01
74 19 0.20
75 9 0.10
76 28 0.30
77 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (69 bp):
CAAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAGCACTAGCAAAATGCCTTCGGACTTAGCCC
AAAT
Done.