Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007277.1 Kokia drynarioides strain JFW-HI SEQ_121893, whole genome shotgun sequence
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: 28549
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:6597 original size:29 final size:29
Alignment explanation
Indices: 6564--6621 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
6554 GAAAAGCTGG
6564 ATCAAAGTTAATAAAGCTTATAGGTTCTT
1 ATCAAAGTTAATAAAGCTTATAGGTTCTT
6593 ATCAAAGTTAATAAAGCTTATAGGTTCTT
1 ATCAAAGTTAATAAAGCTTATAGGTTCTT
6622 TCTTATTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (29 bp):
ATCAAAGTTAATAAAGCTTATAGGTTCTT
Found at i:11283 original size:39 final size:38
Alignment explanation
Indices: 11236--11311 Score: 98
Period size: 39 Copynumber: 2.0 Consensus size: 38
11226 TTTTATGATG
* * *
11236 TAAGCATGTCTATTGTTTTTGTTATTCTGATTACATGA
1 TAAGCATGTCTAGTGTTTTTGATATTCTGATCACATGA
* *
11274 TAAGTCATGTTTAGTGTTTTTGATATTTTGATCACATG
1 TAAG-CATGTCTAGTGTTTTTGATATTCTGATCACATG
11312 TTAAAAACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
38 4 0.12
39 28 0.88
ACGTcount: A:0.24, C:0.09, G:0.17, T:0.50
Consensus pattern (38 bp):
TAAGCATGTCTAGTGTTTTTGATATTCTGATCACATGA
Found at i:12437 original size:24 final size:25
Alignment explanation
Indices: 12404--12466 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
12394 GATGTTCAAC
12404 TTTTCACCTTTCATCACCCTTAACA
1 TTTTCACCTTTCATCACCCTTAACA
**
12429 TTTT-ACCTTTCATCTTCCTTAAC-
1 TTTTCACCTTTCATCACCCTTAACA
* *
12452 TCTTCACATTTCATC
1 TTTTCACCTTTCATC
12467 TCCTTGTAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 3 0.09
24 26 0.79
25 4 0.12
ACGTcount: A:0.21, C:0.33, G:0.00, T:0.46
Consensus pattern (25 bp):
TTTTCACCTTTCATCACCCTTAACA
Found at i:15849 original size:49 final size:50
Alignment explanation
Indices: 15796--15936 Score: 158
Period size: 50 Copynumber: 2.8 Consensus size: 50
15786 CTTCCCAAAT
* ** *
15796 AATATGTCACGTAGGTTTTTAAAATAACTCGCCA-TAAGGCTTTCTAGAA
1 AATATGTCACATAGGCCTTTAAAATAACTCGCCACAAAGGCTTTCTAGAA
* * *
15845 AATATGTCACATAGGCCTTTCAACTAACTCGCCACAAAGGCTTTCTAGAC
1 AATATGTCACATAGGCCTTTAAAATAACTCGCCACAAAGGCTTTCTAGAA
* * * * * *
15895 AATATGCCACATAAGCCTTTTAGATAACTTGTCACAAAGGCT
1 AATATGTCACATAGGCCTTTAAAATAACTCGCCACAAAGGCT
15937 CTGTTTGGTT
Statistics
Matches: 77, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
49 29 0.38
50 48 0.62
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (50 bp):
AATATGTCACATAGGCCTTTAAAATAACTCGCCACAAAGGCTTTCTAGAA
Found at i:15903 original size:25 final size:25
Alignment explanation
Indices: 15831--15936 Score: 69
Period size: 25 Copynumber: 4.2 Consensus size: 25
15821 AACTCGCCAT
* *
15831 AAGGCTTTCTAGA-AAATATGTCACA
1 AAGGCTTTCTAGACAACT-TGCCACA
* *
15856 TAGGCCTTTC-A-ACTAACTCGCCACA
1 AAGG-CTTTCTAGAC-AACTTGCCACA
15881 AAGGCTTTCTAGACAA-TATGCCACA
1 AAGGCTTTCTAGACAACT-TGCCACA
* * *
15906 TAAGCCTTT-TAGATAACTTGTCACA
1 -AAGGCTTTCTAGACAACTTGCCACA
15931 AAGGCT
1 AAGGCT
15937 CTGTTTGGTT
Statistics
Matches: 63, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
24 12 0.19
25 33 0.52
26 18 0.29
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (25 bp):
AAGGCTTTCTAGACAACTTGCCACA
Found at i:16511 original size:14 final size:14
Alignment explanation
Indices: 16492--16520 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
16482 TATAGAAAAA
16492 ACACACATACATAC
1 ACACACATACATAC
16506 ACACACATACATAC
1 ACACACATACATAC
16520 A
1 A
16521 TACAACTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.34, G:0.00, T:0.14
Consensus pattern (14 bp):
ACACACATACATAC
Found at i:22862 original size:21 final size:22
Alignment explanation
Indices: 22803--22862 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 22
22793 TCAACAAAAA
* *
22803 TTATAAAATAATTCAAATTAAT
1 TTATAAAAAAATTCAAAATAAT
* **
22825 TT-T-CAAAAATTTTAAAT-AT
1 TTATAAAAAAATTCAAAATAAT
22844 TTATAAAAAAATTCAAAAT
1 TTATAAAAAAATTCAAAAT
22863 TGATATTTTA
Statistics
Matches: 28, Mismatches: 8, Indels: 5
0.68 0.20 0.12
Matches are distributed among these distances:
19 4 0.14
20 10 0.36
21 12 0.43
22 2 0.07
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (22 bp):
TTATAAAAAAATTCAAAATAAT
Found at i:23505 original size:15 final size:15
Alignment explanation
Indices: 23487--23516 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
23477 TTTTCTTGTC
23487 AAGTATTTATTTCAG
1 AAGTATTTATTTCAG
23502 AAGTATTTATTTCAG
1 AAGTATTTATTTCAG
23517 GTTTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (15 bp):
AAGTATTTATTTCAG
Found at i:26416 original size:45 final size:45
Alignment explanation
Indices: 26343--26541 Score: 206
Period size: 45 Copynumber: 4.5 Consensus size: 45
26333 CCTGTATTAG
* * * * * *
26343 GGAAACATCTTGTTTCCTCTGTCCATATCCTGTTGCTAGCATCAA
1 GGAAACTTCTTGTTTCCTGTATCCATAGCCTGTTTCCAGCATCAA
* * * * *
26388 GGAAACTTCTTGTTTCCTATATCTATATCCTGTTT-GA-CACCAA
1 GGAAACTTCTTGTTTCCTGTATCCATAGCCTGTTTCCAGCATCAA
* * * *
26431 GGAAGCTCCTTGTTTCCTGTATCCATAGCATGTTTCCAGC-TCCAT
1 GGAAACTTCTTGTTTCCTGTATCCATAGCCTGTTTCCAGCAT-CAA
* * *
26476 GGAAACTTCTTGTTTCCTGTATCCATAGCCTGTTTCCGGCTTCAG
1 GGAAACTTCTTGTTTCCTGTATCCATAGCCTGTTTCCAGCATCAA
26521 GGAAACTTCTTGTTTCCTGTA
1 GGAAACTTCTTGTTTCCTGTA
26542 CATGTAGTTT
Statistics
Matches: 129, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
43 34 0.26
44 2 0.02
45 92 0.71
46 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.38
Consensus pattern (45 bp):
GGAAACTTCTTGTTTCCTGTATCCATAGCCTGTTTCCAGCATCAA
Done.