Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2408
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: 12544
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Found at i:384 original size:54 final size:55
Alignment explanation
Indices: 302--418 Score: 204
Period size: 54 Copynumber: 2.2 Consensus size: 55
292 ACAAGGGATG
302 ATGGGCAAAACATGTCATGAAACATGTTGT-TTAATGGAAAA-ATAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAATA-AAATAAGAAGC
356 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAATAAAATAAGAAGC
411 AT-GGCAAA
1 ATGGGCAAA
419 TGAAACATGA
Statistics
Matches: 61, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
54 36 0.59
55 24 0.39
56 1 0.02
ACGTcount: A:0.46, C:0.09, G:0.21, T:0.23
Consensus pattern (55 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAATAAAATAAGAAGC
Found at i:414 original size:21 final size:20
Alignment explanation
Indices: 390--451 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 20
380 TGTTGTGTTA
390 ATGGAAAATAAAATAAGAAGC
1 ATGG-AAATAAAATAAGAAGC
* * *
411 ATGGCAAATGAAACATG-A--
1 ATGG-AAATAAAATAAGAAGC
429 ATGG-AATAAAATAAGAAGC
1 ATGGAAATAAAATAAGAAGC
448 ATGG
1 ATGG
452 GCAATAAACT
Statistics
Matches: 31, Mismatches: 7, Indels: 8
0.67 0.15 0.17
Matches are distributed among these distances:
16 8 0.26
17 1 0.03
18 4 0.13
19 4 0.13
20 1 0.03
21 13 0.42
ACGTcount: A:0.55, C:0.06, G:0.23, T:0.16
Consensus pattern (20 bp):
ATGGAAATAAAATAAGAAGC
Found at i:1728 original size:39 final size:40
Alignment explanation
Indices: 1573--1793 Score: 260
Period size: 39 Copynumber: 5.7 Consensus size: 40
1563 TCGAATGATG
* * * *
1573 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
1613 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
1653 TCC-GGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
1691 TCCGGGTTAAGTCCCGAAGGCATTTG-GCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
1730 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
1770 -CCGGGCTATGT-CCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
1794 AACGAGTAGC
Statistics
Matches: 158, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
38 39 0.25
39 70 0.44
40 41 0.26
41 8 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:1800 original size:117 final size:118
Alignment explanation
Indices: 1573--1826 Score: 261
Period size: 117 Copynumber: 2.2 Consensus size: 118
1563 TCGAATGATG
* *
1573 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* **
1638 GTGCGAGATACTAATTCCGGCTAAGCCCGAAGGCATTGGTGCGAGTTA-CTAAA
66 GTGCGAGATACTAATACCGGCTAAGCCCGAAGGCATTGGAACGAG-TAGCTAAA
* * * **
1691 TCCGGGTTAAGTCCCGAAGGCATTTG-GC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA-
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * *
1752 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCGAAGGCATTTGAACGAGTAGCTATA
64 TTGTGCGAGATACTAAT-ACC-GGCTAAGCCCGAAGGCATTGGAACGAGTAGCTAAA
* *
1808 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
1827 TACGTGATTT
Statistics
Matches: 114, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
115 2 0.02
116 32 0.28
117 54 0.47
118 22 0.19
119 4 0.04
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (118 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGCTAAGCCCGAAGGCATTGGAACGAGTAGCTAAA
Found at i:7612 original size:56 final size:56
Alignment explanation
Indices: 7526--7700 Score: 334
Period size: 56 Copynumber: 3.1 Consensus size: 56
7516 ACAAGGGATG
7526 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
7582 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGG-AAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
7637 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
7693 ATGGGCAA
1 ATGGGCAA
7701 TAAACTAATA
Statistics
Matches: 117, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
55 55 0.47
56 62 0.53
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:9066 original size:40 final size:40
Alignment explanation
Indices: 8828--9052 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
8818 TCGAATGATG
* * * *
8828 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
8868 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
8908 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
8947 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
8987 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
9028 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
9053 AACGAGTAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:9074 original size:119 final size:119
Alignment explanation
Indices: 8828--9085 Score: 292
Period size: 119 Copynumber: 2.2 Consensus size: 119
8818 TCGAATGATG
* *
8828 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* **
8893 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
* * * **
8947 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
9010 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAAA
* *
9067 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
9086 TACGTGATTT
Statistics
Matches: 118, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
118 3 0.03
119 84 0.71
120 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
Done.