Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3033
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: 33721
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:3571 original size:15 final size:15
Alignment explanation
Indices: 3545--3600 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
3535 CAAGGAAACC
3545 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
*
3560 -AGATAGAGAAATCCA
1 GA-ATAAAGAAATCCA
3575 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
3590 GAATAAAGAAA
1 GAATAAAGAAA
3601 CCCAAGATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
14 1 0.03
15 35 0.95
16 1 0.03
ACGTcount: A:0.61, C:0.11, G:0.16, T:0.12
Consensus pattern (15 bp):
GAATAAAGAAATCCA
Found at i:6656 original size:46 final size:45
Alignment explanation
Indices: 6500--6667 Score: 142
Period size: 46 Copynumber: 3.6 Consensus size: 45
6490 GCCCATAAGC
* * * * *
6500 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCAT-AAT
* * * * * *
6546 GAACTCGGACTTAACTCAATGAGTTCGGATGCCTAGTTACAT-C-TCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCATAAT
*
6593 GAACTCAGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAAT
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCAT-AAT
* *
6639 AAACTCGGACTCAACTCAATGAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGTTCGGA
6668 TGCTCAACCA
Statistics
Matches: 94, Mismatches: 21, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 1 0.01
46 52 0.55
47 26 0.28
48 1 0.01
49 2 0.02
50 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAT
Found at i:6658 original size:93 final size:93
Alignment explanation
Indices: 6499--6670 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
6489 TGCCCATAAG
* * * * * * *
6499 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGGACTTAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATAAACTCGGACTCAACTCA
6564 ATGAGTTCGGATGCCTAGTTACATCTCA
66 ATGAGTTCGGATGCCTAGTTACATCTCA
* *
6592 CGAACTCAGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAATAAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATAAACTCGGACTCAACTCA
6657 ATGAGTTCGGATGC
66 ATGAGTTCGGATGC
6671 TCAACCATCC
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATAAACTCGGACTCAACTCA
ATGAGTTCGGATGCCTAGTTACATCTCA
Found at i:11768 original size:22 final size:21
Alignment explanation
Indices: 11743--11807 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 21
11733 GTCGAACCTT
11743 TTCTCTTTTTTTTCTTTTTTTA
1 TTCT-TTTTTTTTCTTTTTTTA
*
11765 TTCTTTATTTATTCTTTATTTTA
1 TTCTTT-TTTTTTCTTT-TTTTA
*
11788 TT-TTATTTTATTTATTTTTT
1 TTCTT-TTTT-TTTCTTTTTT
11808 AGGGCATTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 2 0.06
22 21 0.58
23 13 0.36
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (21 bp):
TTCTTTTTTTTTCTTTTTTTA
Found at i:12640 original size:3 final size:3
Alignment explanation
Indices: 12634--12674 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
12624 TATTATTATT
12634 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
12675 TCATTTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:12826 original size:20 final size:20
Alignment explanation
Indices: 12801--12839 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
12791 CTTGTTTTTT
12801 TTATTTATTTA-TCTTATTAA
1 TTATTT-TTTACTCTTATTAA
12821 TTATTTTTTACTCTTATTA
1 TTATTTTTTACTCTTATTA
12840 TTGTTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTTTACTCTTATTAA
Found at i:19747 original size:19 final size:19
Alignment explanation
Indices: 19723--19769 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
19713 AATGCCTCTT
*
19723 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTGCAT-CA
19742 TTTGCATTACATTGCATCA
1 TTTGCATTACATTGCATCA
*
19761 TATGCATTA
1 TTTGCATTA
19770 AACTTCACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTGCATCA
Found at i:24812 original size:39 final size:39
Alignment explanation
Indices: 24764--24926 Score: 100
Period size: 40 Copynumber: 4.1 Consensus size: 39
24754 CGGAATTTAA
* * *
24764 CCGGATATAGCT-CCTCGTTCAAGTGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCATTCAA-TGCCTTCGGGACATAAC
*
24804 CCGG-TATAGTAACTCATTCAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCATTCAATGCCTTCGGGACATAAC
* * *** *
24842 CCGGATTTTA-AAACTCGCACGAATGCCTTCGGGACTTAAC
1 CCGGA-TATAGTAACTCATTC-AATGCCTTCGGGACATAAC
* *** * *
24882 CCGGA-ATTAGTATCTCGCACAAAGGCCTTCGGGACTTAAC
1 CCGGATA-TAGTAACTCATTC-AATGCCTTCGGGACATAAC
24922 CCGGA
1 CCGGA
24927 ATTAATAACT
Statistics
Matches: 103, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
38 20 0.19
39 21 0.20
40 62 0.60
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
CCGGATATAGTAACTCATTCAATGCCTTCGGGACATAAC
Found at i:24925 original size:80 final size:80
Alignment explanation
Indices: 24826--25006 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
24816 CTCATTCAAT
* * *
24826 GCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-A
1 GCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA
*
24888 TTAGT-A-TCTCGCACAAA
64 -TAGTCACT-TAGCACAAA
**
24905 GGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATAT
1 -GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAACCCGGATAT
24970 AGTCACTTAGCACAAA
65 AGTCACTTAGCACAAA
*
24986 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
25007 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):
GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:24966 original size:40 final size:40
Alignment explanation
Indices: 24823--25006 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
24813 TAACTCATTC
* *
24823 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
24863 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
24903 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
24943 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
24984 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
25007 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
Done.