Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014570.1 Kokia drynarioides strain JFW-HI SEQ_129609, 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: 57745
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:2404 original size:3 final size:3
Alignment explanation
Indices: 2390--2425 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
2380 TCTGTAGACT
*
2390 TTG TTT TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
2426 CAGTTGTGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:3163 original size:2 final size:2
Alignment explanation
Indices: 3158--3195 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
3148 ACACACACAC
3158 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3196 CAAGAATAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:21564 original size:19 final size:20
Alignment explanation
Indices: 21542--21585 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
21532 TATTAAAAAC
*
21542 ATTTTCATGAA-AATTTGAA
1 ATTTTCATAAATAATTTGAA
*
21561 ATTTTTATAAATAATTTGAA
1 ATTTTCATAAATAATTTGAA
21581 ATTTT
1 ATTTT
21586 GAAAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (20 bp):
ATTTTCATAAATAATTTGAA
Found at i:21592 original size:20 final size:20
Alignment explanation
Indices: 21553--21593 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
21543 TTTTCATGAA
* *
21553 AATTTGAAATTTTTATAAAT
1 AATTTGAAATTTTGAAAAAT
21573 AATTTGAAATTTTGAAAAAT
1 AATTTGAAATTTTGAAAAAT
21593 A
1 A
21594 TTTTAATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (20 bp):
AATTTGAAATTTTGAAAAAT
Found at i:23523 original size:11 final size:11
Alignment explanation
Indices: 23509--23586 Score: 51
Period size: 11 Copynumber: 7.5 Consensus size: 11
23499 GTTGTTTTGG
23509 TGTTTTTTTAC
1 TGTTTTTTTAC
* *
23520 TGTTTTGATTGC
1 TGTTTT-TTTAC
*
23532 TATTTTTTT-C
1 TGTTTTTTTAC
*
23542 TG--TTTTT-G
1 TGTTTTTTTAC
23550 TGTTTTTTTAC
1 TGTTTTTTTAC
**
23561 TGTTTTGGTAC
1 TGTTTTTTTAC
23572 T-TTTTTTTA-
1 TGTTTTTTTAC
23581 TGTTTT
1 TGTTTT
23587 GATTATTGTT
Statistics
Matches: 51, Mismatches: 11, Indels: 11
0.70 0.15 0.15
Matches are distributed among these distances:
8 7 0.14
9 1 0.02
10 17 0.33
11 18 0.35
12 8 0.16
ACGTcount: A:0.08, C:0.06, G:0.14, T:0.72
Consensus pattern (11 bp):
TGTTTTTTTAC
Found at i:23525 original size:19 final size:19
Alignment explanation
Indices: 23501--23587 Score: 86
Period size: 19 Copynumber: 4.4 Consensus size: 19
23491 TTTATATTGT
23501 TGTTTTGGTGTTTTTTTAC
1 TGTTTTGGTGTTTTTTTAC
* *
23520 TGTTTTGATTGCTATTTTTTTC
1 TGTTTTG-GTG-T-TTTTTTAC
*
23542 TGTTTTTGTGTTTTTTTAC
1 TGTTTTGGTGTTTTTTTAC
*
23561 TGTTTTGGTACTTTTTTTTA-
1 TGTTTTGGT--GTTTTTTTAC
23581 TGTTTTG
1 TGTTTTG
23588 ATTATTGTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
19 22 0.39
20 10 0.18
21 11 0.20
22 13 0.23
ACGTcount: A:0.07, C:0.06, G:0.17, T:0.70
Consensus pattern (19 bp):
TGTTTTGGTGTTTTTTTAC
Found at i:23579 original size:41 final size:41
Alignment explanation
Indices: 23501--23587 Score: 124
Period size: 41 Copynumber: 2.2 Consensus size: 41
23491 TTTATATTGT
* *
23501 TGTTTTGGTGTTTTTTTACTGTTTTGATTGCTATTTTTTTC
1 TGTTTTGGTGTTTTTTTACTGTTTTGAGTACTATTTTTTTC
* *
23542 TGTTTTTGTGTTTTTTTACTGTTTTG-GTACT-TTTTTTTA
1 TGTTTTGGTGTTTTTTTACTGTTTTGAGTACTATTTTTTTC
23581 TGTTTTG
1 TGTTTTG
23588 ATTATTGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
39 13 0.32
40 3 0.07
41 25 0.61
ACGTcount: A:0.07, C:0.06, G:0.17, T:0.70
Consensus pattern (41 bp):
TGTTTTGGTGTTTTTTTACTGTTTTGAGTACTATTTTTTTC
Found at i:23640 original size:21 final size:21
Alignment explanation
Indices: 23589--23654 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
23579 TATGTTTTGA
*
23589 TTATTGTTTTCGTGTTGTTATTG
1 TTATTGTTTT--TGTTGTTATTT
**
23612 TTGCTGTTTTTGTTGTTATTT
1 TTATTGTTTTTGTTGTTATTT
**
23633 TTATTGTTTTTAATGTTATTT
1 TTATTGTTTTTGTTGTTATTT
23654 T
1 T
