Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005753.1 Kokia drynarioides strain JFW-HI SEQ_120007, 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: 54873
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:2683 original size:20 final size:20
Alignment explanation
Indices: 2658--2701 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2648 AAGTATTCAG
*
2658 GTGCCGATGTATCAGGCTTT
1 GTGCCGATGTAACAGGCTTT
*
2678 GTGCCGGTGTAACAGGCTTT
1 GTGCCGATGTAACAGGCTTT
2698 GTGC
1 GTGC
2702 AGGATATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.20, G:0.34, T:0.32
Consensus pattern (20 bp):
GTGCCGATGTAACAGGCTTT
Found at i:3610 original size:21 final size:20
Alignment explanation
Indices: 3580--3628 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
3570 AAAAATTTCG
* *
3580 AATCAAGTCGAGTAAAATGA
1 AATCGAGTCGAGTAAAATCA
*
3600 AATTCGAGTCGAGTCAAATCA
1 AA-TCGAGTCGAGTAAAATCA
3621 AATCGAGT
1 AATCGAGT
3629 TAAATTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.22
Consensus pattern (20 bp):
AATCGAGTCGAGTAAAATCA
Found at i:3861 original size:19 final size:20
Alignment explanation
Indices: 3832--3869 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3822 ATATTAACTC
*
3832 TTTATATATTTTTTAAAATT
1 TTTATATATTTTTAAAAATT
3852 TTTATA-ATTTTTAAAAAT
1 TTTATATATTTTTAAAAAT
3870 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTATATATTTTTAAAAATT
Found at i:11021 original size:16 final size:17
Alignment explanation
Indices: 11000--11033 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
10990 TTAAATTAAC
11000 TAAATTA-TTTCTCAAT
1 TAAATTATTTTCTCAAT
11016 TAAATTATTTTCTCAAT
1 TAAATTATTTTCTCAAT
11033 T
1 T
11034 CAATCTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAATTATTTTCTCAAT
Found at i:11633 original size:19 final size:19
Alignment explanation
Indices: 11611--11655 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
11601 TTATATTAGG
11611 ATTTAATATTTAAGATGT-T
1 ATTTAATATTTAA-ATGTGT
* *
11630 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATGTGT
11649 ATTTAAT
1 ATTTAAT
11656 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATGTGT
Found at i:12475 original size:15 final size:16
Alignment explanation
Indices: 12455--12484 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12445 CTTCCCTATT
12455 TTCTATTTA-TTTTAA
1 TTCTATTTACTTTTAA
12470 TTCTATTTACTTTTA
1 TTCTATTTACTTTTA
12485 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (16 bp):
TTCTATTTACTTTTAA
Found at i:12510 original size:21 final size:22
Alignment explanation
Indices: 12450--12510 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
12440 TCTGACTTCC
*
12450 CTATTTTCTATTTA-TTTTAATT
1 CTATTTACT-TTTATTTTTAATT
12472 CTATTTACTTTTATTTTTAATT
1 CTATTTACTTTTATTTTTAATT
12494 CTATTTA-TTTTATTTTT
1 CTATTTACTTTTATTTTT
12511 CCTTAGATCG
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
21 14 0.38
22 23 0.62
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.70
Consensus pattern (22 bp):
CTATTTACTTTTATTTTTAATT
Found at i:20711 original size:83 final size:83
Alignment explanation
Indices: 20609--20766 Score: 255
Period size: 83 Copynumber: 1.9 Consensus size: 83
20599 TATACTTCGA
* *
20609 ATGCAAATCGAGATATATGAGTTCATACAGCATGTTTATCAGAAAAAGTTAATGAATTGAAATAC
1 ATGCAAATCGAGATATATGAGTTCATACAGCATGTTTATCAGAAAAACTTAATGAACTGAAATAC
20674 TAAAATACTACAAAAGAT
66 TAAAATACTACAAAAGAT
* *
20692 ATGCAAATCGAGA-AGTATGAGTTCATACAGCATGTTTATCTGAAAAACTTAATGAACTGATATA
1 ATGCAAATCGAGATA-TATGAGTTCATACAGCATGTTTATCAGAAAAACTTAATGAACTGAAATA
*
20756 CTGAAATACTA
65 CTAAAATACTA
20767 AAGTACTACA
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
82 1 0.01
83 68 0.99
