Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1257
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: 42074
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2312 original size:20 final size:20
Alignment explanation
Indices: 2289--2335 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2279 GGGTTAAGAT
*
2289 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
2309 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
2329 TGAGCTG
1 TGAGCTG
2336 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:4044 original size:48 final size:48
Alignment explanation
Indices: 3989--4094 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
3979 TTGTCTTTTC
*
3989 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
4037 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
4085 TTTCTTTTTC
1 TTTCTTTTTC
4095 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:5140 original size:15 final size:15
Alignment explanation
Indices: 5122--5172 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
5112 TTAACTTGAT
5122 TTTTTTTTTGCTCAC
1 TTTTTTTTTGCTCAC
**
5137 TTTTTTTTT-CTTTC
1 TTTTTTTTTGCTCAC
5151 TTTTTTTTTGCTCGA-
1 TTTTTTTTTGCTC-AC
5166 TTTTTTT
1 TTTTTTT
5173 CACTTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 12 0.40
15 18 0.60
ACGTcount: A:0.04, C:0.14, G:0.06, T:0.76
Consensus pattern (15 bp):
TTTTTTTTTGCTCAC
Found at i:5140 original size:31 final size:29
Alignment explanation
Indices: 5102--5184 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 29
5092 GCAAGACTTT
5102 TCACTTTTTTTTAACTTGAT-TTTTTTTTTGC
1 TCACTTTTTTTT-ACTT--TCTTTTTTTTTGC
*
5133 TCACTTTTTTTTTCTTTCTTTTTTTTTGC
1 TCACTTTTTTTTACTTTCTTTTTTTTTGC
*
5162 TCGA-TTTTTTTCACTTT-TTTTTT
1 TC-ACTTTTTTTTACTTTCTTTTTT
5185 GAATTTTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
28 7 0.15
29 24 0.51
30 4 0.09
31 12 0.26
ACGTcount: A:0.08, C:0.14, G:0.05, T:0.72
Consensus pattern (29 bp):
TCACTTTTTTTTACTTTCTTTTTTTTTGC
Found at i:6696 original size:20 final size:20
Alignment explanation
Indices: 6673--6719 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
6663 GGGTTAAGAT
*
6673 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
6693 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
6713 TGAGCTG
1 TGAGCTG
6720 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:7051 original size:24 final size:23
Alignment explanation
Indices: 7023--7069 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
7013 CAAAAAAGTC
*
7023 AAAAAATCAAAAAAACGAATTCAAT
1 AAAAATTCAAAAAAA-G-ATTCAAT
*
7048 AAAAATTTAAAAAAAGATTCAA
1 AAAAATTCAAAAAAAGATTCAA
7070 CGGGTTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 1 0.05
25 13 0.65
ACGTcount: A:0.68, C:0.09, G:0.04, T:0.19
Consensus pattern (23 bp):
AAAAATTCAAAAAAAGATTCAAT
Found at i:17074 original size:79 final size:81
Alignment explanation
Indices: 16965--17147 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
16955 TACTCGTTCA
* *
16965 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
17028 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
17045 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
17108 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
17124 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
17148 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:17147 original size:40 final size:40
Alignment explanation
Indices: 16944--17147 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
16934 CAGAATTTAA
** *
16944 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
16984 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
17024 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
17063 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
17103 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
17143 CCGGA
1 CCGGA
17148 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:27736 original size:22 final size:22
Alignment explanation
Indices: 27708--27751 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
27698 TTTTGAACCA
*
27708 TTACCATTTTGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
27730 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
27752 AATACCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.34, G:0.05, T:0.36
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:28740 original size:23 final size:22
Alignment explanation
Indices: 28688--28741 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
28678 TCCACGTCTT
*
28688 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
28710 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
28733 TTTCTTTTC
1 TTTCTTTTC
28742 ACTCTCAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 3 0.11
22 5 0.19
23 13 0.48
24 6 0.22
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:38103 original size:23 final size:23
Alignment explanation
Indices: 38072--38116 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
38062 TTTGGTATTT
*
38072 GGGAATTGGTACGAAATGGTAAG
1 GGGAATTGGTACAAAATGGTAAG
*
38095 GGGATTTGGTACAAAATGGTAA
1 GGGAATTGGTACAAAATGGTAA
38117 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.04, G:0.36, T:0.24
Consensus pattern (23 bp):
GGGAATTGGTACAAAATGGTAAG
Found at i:40165 original size:17 final size:17
Alignment explanation
Indices: 40136--40168 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40126 TGTAAAGTTT
40136 TATTTTTATTTTATTTA
1 TATTTTTATTTTATTTA
40153 TATTATTTA-TTTATTT
1 TATT-TTTATTTTATTT
40169 TTACTTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TATTTTTATTTTATTTA
Found at i:40180 original size:28 final size:27
Alignment explanation
Indices: 40134--40189 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
40124 GTTGTAAAGT
* *
40134 TTTATTTTTATTTTATTTATATTATTTA
1 TTTATTTTTATCTTATTTAAATT-TTTA
40162 TTTATTTTTA-CTTAGTTTAAATTTTTA
1 TTTATTTTTATCTTA-TTTAAATTTTTA
40189 T
1 T
40190 GTCAATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTATTTTTATCTTATTTAAATTTTTA
Done.