Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2481
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: 48173
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:4173 original size:79 final size:80
Alignment explanation
Indices: 4038--4257 Score: 238
Period size: 79 Copynumber: 2.8 Consensus size: 80
4028 CCGAATCACG
* * * * *
4038 TGCCTTCGGAACTTAA-CCGGATATAGCT-ACTCATTCA-AATGCCTTCGGGACATAGCCCGG-T
1 TGCCTTCGGATCTTAACCCGGATATAG-TAACTTA-GCACAATGCCTTCGGGACTTAGCCCGGAA
4099 TATAGTAACTCGCACAAA
64 T-TAGTAACTCGCACAAA
* *
4117 TGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCACCAATGCCTTCGGG-CTTAGCCCGGAA
1 TGCCTTC-GGATCTTAACCCGGATATAGTAACTTAGCA-CAATGCCTTCGGGACTTAGCCCGGAA
4179 TTAGTAACTCGCACAAA
64 TTAGTAACTCGCACAAA
** * * *
4196 TGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAATGCCTTCGGGACTTAGCCCGGA
4258 CATCATTCGA
Statistics
Matches: 119, Mismatches: 13, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
78 5 0.04
79 72 0.61
80 42 0.35
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
TGCCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAATGCCTTCGGGACTTAGCCCGGAATT
AGTAACTCGCACAAA
Found at i:4257 original size:40 final size:40
Alignment explanation
Indices: 4038--4257 Score: 236
Period size: 40 Copynumber: 5.5 Consensus size: 40
4028 CCGAATCACG
* * ***
4038 TGCCTTCGGAACTTA-ACCGGATATAGCT-ACTCATTCAAA
1 TGCCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAA
* *
4077 TGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA
* * *
4117 TGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA
4157 TGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAA
* * * *
4196 TGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA
1 TGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCACAAA
4237 -GCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGACTTAGCCCGGA
4258 CATCATTCGA
Statistics
Matches: 153, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 46 0.30
40 93 0.61
41 12 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA
Found at i:7018 original size:40 final size:40
Alignment explanation
Indices: 6981--7204 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
6971 GCTACTCGTT
* *
6981 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
7021 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
7061 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
7101 C-AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
7139 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
7180 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
7205 CATCATTCGA
Statistics
Matches: 165, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
38 25 0.15
39 21 0.13
40 106 0.64
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:7164 original size:118 final size:119
Alignment explanation
Indices: 6983--7204 Score: 299
Period size: 118 Copynumber: 1.9 Consensus size: 119
6973 TACTCGTTCA
*
6983 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
7048 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * **
7102 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
7164 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
7205 CATCATTCGA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
117 4 0.04
118 66 0.73
119 20 0.22
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:8397 original size:56 final size:56
Alignment explanation
Indices: 8330--8449 Score: 222
Period size: 56 Copynumber: 2.1 Consensus size: 56
8320 TATTAGTTTA
*
8330 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATTACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
8386 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
8442 TTGCCCAT
1 TTGCCCAT
8450 CATCCCTTGT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:14349 original size:79 final size:81
Alignment explanation
Indices: 14240--14422 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
14230 TACTCGTTCA
* *
14240 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
14303 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
14320 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
14383 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
14399 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
14423 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:14422 original size:40 final size:40
Alignment explanation
Indices: 14219--14422 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
14209 CGGAATTTAA
** *
14219 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
14259 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
14299 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
14338 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
14378 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
14418 CCGGA
1 CCGGA
14423 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:34582 original size:29 final size:30
Alignment explanation
Indices: 34525--34582 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