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.28
Consensus pattern (83 bp):
ATGCAAATCGAGATATATGAGTTCATACAGCATGTTTATCAGAAAAACTTAATGAACTGAAATAC
TAAAATACTACAAAAGAT
Found at i:22713 original size:9 final size:8
Alignment explanation
Indices: 22670--22711 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
22660 AATAGTAAAA
22670 TTATATTT
1 TTATATTT
22678 TTATTATTT
1 TTA-TATTT
* *
22687 TAATA-GT
1 TTATATTT
22694 TTATATTT
1 TTATATTT
22702 TTATATTT
1 TTATATTT
22710 TT
1 TT
22712 TAAAGGATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 5 0.18
8 16 0.57
9 7 0.25
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (8 bp):
TTATATTT
Found at i:25092 original size:12 final size:12
Alignment explanation
Indices: 25075--25109 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
25065 AAAGTTCAAA
25075 GAGAGAGAGAGG
1 GAGAGAGAGAGG
*
25087 GAGAGAGGGAGG
1 GAGAGAGAGAGG
*
25099 GAGAGAAAGAG
1 GAGAGAGAGAG
25110 ATTATCAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (12 bp):
GAGAGAGAGAGG
Found at i:29167 original size:21 final size:22
Alignment explanation
Indices: 29141--29191 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
29131 TAAAAAGTGT
29141 ATAAAATTAT-TAAATATTAAA
1 ATAAAATTATATAAATATTAAA
* *
29162 ATAAAATAATATAAATATTTAA
1 ATAAAATTATATAAATATTAAA
29184 A-AAAATTA
1 ATAAAATTA
29192 AAAATAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
ATAAAATTATATAAATATTAAA
Found at i:34703 original size:17 final size:17
Alignment explanation
Indices: 34681--34719 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
34671 AATAAATCCT
* *
34681 AATAATAATTCATAATG
1 AATAATAAATCAAAATG
*
34698 AATAATAAATGAAAATG
1 AATAATAAATCAAAATG
34715 AATAA
1 AATAA
34720 ATAGAAGGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.28
Consensus pattern (17 bp):
AATAATAAATCAAAATG
Found at i:35822 original size:27 final size:27
Alignment explanation
Indices: 35792--35843 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
35782 GGTCGAGTCG
*
35792 GTCAACTCAAGTCAACGAGTTGGGTTT
1 GTCAACTCAAGTCAACGAGTCGGGTTT
**
35819 GTCAACTCGGGTCAACGAGTCGGGT
1 GTCAACTCAAGTCAACGAGTCGGGT
35844 CGATCAATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.25
Consensus pattern (27 bp):
GTCAACTCAAGTCAACGAGTCGGGTTT
Found at i:35850 original size:27 final size:26
Alignment explanation
Indices: 35783--35850 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 26
35773 CGATCAATGG
*
35783 GTCGAGTCGGTCAACTCAAGTCAACGA
1 GTCGGGTC-GTCAACTCAAGTCAACGA
* * **
35810 GTTGGGTTTGTCAACTCGGGTCAACGA
1 GTCGGG-TCGTCAACTCAAGTCAACGA
35837 GTCGGGTCGATCAA
1 GTCGGGTCG-TCAA
35851 TGCGAGTTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
26 2 0.06
27 29 0.91
28 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.24
Consensus pattern (26 bp):
GTCGGGTCGTCAACTCAAGTCAACGA
Found at i:47338 original size:17 final size:17
Alignment explanation
Indices: 47296--47329 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
47286 CAGTATAATG
* *
47296 ACAAACAGTTTCACATA
1 ACAAACAATCTCACATA
47313 ACAAACAATCTCACATA
1 ACAAACAATCTCACATA
47330 TCAATCAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.26, G:0.03, T:0.21
Consensus pattern (17 bp):
ACAAACAATCTCACATA
Found at i:48338 original size:29 final size:29
Alignment explanation
Indices: 48296--48453 Score: 147
Period size: 29 Copynumber: 5.4 Consensus size: 29
48286 AAGAATAGTA
* *
48296 GCAAAACTGTAAAATATGGAAAATCAGTG
1 GCAAAACTGTAAAATCTGGAAAAACAGTG
* * *
48325 GCAAAATTGTAAAATCTAGAAAAATAGTG
1 GCAAAACTGTAAAATCTGGAAAAACAGTG
* * * * **
48354 GTAGAACTATAAAATTTTAAAAAACTAGTG
1 GCAAAACTGTAAAATCTGGAAAAAC-AGTG
* *
48384 GCAAAATTATAAAATCT-GAAAAACAGTG
1 GCAAAACTGTAAAATCTGGAAAAACAGTG
