Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3765
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: 31877
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Found at i:6587 original size:104 final size:103
Alignment explanation
Indices: 6407--6774 Score: 623
Period size: 104 Copynumber: 3.6 Consensus size: 103
6397 TGTATATAAA
** * * *
6407 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGT-ATCCACCATATCTT
6472 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
6511 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCG-TATCCACCATATCTT
6576 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
6615 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCG-TATCCACCATATCTT
*
6680 TGAAA--TAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
6717 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTATCCACCA
6775 ATAACGGTTA
Statistics
Matches: 255, Mismatches: 8, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
101 8 0.03
102 79 0.31
104 167 0.65
105 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.30
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTATCCACCATATCTTT
GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:8229 original size:20 final size:20
Alignment explanation
Indices: 8204--8243 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
8194 AAATAAAGTT
8204 AATTTCACATTTCACTATTA
1 AATTTCACATTTCACTATTA
8224 AATTTCACATTTCACTATTA
1 AATTTCACATTTCACTATTA
8244 TGTCTTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTTCACATTTCACTATTA
Found at i:9963 original size:31 final size:29
Alignment explanation
Indices: 9928--9985 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
9918 AATAGTATTT
*
9928 TATTAATTTAATATTAAAGTGATTATCTTAA
1 TATTAAATTAA-ATTAAA-TGATTATCTTAA
* *
9959 TATTAAATTAAATTTAATGTTTATCTT
1 TATTAAATTAAATTAAATGATTATCTT
9986 GTAGATAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.38
30 5 0.21
31 10 0.42
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (29 bp):
TATTAAATTAAATTAAATGATTATCTTAA
Found at i:19612 original size:13 final size:13
Alignment explanation
Indices: 19594--19621 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19584 CTGCCAAAGA
19594 GACACGGCCGTGT
1 GACACGGCCGTGT
19607 GACACGGCCGTGT
1 GACACGGCCGTGT
19620 GA
1 GA
19622 GGAAGTCCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.18, C:0.29, G:0.39, T:0.14
Consensus pattern (13 bp):
GACACGGCCGTGT
Found at i:24459 original size:29 final size:29
Alignment explanation
Indices: 24426--24482 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
24416 TTGAATTGTG
24426 TTAGGTTTCAGTTCAAAAGTATTTGCAGT
1 TTAGGTTTCAGTTCAAAAGTATTTGCAGT
24455 TTAGGTTTCAGTTCAAAAGTATTTGCAG
1 TTAGGTTTCAGTTCAAAAGTATTTGCAG
24483 CTACAGCAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (29 bp):
TTAGGTTTCAGTTCAAAAGTATTTGCAGT
Found at i:26126 original size:56 final size:56
Alignment explanation
Indices: 26040--26159 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
26030 ACAAGGGATG
26040 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
26096 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
26152 ATGGGCAA
1 ATGGGCAA
26160 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:27519 original size:40 final size:39
Alignment explanation
Indices: 27283--27505 Score: 279
Period size: 39 Copynumber: 5.6 Consensus size: 39
27273 TCGAATGATG
* * * *
27283 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
27323 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
27363 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
27402 TCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
27441 TCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTA-AA
*
27481 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
27506 AACGAGTAGC
Statistics
Matches: 162, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
39 106 0.65
40 48 0.30
41 8 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Done.