Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009834.1 Kokia drynarioides strain JFW-HI SEQ_124555, 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: 36299
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:4578 original size:12 final size:13
Alignment explanation
Indices: 4556--4581 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4546 CTATATTTTG
4556 AAAGAAAAAAAAA
1 AAAGAAAAAAAAA
4569 AAAGAAAAAAAAA
1 AAAGAAAAAAAAA
4582 GACCAATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAA
Found at i:8531 original size:4 final size:4
Alignment explanation
Indices: 8524--8552 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
8514 TCCCCCACAC
8524 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
8553 TAGTTGCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:13065 original size:38 final size:38
Alignment explanation
Indices: 13014--13127 Score: 165
Period size: 38 Copynumber: 3.0 Consensus size: 38
13004 CTGATGAATA
* *
13014 GCCAAGCAGTAACACATGGCATTCCACGTGTGTCACAT
1 GCCAAACAGTAACACATGGCATACCACGTGTGTCACAT
* * *
13052 GCCAAACAATAACACATGGCATACCACCTGTATCACAT
1 GCCAAACAGTAACACATGGCATACCACGTGTGTCACAT
* *
13090 GCCAGACAGTAACACATGGCATGCCACGTGTGTCACAT
1 GCCAAACAGTAACACATGGCATACCACGTGTGTCACAT
13128 TTTAACATAC
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 66 1.00
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.19
Consensus pattern (38 bp):
GCCAAACAGTAACACATGGCATACCACGTGTGTCACAT
Found at i:18058 original size:52 final size:52
Alignment explanation
Indices: 17979--18314 Score: 453
Period size: 52 Copynumber: 6.5 Consensus size: 52
17969 GAGAAAGCTT
* *
17979 CGATGACTATGTGTCATCGTGAATATATGAATCCTTTACGGATTAT-AGGGTC
1 CGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA-GGTC
* * *
18031 TGATGACTACATATCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC
1 CGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC
* *
18083 CGATGACTACTTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTC
1 CGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC
* * *
18135 TGATGACTACGTGTCATCATGAGTATATGAATCCTTTACAGATTATGAGGTC
1 CGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC
*
18187 CGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTT
1 CGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC
* * * * * ** * *
18239 CGGTGAC-ATGTGTCATCGTGAGTGTATGATTCTTTTACGGAACAAGAGGTT
1 CGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC
*
18290 C-ATGACTATGTGTCATCGTGAGTAT
1 CGATGACTACGTGTCATCGTGAGTAT
18315 TAAGTGTAAT
Statistics
Matches: 254, Mismatches: 28, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
50 4 0.02
51 55 0.22
52 194 0.76
53 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (52 bp):
CGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC
Found at i:19033 original size:21 final size:21
Alignment explanation
Indices: 18974--19026 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
18964 GTATGTGGAA
* *
18974 GTATCGGTAGATTGTGTACTT
1 GTATCGGTAGATTATGCACTT
*
18995 GTATTGGTAGATTATGCACTT
1 GTATCGGTAGATTATGCACTT
19016 GTATCGGTAGA
1 GTATCGGTAGA
19027 AGTTGCAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.23, C:0.09, G:0.28, T:0.40
Consensus pattern (21 bp):
GTATCGGTAGATTATGCACTT
Found at i:21472 original size:23 final size:23
Alignment explanation
Indices: 21446--21497 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
21436 AAAATTATAT
21446 TGTTGTTT-TGGTGCTTTTTTTAC
1 TGTT-TTTGTGGTGCTTTTTTTAC
* *
21469 TGTTTTTGTGTTGTTTTTTTTAC
1 TGTTTTTGTGGTGCTTTTTTTAC
21492 TGTTTT
1 TGTTTT
21498 GATGTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.04, C:0.06, G:0.19, T:0.71