23655 ACTGTTATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 28 0.78
23 8 0.22
ACGTcount: A:0.11, C:0.03, G:0.17, T:0.70
Consensus pattern (21 bp):
TTATTGTTTTTGTTGTTATTT
Found at i:23641 original size:56 final size:56
Alignment explanation
Indices: 23575--23697 Score: 135
Period size: 56 Copynumber: 2.2 Consensus size: 56
23565 TTGGTACTTT
* * * *
23575 TTTTTA-TGTTTTGATTATTGTTTT-CGTGTTGTTATTGTTGCTGTTTTTG-TTGTTA
1 TTTTTATTGTTTTGAATATTATTTTAC-TGTTATTATTGCTGCTG-TTTTGATTGTTA
* * *
23630 TTTTTATTGTTTTTAATGTTATTTTACTGTTATTTTTGCTGCTGTTTTGATTGTTA
1 TTTTTATTGTTTTGAATATTATTTTACTGTTATTATTGCTGCTGTTTTGATTGTTA
*
23686 TTTTTGTTGTTT
1 TTTTTATTGTTT
23698 GGATGTTATT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
55 11 0.19
56 45 0.79
57 1 0.02
ACGTcount: A:0.11, C:0.04, G:0.17, T:0.68
Consensus pattern (56 bp):
TTTTTATTGTTTTGAATATTATTTTACTGTTATTATTGCTGCTGTTTTGATTGTTA
Found at i:23704 original size:20 final size:23
Alignment explanation
Indices: 23657--23710 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
23647 GTTATTTTAC
*
23657 TGTTATTTTTGCTGCTGTTTTGAT
1 TGTTATTTTTGCT-CTGTTTGGAT
23681 TGTTATTTTTG-T-TGTTTGGA-
1 TGTTATTTTTGCTCTGTTTGGAT
23701 TGTTATTTTT
1 TGTTATTTTT
23711 TATGCGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 10 0.34
21 7 0.24
23 1 0.03
24 11 0.38
ACGTcount: A:0.09, C:0.04, G:0.20, T:0.67
Consensus pattern (23 bp):
TGTTATTTTTGCTCTGTTTGGAT
Found at i:23710 original size:21 final size:22
Alignment explanation
Indices: 23657--23711 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
23647 GTTATTTTAC
*
23657 TGTTATTTTTGCTGCTGTTTTGAT
1 TGTTATTTTT--TGCTGTTTGGAT
*
23681 TGTTA-TTTTTGTTGTTTGGA-
1 TGTTATTTTTTGCTGTTTGGAT
23701 TGTTATTTTTT
1 TGTTATTTTTT
23712 ATGCGTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 5 0.18
21 14 0.50
23 4 0.14
24 5 0.18
ACGTcount: A:0.09, C:0.04, G:0.20, T:0.67
Consensus pattern (22 bp):
TGTTATTTTTTGCTGTTTGGAT
Found at i:37650 original size:162 final size:163
Alignment explanation
Indices: 37383--37686 Score: 538
Period size: 162 Copynumber: 1.9 Consensus size: 163
37373 AGTGTCAAAA
*
37383 TAATGGATTATGAAAATAAATTAACAGATAATGTGGTGTGGCAGTAATTCGCATAGATAGCACAA
1 TAATGGATTATGAAAATAAATTAACAGATAATGTGGTGTGGCAGTAATTAGCATAGATAGCACAA
* * *
37448 ACACATGTTGGAATACAATAATGTTTACAAACTTCCCCTGTTACCCCAAAA-TTTGATATGTACT
66 ACACATGATGGAATACAATAATGTTTACAAACCTCCCCTGTTACCCCAAAATTTTAATATGTACT
37512 TATTCTCATGATGTTGGTGGGTACTTATTGATT
131 TATTCTCATGATGTTGGTGGGTACTTATTGATT
* *
37545 TAATGGATTATGAAAATGAATTAACAGATAATGTGGTGTGGCAGTAATTAGCATAGATAGTACAA
1 TAATGGATTATGAAAATAAATTAACAGATAATGTGGTGTGGCAGTAATTAGCATAGATAGCACAA
*
37610 ACACATGATGGAATACAATGATGTTTACAAACCTCCCCTGTTACCCCAAAATTTTAATATGTACT
66 ACACATGATGGAATACAATAATGTTTACAAACCTCCCCTGTTACCCCAAAATTTTAATATGTACT
37675 TATTCTCATGAT
131 TATTCTCATGAT
37687 TGACACTATA
Statistics
Matches: 134, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
162 110 0.82
163 24 0.18
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (163 bp):
TAATGGATTATGAAAATAAATTAACAGATAATGTGGTGTGGCAGTAATTAGCATAGATAGCACAA
ACACATGATGGAATACAATAATGTTTACAAACCTCCCCTGTTACCCCAAAATTTTAATATGTACT
TATTCTCATGATGTTGGTGGGTACTTATTGATT
Found at i:47810 original size:5 final size:5
Alignment explanation
Indices: 47802--47826 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
47792 AAAATTTTAA
47802 ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT
47827 TTTTTATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:56177 original size:21 final size:21
Alignment explanation
Indices: 56148--56188 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
56138 TGTAATTTAG
*
56148 ATTTATAAACTTTATGTTTGA
1 ATTTATAAACTTTATATTTGA
* *
56169 ATTTCTAAATTTTATATTTG
1 ATTTATAAACTTTATATTTG
56189 GATTATGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (21 bp):
ATTTATAAACTTTATATTTGA
Done.