34515 CTTTTGAAAA
* * * *
34525 TATTTACAAAAAGAGGTATCTAATTTTTAT
1 TATTTACAAAAAGAGGCAACCAAGTTTTAT
34555 TATTTACAAAAAGA-GCAACCAAGTTTTA
1 TATTTACAAAAAGAGGCAACCAAGTTTTA
34583 AAATTAGTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (30 bp):
TATTTACAAAAAGAGGCAACCAAGTTTTAT
Found at i:38768 original size:103 final size:102
Alignment explanation
Indices: 38589--38956 Score: 587
Period size: 103 Copynumber: 3.6 Consensus size: 102
38579 TAGCCGTTAT
** *
38589 TGGTGGATCCCGCACTTAGCACCACCACTAAATCGGGGAATCAGCACTTAGCAACCCCTCAGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATAAATCGGGGAATCAGCACTTAGCAACCCCTC-GGGG
*
38654 AATCAGCACATAGCAACCCCCTTTTTATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
*
38692 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATAAATCGGGGAATCAGCACTTAGCAACCCCTC-GGGG
38757 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
38795 TGGTGGATATCGCACTTAGCA-CACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATATCGCACTTAGCACCACCAAT-AAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
*
38859 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATA
* * **
38898 TGGTGGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATAAATCGGGGAATCAGCACTTAGCAACCCCT
38957 TTTATATACA
Statistics
Matches: 249, Mismatches: 12, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
102 35 0.14
103 207 0.83
104 7 0.03
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.20
Consensus pattern (102 bp):
TGGTGGATATCGCACTTAGCACCACCAATAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
ATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
Found at i:38857 original size:26 final size:26
Alignment explanation
Indices: 38827--38878 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
38817 ACCAATGAAA
*
38827 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
38853 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
38879 CTTTCACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:46690 original size:100 final size:101
Alignment explanation
Indices: 46478--46834 Score: 400
Period size: 100 Copynumber: 3.6 Consensus size: 101
46468 TATATAAAAG
** *
46478 GGGTTGCTGTGTGCTGATTCTCCCGATTT-ATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 GGGTTGCTAAGTGCTGATTC-CCCGATTTCATTGGTGGTGCTA-GTGCGAT-ATCCACCATATCT
* *
46541 TTGAAATGTGGAAAGGGGGTTG-CTAT-TGCTGATTCCTCCGA
63 TTGAAA--TGAAAAGGGGGTTGTCT-TGTGCTGA-TCCCCCGA
46582 GGGTTGCTAAGTGCTGA-TCTCCCGATTTCATTGGTGGT-CTAGTGCGATATCCACC-TAATCTT
1 GGGTTGCTAAGTGCTGATTC-CCCGATTTCATTGGTGGTGCTAGTGCGATATCCACCAT-ATCTT
46644 TGAAATGAAAAGGGGGTTGTCTTGTGCTGATCCCCCGA
64 TGAAATGAAAAGGGGGTTGTCTTGTGCTGATCCCCCGA
* *
46682 GGGTTGCTAAGTTCTGATTCCCCGA-TTCA-TGCTGGTGCTAAGTGCGATATCCACCATATCTTT
1 GGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCT-AGTGCGATATCCACCATATCTTT
* * *
46745 GAAAT-AAAAAGGGG-T-TCATGTGCTGATCCCCTGA
65 GAAATGAAAAGGGGGTTGTCTTGTGCTGATCCCCCGA
* **
46779 GGGTTGCTAAGTGCTGATTCCCCGA-TT-AGTGGTGGTGCTAAGTGCGGGATCCACCA
1 GGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCT-AGTGCGATATCCACCA
46835 ATAACGGCTA
Statistics
Matches: 229, Mismatches: 14, Indels: 27
0.85 0.05 0.10
Matches are distributed among these distances:
96 1 0.00
97 67 0.29
98 7 0.03
99 14 0.06
100 68 0.30
101 12 0.05
102 22 0.10
103 15 0.07
104 23 0.10
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (101 bp):
GGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAGTGCGATATCCACCATATCTTTG
AAATGAAAAGGGGGTTGTCTTGTGCTGATCCCCCGA
Found at i:46805 original size:97 final size:99
Alignment explanation
Indices: 46478--46834 Score: 396
Period size: 97 Copynumber: 3.6 Consensus size: 99
46468 TATATAAAAG
** * *
46478 GGGTTGCTGTGTGCTGATTCTCCCGATTTA-TGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 GGGTTGCTAAGTGCTGATTCTCCCGATTCAGT-GGTGGTGCTAAGTGCGAT-ATCCACCATATCT
*
46541 TTGAAATGTGGAAAGGGGGTTGCTAT-TGCTGATTCCTCCGA
64 TTGAAA--TGAAAAGGGGGTT-C-ATGTGCTGA-TCC-CCGA
*
46582 GGGTTGCTAAGTGCTGA-TCTCCCGATTTCATTGGTGGT-CT-AGTGCGATATCCACC-TAATCT
1 GGGTTGCTAAGTGCTGATTCTCCCGA-TTCAGTGGTGGTGCTAAGTGCGATATCCACCAT-ATCT
*
46643 TTGAAATGAAAAGGGGGTTGTCTTGTGCTGATCCCCCGA
64 TTGAAATGAAAAGGGGG-T-TCATGTGCTGAT-CCCCGA
* *
46682 GGGTTGCTAAGTTCTGATTC-CCCGATTCA-TGCTGGTGCTAAGTGCGATATCCACCATATCTTT
1 GGGTTGCTAAGTGCTGATTCTCCCGATTCAGTGGTGGTGCTAAGTGCGATATCCACCATATCTTT
*
46745 GAAAT-AAAAAGGGGTTCATGTGCTGATCCCCTGA
66 GAAATGAAAAGGGGGTTCATGTGCTGATCCCC-GA
**
46779 GGGTTGCTAAGTGCTGATTC-CCCGATT-AGTGGTGGTGCTAAGTGCGGGATCCACCA
1 GGGTTGCTAAGTGCTGATTCTCCCGATTCAGTGGTGGTGCTAAGTGCGATATCCACCA
46835 ATAACGGCTA
Statistics
Matches: 225, Mismatches: 14, Indels: 35
0.82 0.05 0.13
Matches are distributed among these distances:
96 5 0.02
97 63 0.28
98 7 0.03
99 14 0.06
100 63 0.28
101 14 0.06
102 23 0.10
103 11 0.05
104 24 0.11
105 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (99 bp):
GGGTTGCTAAGTGCTGATTCTCCCGATTCAGTGGTGGTGCTAAGTGCGATATCCACCATATCTTT
GAAATGAAAAGGGGGTTCATGTGCTGATCCCCGA
Done.