Consensus pattern (23 bp):
TGTTTTTGTGGTGCTTTTTTTAC
Found at i:21507 original size:19 final size:19
Alignment explanation
Indices: 21449--21541 Score: 96
Period size: 19 Copynumber: 4.6 Consensus size: 19
21439 ATTATATTGT
*
21449 TGTTTTGGTGCTTTTTTTAC
1 TGTTTTGATG-TTTTTTTAC
*
21469 TGTTTTTGTGTTGTTTTTTTTAC
1 TG--TTT-TGATG-TTTTTTTAC
*
21492 TGTTTTGATGTTTTTTTAT
1 TGTTTTGATGTTTTTTTAC
* *
21511 TGTTTTGCTATTTTTTTAC
1 TGTTTTGATGTTTTTTTAC
21530 TGTTTTGATGTT
1 TGTTTTGATGTT
21542 GTTATTTTTG
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
19 34 0.56
20 6 0.10
21 3 0.05
22 3 0.05
23 15 0.25
ACGTcount: A:0.08, C:0.05, G:0.17, T:0.70
Consensus pattern (19 bp):
TGTTTTGATGTTTTTTTAC
Found at i:21565 original size:24 final size:24
Alignment explanation
Indices: 21519--21613 Score: 83
Period size: 24 Copynumber: 4.0 Consensus size: 24
21509 ATTGTTTTGC
21519 TATTTTT-TTACTGTTTTGATGTTGT
1 TATTTTTGTTACTGTTTT--TGTTGT
**
21544 TATTTTTGTTACTGTTTTTGTTAC
1 TATTTTTGTTACTGTTTTTGTTGT
* **
21568 TATTTTTGCTGTTGTTTTTGTT-T
1 TATTTTTGTTACTGTTTTTGTTGT
21591 CTATTTTTG-T--TGTTTTTGTTGT
1 -TATTTTTGTTACTGTTTTTGTTGT
21613 T
1 T
21614 GTTGTGCTGT
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
21 11 0.18
22 1 0.02
23 1 0.02
24 31 0.51
25 7 0.11
26 10 0.16
ACGTcount: A:0.08, C:0.05, G:0.16, T:0.71
Consensus pattern (24 bp):
TATTTTTGTTACTGTTTTTGTTGT
Found at i:21568 original size:38 final size:36
Alignment explanation
Indices: 21471--21601 Score: 115
Period size: 38 Copynumber: 3.5 Consensus size: 36
21461 TTTTTTACTG
*
21471 TTTTTGTGT-TGTTTTTTTTACTGTTTTGATGTT-TT
1 TTTTTGT-TCTGTTTTTGTTACTGTTTTGATGTTGTT
* *
21506 TTTATTGTTTTGCTATTTTTTTACTGTTTTGATGTTGTT
1 TTT-TTGTTCTG-T-TTTTGTTACTGTTTTGATGTTGTT
* *
21545 ATTTTTGTTACTGTTTTTGTTACTATTTTTGCTGTTGTT
1 -TTTTTGTT-CTGTTTTTGTTACT-GTTTTGATGTTGTT
* *
21584 TTTGT-TTCTATTTTTGTT
1 TTTTTGTTCTGTTTTTGTT
21602 GTTTTTGTTG
Statistics
Matches: 82, Mismatches: 6, Indels: 15
0.80 0.06 0.15
Matches are distributed among these distances:
35 4 0.05
36 16 0.20
37 3 0.04
38 34 0.41
39 20 0.24
40 5 0.06
ACGTcount: A:0.08, C:0.05, G:0.15, T:0.71
Consensus pattern (36 bp):
TTTTTGTTCTGTTTTTGTTACTGTTTTGATGTTGTT
Found at i:21612 original size:12 final size:12
Alignment explanation
Indices: 21538--21616 Score: 63
Period size: 12 Copynumber: 6.6 Consensus size: 12
21528 ACTGTTTTGA
21538 TGTTGTTATTTT
1 TGTTGTTATTTT
** *
21550 TGTTACTGTTTT
1 TGTTGTTATTTT
**
21562 TGTTACTATTTT
1 TGTTGTTATTTT
* *
21574 TGCTGTTGTTTT
1 TGTTGTTATTTT
21586 TGTT-TCTATTTT
1 TGTTGT-TATTTT
21598 TGTTGTT-TTTGT
1 TGTTGTTATTT-T
21610 TGTTGTT
1 TGTTGTT
21617 GTGCTGTTAT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
11 4 0.07
12 49 0.91
13 1 0.02
ACGTcount: A:0.06, C:0.05, G:0.18, T:0.71
Consensus pattern (12 bp):
TGTTGTTATTTT
Found at i:21617 original size:36 final size:37
Alignment explanation
Indices: 21518--21618 Score: 109
Period size: 36 Copynumber: 2.8 Consensus size: 37
21508 TATTGTTTTG
* *
21518 CTATTTTT-TTACTGTTTTGATGTTGTTATTTTTGTTA
1 CTATTTTTGTTACT-TTTTGTTGTTGTTGTTTTTGTTA
* * * *
21555 CTGTTTTTGTTACTATTT-TTGCTGTTGTTTTTGTTT
1 CTATTTTTGTTACTTTTTGTTGTTGTTGTTTTTGTTA
*
21591 CTATTTTTGTT-GTTTTTGTTGTTGTTGT
1 CTATTTTTGTTACTTTTTGTTGTTGTTGT
21619 GCTGTTATTT
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
35 4 0.08
36 33 0.63
37 10 0.19
38 5 0.10
ACGTcount: A:0.08, C:0.06, G:0.17, T:0.69
Consensus pattern (37 bp):
CTATTTTTGTTACTTTTTGTTGTTGTTGTTTTTGTTA
Found at i:21953 original size:20 final size:20
Alignment explanation
Indices: 21928--21981 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