* * *
48412 GCAGAACTGTAAAATCTGGAAAACCAATG
1 GCAAAACTGTAAAATCTGGAAAAACAGTG
*
48441 GCAAAAATGTAAA
1 GCAAAACTGTAAA
48454 TGTCACACCC
Statistics
Matches: 102, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
28 18 0.18
29 67 0.66
30 17 0.17
ACGTcount: A:0.51, C:0.10, G:0.17, T:0.22
Consensus pattern (29 bp):
GCAAAACTGTAAAATCTGGAAAAACAGTG
Found at i:48448 original size:58 final size:58
Alignment explanation
Indices: 48300--48446 Score: 179
Period size: 58 Copynumber: 2.5 Consensus size: 58
48290 ATAGTAGCAA
* * * *
48300 AACTGTAAAATATGGAAAATCAGTGGCAAAATTGTAAAATCTAGAAAAATAGTGGTAG
1 AACTGTAAAATATGGAAAACCAGTGGCAAAATTATAAAATCTAGAAAAACAGTGGCAG
* * ** *
48358 AACTATAAAATTTTAAAAAACTAGTGGCAAAATTATAAAATCT-GAAAAACAGTGGCAG
1 AACTGTAAAA-TATGGAAAACCAGTGGCAAAATTATAAAATCTAGAAAAACAGTGGCAG
* *
48416 AACTGTAAAATCTGGAAAACCAATGGCAAAA
1 AACTGTAAAATATGGAAAACCAGTGGCAAAA
48447 ATGTAAATGT
Statistics
Matches: 73, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
57 16 0.22
58 31 0.42
59 26 0.36
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.22
Consensus pattern (58 bp):
AACTGTAAAATATGGAAAACCAGTGGCAAAATTATAAAATCTAGAAAAACAGTGGCAG
Found at i:51409 original size:33 final size:33
Alignment explanation
Indices: 51353--51417 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
51343 ATAAATTCTA
51353 TTAGAATTTGAAAAAGAGTAATTTGAATTTTAG
1 TTAGAATTTGAAAAAGAGTAATTTGAATTTTAG
* *
51386 TTAGGATTT-AAAAAGGATTAATTTGAATTTTA
1 TTAGAATTTGAAAAA-GAGTAATTTGAATTTTA
51418 AATTAAGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 5 0.17
33 24 0.83
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.42
Consensus pattern (33 bp):
TTAGAATTTGAAAAAGAGTAATTTGAATTTTAG
Found at i:52931 original size:18 final size:18
Alignment explanation
Indices: 52893--52931 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
52883 CTAGTAATAC
* **
52893 TTTTATCTCAAAAGTGTT
1 TTTTATCCCAAAAGTACT
52911 TTTTATCCCAAAAGTACT
1 TTTTATCCCAAAAGTACT
52929 TTT
1 TTT
52932 AAGAGGTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.49
Consensus pattern (18 bp):
TTTTATCCCAAAAGTACT
Found at i:53459 original size:17 final size:17
Alignment explanation
Indices: 53431--53503 Score: 103
Period size: 17 Copynumber: 4.4 Consensus size: 17
53421 TTGGAAATTG
53431 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
*
53447 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
53464 AATTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
53481 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
53498 AATTTA
1 AATTTA
53504 GAAAGTCCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
16 5 0.10
17 45 0.90
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:53479 original size:7 final size:6
Alignment explanation
Indices: 53436--53503 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
53426 AATTGAATTT
* *
53436 ATTTAA ATTTAA GTTT-A TTTTAA ATTTAA ATTT-- ATTTGAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA
*
53482 ATTT-- ATTATAA AATTAA ATTTA
1 ATTTAA ATT-TAA ATTTAA ATTTA
53504 GAAAGTCCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
4 7 0.14
5 5 0.10
6 32 0.64
7 6 0.12
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:53559 original size:15 final size:15
Alignment explanation
Indices: 53535--53590 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
53525 AAAACAAAGT
53535 CCAATTACAAATGGC
1 CCAATTACAAATGGC
*
53550 CCAATAACAAATGGC
1 CCAATTACAAATGGC
* *
53565 CCAGTTACAGATGGC
1 CCAATTACAAATGGC
53580 CCAATTACAAA
1 CCAATTACAAA
53591 CTACCTAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.41, C:0.27, G:0.14, T:0.18
Consensus pattern (15 bp):
CCAATTACAAATGGC
Done.