Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2594
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: 18159
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Found at i:365 original size:28 final size:28
Alignment explanation
Indices: 308--441 Score: 177
Period size: 27 Copynumber: 4.9 Consensus size: 28
298 GAGGAAGCGT
*
308 TCTGGTGGCTCTGCCACAAATATCT-CA
1 TCTGGTGGCTCTGCCACAAATATCTGTA
*
335 TCTGGTGGCTTTGCCCACAAATATCTG-A
1 TCTGGTGGCTCTG-CCACAAATATCTGTA
* *
363 TCTGGTGGCTTTGCCACAAATATCTGTT
1 TCTGGTGGCTCTGCCACAAATATCTGTA
391 TCTGGTGGCTCTGCCAC-AATATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTGTA
* *
418 TCTGGTGACTCTGTCAC-AATATCT
1 TCTGGTGGCTCTGCCACAAATATCT
442 TGTTTTGGCA
Statistics
Matches: 98, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
27 56 0.57
28 42 0.43
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.34
Consensus pattern (28 bp):
TCTGGTGGCTCTGCCACAAATATCTGTA
Found at i:408 original size:55 final size:56
Alignment explanation
Indices: 308--446 Score: 178
Period size: 55 Copynumber: 2.5 Consensus size: 56
298 GAGGAAGCGT
** *
308 TCTGGTGGCTCTGCCACAAATATCT-CATCTGGTGGCTTTGCCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACAAATATCTGTTTCTGGTGGCTCTGCCCAC-AATATCTGTA
*
363 TCTGGTGGCTTTGCCACAAATATCTGTTTCTGGTGGCTCTG-CCACAATATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTGTTTCTGGTGGCTCTGCCCACAATATCTGTA
* *
418 TCTGGTGACTCTGTCAC-AATATCTTGTTT
1 TCTGGTGGCTCTGCCACAAATATC-TGTTT
447 TGGCAGCCAT
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
54 14 0.19
55 48 0.65
56 12 0.16
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.36
Consensus pattern (56 bp):
TCTGGTGGCTCTGCCACAAATATCTGTTTCTGGTGGCTCTGCCCACAATATCTGTA
Found at i:2793 original size:40 final size:40
Alignment explanation
Indices: 2555--2779 Score: 305
Period size: 40 Copynumber: 5.7 Consensus size: 40
2545 TTGAATGATG
* * * *
2555 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
2595 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
2635 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
2674 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
2714 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
2755 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
2780 AACGAGTAGC
Statistics
Matches: 167, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
39 35 0.21
40 122 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:2801 original size:119 final size:119
Alignment explanation
Indices: 2555--2812 Score: 301
Period size: 119 Copynumber: 2.2 Consensus size: 119
2545 TTGAATGATG
* *
2555 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* **
2620 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAA
* * * **
2674 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * *
2737 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-CTAAA
* *
2794 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
2813 TACGTGATTT
Statistics
Matches: 119, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
118 3 0.03
119 84 0.71
120 32 0.27
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAA
Found at i:10771 original size:40 final size:40
Alignment explanation
Indices: 10533--10757 Score: 305
Period size: 40 Copynumber: 5.7 Consensus size: 40
10523 TTGAATGATG
* * * *
10533 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
10573 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
10613 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
10652 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
10692 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
10733 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
10758 AACGAGTAGC
Statistics
Matches: 167, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
39 35 0.21
40 122 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:10779 original size:119 final size:119
Alignment explanation
Indices: 10533--10790 Score: 301
Period size: 119 Copynumber: 2.2 Consensus size: 119
10523 TTGAATGATG
* *
10533 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* **
10598 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAA
* * * **
10652 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * *
10715 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-CTAAA
* *
10772 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
10791 TACGTGATTT
Statistics
Matches: 119, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
118 3 0.03
119 84 0.71
120 32 0.27
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAA
Found at i:17698 original size:27 final size:27
Alignment explanation
Indices: 17667--17841 Score: 199
Period size: 27 Copynumber: 6.4 Consensus size: 27
17657 TAAATTGTAC
17667 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
17694 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
17720 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
17748 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
17776 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
17803 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
17830 AGCACTGAGTGT
1 AGCACTAAGTGT
17842 ACGGACTCAA
Statistics
Matches: 126, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 103 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:17781 original size:82 final size:81
Alignment explanation
Indices: 17668--17823 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
17658 AAATTGTACA
* *
17668 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
17732 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
17749 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
17814 TGCGAGTTGA
65 TGCGAATTGA
17824 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:17835 original size:82 final size:81
Alignment explanation
Indices: 17664--17841 Score: 223
Period size: 82 Copynumber: 2.2 Consensus size: 81
17654 GATTAAATTG
* *
17664 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
17729 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
17745 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
17809 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
17827 TATAGCACTGAGTGT
1 TACAGCACTAAGTGT
17842 ACGGACTCAA
Statistics
Matches: 81, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.22
82 63 0.78
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.