21918 CTCCAGTGAG
** *
21928 ACTTCTACCGGTAGAACTCC
1 ACTTCTACCAATACAACTCC
*
21948 ACTTCTACCAATACAACTCT
1 ACTTCTACCAATACAACTCC
21968 ACTTCTACCAATAC
1 ACTTCTACCAATAC
21982 CTTGAAGACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.35, G:0.06, T:0.28
Consensus pattern (20 bp):
ACTTCTACCAATACAACTCC
Found at i:24954 original size:14 final size:14
Alignment explanation
Indices: 24935--24963 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
24925 TATATAAAAA
24935 AGGGGGAGATTGTT
1 AGGGGGAGATTGTT
24949 AGGGGGAGATTGTT
1 AGGGGGAGATTGTT
24963 A
1 A
24964 AACTAAGCCT
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:0.24, C:0.00, G:0.48, T:0.28
Consensus pattern (14 bp):
AGGGGGAGATTGTT
Found at i:25102 original size:20 final size:20
Alignment explanation
Indices: 25063--25102 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
25053 CTACCGGTAG
**
25063 AACTCCACTTTTACTGATAC
1 AACTCCACTTTTACCAATAC
*
25083 AACTCTACTTTTACCAATAC
1 AACTCCACTTTTACCAATAC
25103 CTTGAAGACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.35
Consensus pattern (20 bp):
AACTCCACTTTTACCAATAC
Found at i:30738 original size:52 final size:52
Alignment explanation
Indices: 30629--30866 Score: 284
Period size: 52 Copynumber: 4.6 Consensus size: 52
30619 TAAATGTAAA
* * * *
30629 AGGTTCGATGACTCTGTGTCATCATGAGTTATATGAATCCTTTA-AGGATTATA
1 AGGTCCGATGACTATGTGTCATCGTGAG-TATATGAATCCTTTACA-GATTATG
* **
30682 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
* * * *
30734 AGGTCCGATGACTATGTGCCATCATGAGTATATGAATCTTTTACAGATTACG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
* * * *
30786 AGGTTCGATGAC--TGTTTCATCGTGATTATATGAATCTTTTACAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
* *
30836 AGGTCCAATGACCATGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
30867 TAAATGAGAA
Statistics
Matches: 159, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
50 43 0.27
52 92 0.58
53 24 0.15
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
Found at i:30833 original size:102 final size:103
Alignment explanation
Indices: 30629--30866 Score: 293
Period size: 102 Copynumber: 2.3 Consensus size: 103
30619 TAAATGTAAA
* * *
30629 AGGTTCGATGACTCTGTGTCATCATGAGTTATATGAATCCTTTAAGGATTATAAGGTCTGATGAC
1 AGGTCCGATGACTATGTGTCATCATGAG-TATATGAATCCTTTAAGGATTACAAGGTCTGATGAC
**
30694 TATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
65 -ATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
* * *
30734 AGGTCCGATGACTATGTGCCATCATGAGTATATGAATCTTTTACA-GATTACGAGGT-TCGATGA
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTA-AGGATTACAAGGTCT-GATGA
* * *
30797 C-TGTTTCATCGTGATTATATGAATCTTTTACAGATTATG
64 CATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
* * *
30836 AGGTCCAATGACCATGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCATGAGTAT
30867 TAAATGAGAA
Statistics
Matches: 116, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
102 60 0.52
103 1 0.01
104 29 0.25
105 26 0.22
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (103 bp):
AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTAAGGATTACAAGGTCTGATGACA
TGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
Found at i:31635 original size:21 final size:21
Alignment explanation
Indices: 31609--31656 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
31599 TTTAGTACCG
*
31609 GTAGAAACATGATTTGTTTCA
1 GTAGAAACATGATTTGTATCA
* * *
31630 GTAGAAGCTTTATTTGTATCA
1 GTAGAAACATGATTTGTATCA
31651 GTAGAA
1 GTAGAA
31657 CTGTCATAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (21 bp):
GTAGAAACATGATTTGTATCA
Done.