Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1180
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: 16056
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Found at i:1552 original size:39 final size:40
Alignment explanation
Indices: 1475--1621 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
1465 TTAGCTCTCG
* * *
1475 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
1515 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
1554 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
1594 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
1622 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:1632 original size:80 final size:80
Alignment explanation
Indices: 1521--1701 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
1511 CTCATTCAAT
* * *
1521 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
1584 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
1600 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
1664 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
1681 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
1702 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:1661 original size:40 final size:40
Alignment explanation
Indices: 1518--1701 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
1508 TAACTCATTC
* *
1518 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
1558 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
1598 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
1638 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
1679 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
1702 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:8758 original size:39 final size:40
Alignment explanation
Indices: 8681--8827 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
8671 TAGCTCCTCG
* * *
8681 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
8721 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
8760 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
8800 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
8828 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:8838 original size:80 final size:80
Alignment explanation
Indices: 8727--8907 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
8717 CTCATTCAAT
* * *
8727 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
8790 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
8806 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
8870 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
8887 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
8908 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:8867 original size:40 final size:40
Alignment explanation
Indices: 8724--8907 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
8714 TAACTCATTC
* *
8724 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
8764 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
8804 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
8844 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
8885 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
8908 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:13653 original size:104 final size:104
Alignment explanation
Indices: 13531--13754 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
13521 AATGGATATC
13531 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
13596 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
13635 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
13700 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
13739 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
13755 TTTATATACA
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:14116 original size:29 final size:29
Alignment explanation
Indices: 14083--14146 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
14073 TAATCCACCA
14083 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
14112 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
14142 CCCAA
1 CCCAA
14147 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:14120 original size:30 final size:30
Alignment explanation
Indices: 14090--14146 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
14080 CCACCCAACT
14090 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
14119 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
14147 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Done.