Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2425
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: 36787
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:1825 original size:22 final size:26
Alignment explanation
Indices: 1781--1831 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
1771 AAATTGATTC
1781 ATAAATGTATTAAAATGTTGGTG-GAA
1 ATAAATGTATTAAAATG-TGGTGAGAA
1807 ATAAATG-ATT-AAATG-GGTGAGAA
1 ATAAATGTATTAAAATGTGGTGAGAA
1830 AT
1 AT
1832 TTGGCTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.17
23 5 0.21
24 5 0.21
25 3 0.12
26 7 0.29
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.31
Consensus pattern (26 bp):
ATAAATGTATTAAAATGTGGTGAGAA
Found at i:4721 original size:79 final size:82
Alignment explanation
Indices: 4610--4794 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
4600 GCTACTCGTT
* * *
4610 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
4673 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
4690 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
4753 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
4770 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
4795 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:4794 original size:40 final size:40
Alignment explanation
Indices: 4591--4794 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
4581 CGGAATTTAA
** *
4591 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
4631 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
4671 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
4710 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
4750 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
4790 CCGGA
1 CCGGA
4795 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:12628 original size:79 final size:82
Alignment explanation
Indices: 12517--12701 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
12507 GCTACTCGTT
* * *
12517 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
12580 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
12597 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
12660 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
12677 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
12702 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:12701 original size:40 final size:40
Alignment explanation
Indices: 12498--12701 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
12488 CGGAATTTAA
** *
12498 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
12538 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
12578 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
12617 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
12657 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
12697 CCGGA
1 CCGGA
12702 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:22462 original size:19 final size:18
Alignment explanation
Indices: 22426--22465 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
22416 TTTCCACTCG
*
22426 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
22444 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
22463 TTT
1 TTT
22466 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:23538 original size:15 final size:14
Alignment explanation
Indices: 23518--23573 Score: 85
Period size: 14 Copynumber: 3.9 Consensus size: 14
23508 AGCTTCTTCT
23518 TTTTTTTTCACGAAA
1 TTTTTTTTCAC-AAA
23533 TTTTTTTTCACAAA
1 TTTTTTTTCACAAA
**
23547 TTTTTTTTTTCAAA
1 TTTTTTTTCACAAA
23561 TTTTTTTTCACAA
1 TTTTTTTTCACAA
23574 CTTGATATCC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
14 26 0.70
15 11 0.30
ACGTcount: A:0.25, C:0.12, G:0.02, T:0.61
Consensus pattern (14 bp):
TTTTTTTTCACAAA
Found at i:23627 original size:11 final size:11
Alignment explanation
Indices: 23611--23652 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
23601 TGGAAACTAG
23611 TTTTTTTTGAA
1 TTTTTTTTGAA
23622 TTTTTTTT-AA
1 TTTTTTTTGAA
*
23632 TTTTGTTTTCGAG
1 TTTT-TTTT-GAA
23645 TTTTTTTT
1 TTTTTTTT
23653 CGAGAAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 6 0.22
11 12 0.44
12 4 0.15
13 5 0.19
ACGTcount: A:0.12, C:0.02, G:0.10, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:26747 original size:19 final size:18
Alignment explanation
Indices: 26711--26750 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
26701 TTTCCACTCG
*
26711 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
26729 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
26748 TTT
1 TTT
26751 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:26856 original size:17 final size:18
Alignment explanation
Indices: 26834--26869 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
26824 TTTCTTTCTC
26834 CAATTTTT-TCTCTTTTT
1 CAATTTTTGTCTCTTTTT
*
26851 CAATTTTTGTTTCTTTTT
1 CAATTTTTGTCTCTTTTT
26869 C
1 C
26870 GGTTTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.11, C:0.17, G:0.03, T:0.69
Consensus pattern (18 bp):
CAATTTTTGTCTCTTTTT
Found at i:27818 original size:13 final size:12
Alignment explanation
Indices: 27801--27848 Score: 80
Period size: 12 Copynumber: 4.0 Consensus size: 12
27791 ACTAGCTTCT
27801 TTTTTTTCACAA
1 TTTTTTTCACAA
27813 TTTTTTTCACAA
1 TTTTTTTCACAA
27825 TTTTTTTTCA-AA
1 -TTTTTTTCACAA
27837 TTTTTTTCACAA
1 TTTTTTTCACAA
27849 CTTGATATCC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 9 0.26
12 16 0.47
13 9 0.26
ACGTcount: A:0.25, C:0.15, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTTTTCACAA
Found at i:27838 original size:24 final size:25
Alignment explanation
Indices: 27800--27848 Score: 91
Period size: 24 Copynumber: 2.0 Consensus size: 25
27790 AACTAGCTTC
27800 TTTTTTTTCACAATTTTTTTCACAA
1 TTTTTTTTCACAATTTTTTTCACAA
27825 TTTTTTTTCA-AATTTTTTTCACAA
1 TTTTTTTTCACAATTTTTTTCACAA
27849 CTTGATATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTTTTTTCACAATTTTTTTCACAA
Found at i:27909 original size:18 final size:18
Alignment explanation
Indices: 27886--27921 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
27876 TGGAAACTAG
27886 TTTTTTTGAATTTTTTTT
1 TTTTTTTGAATTTTTTTT
*
27904 TTTTTTTGAGTTTTTTTT
1 TTTTTTTGAATTTTTTTT
27922 CGAGAAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.83
Consensus pattern (18 bp):
TTTTTTTGAATTTTTTTT
Found at i:29829 original size:28 final size:30
Alignment explanation
Indices: 29785--29843 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
29775 AGAGATTGAG
* *
29785 AGTGAAAGGAATGTGAA-ACAGAA-AGAAA
1 AGTGAAAAGAATGTGAAGAAAGAAGAGAAA
29813 AGTGAAAAAGAAT-TGAAGAAAGAAGAGAAA
1 AGTG-AAAAGAATGTGAAGAAAGAAGAGAAA
29843 A
1 A
29844 TAGTTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 8 0.31
29 12 0.46
30 6 0.23
ACGTcount: A:0.61, C:0.02, G:0.27, T:0.10
Consensus pattern (30 bp):
AGTGAAAAGAATGTGAAGAAAGAAGAGAAA
Done.