Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001227.1 Kokia drynarioides strain JFW-HI SEQ_112585, 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: 100743
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 99 characters in sequence are not A, C, G, or T
Found at i:50 original size:23 final size:23
Alignment explanation
Indices: 23--146 Score: 115
Period size: 23 Copynumber: 5.3 Consensus size: 23
13 CTAGCGCGCG
23 CTCTGTTTAGCAC-GTCTCGTGCT
1 CTCTGTTTAGCACTGTCT-GTGCT
*
46 CTCTGTTATTAGCACTGTGTGTGCT
1 CTCTG-T-TTAGCACTGTCTGTGCT
* * *
71 CTCTGATTAGCACTTTGTGTGCT
1 CTCTGTTTAGCACTGTCTGTGCT
* ** * * *
94 CTCTGATTAGTGCTTTGTGTACT
1 CTCTGTTTAGCACTGTCTGTGCT
*
117 CTCTGTTTAGCACTGTGTGTGCT
1 CTCTGTTTAGCACTGTCTGTGCT
140 CTCTGTT
1 CTCTGTT
147 GCCCAGCACT
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
23 66 0.76
24 1 0.01
25 17 0.20
26 3 0.03
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.44
Consensus pattern (23 bp):
CTCTGTTTAGCACTGTCTGTGCT
Found at i:133 original size:69 final size:68
Alignment explanation
Indices: 44--189 Score: 190
Period size: 69 Copynumber: 2.1 Consensus size: 68
34 ACGTCTCGTG
* *
44 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATT-AGCACTTTGTGTGCTCTCTGATTAGTGCT
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTG-TTCAGCAC-TTATGTGCTCTCTG-TTAGTACT
108 TTGTGTA
63 TTG-GTA
115 CTCTCTG-T-TTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTAGTACT
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGTT---CAGCACTTATGTGCTCTCTGTTAGTACT
178 TTGGTA
63 TTGGTA
184 CTCTCT
1 CTCTCT
190 TTTTGTTCCG
Statistics
Matches: 69, Mismatches: 2, Indels: 10
0.85 0.02 0.12
Matches are distributed among these distances:
68 2 0.03
69 31 0.45
70 11 0.16
71 20 0.29
72 5 0.07
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (68 bp):
CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGTTCAGCACTTATGTGCTCTCTGTTAGTACTTTG
GTA
Found at i:20257 original size:14 final size:13
Alignment explanation
Indices: 20222--20260 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
20212 CTTAGTCAAG
20222 ATAAATTA-TTTT
1 ATAAATTATTTTT
*
20234 ATAGATTATTTTT
1 ATAAATTATTTTT
20247 ATAATATTATTTTT
1 ATAA-ATTATTTTT
20261 GGTTTCGCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 7 0.30
13 7 0.30
14 9 0.39
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (13 bp):
ATAAATTATTTTT
Found at i:22950 original size:17 final size:17
Alignment explanation
Indices: 22878--22950 Score: 50
Period size: 17 Copynumber: 4.6 Consensus size: 17
22868 ATAAAATAAT
22878 TGACTTAAATATTGTAG
1 TGACTTAAATATTGTAG
* *
22895 TGAC--AAATA-T-AAA
1 TGACTTAAATATTGTAG
22908 TGA--TAAATATTGTAG
1 TGACTTAAATATTGTAG
* * * *
22923 TGATTTTAATATTTTAT
1 TGACTTAAATATTGTAG
22940 TGACTTAAATA
1 TGACTTAAATA
22951 AAAAAATTCA
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
13 9 0.21
14 2 0.05
15 9 0.21
17 22 0.52
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.42
Consensus pattern (17 bp):
TGACTTAAATATTGTAG
Found at i:24701 original size:28 final size:28
Alignment explanation
Indices: 24624--24703 Score: 71
Period size: 28 Copynumber: 3.0 Consensus size: 28
24614 CGTTCTTTGA
* * * *
24624 TTTTTATTT-TTTTATAAAATTGTAAGTT
1 TTTTTATTTATATT-TAAAATTATAAATG
24652 TTTTTCA-TTA-ATTT-AAA-TATAAATG
1 TTTTT-ATTTATATTTAAAATTATAAATG
24677 TTTTTATTTATATTTAAAATTATAAAT
1 TTTTTATTTATATTTAAAATTATAAAT
24704 TAAATTAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
24 1 0.02
25 13 0.31
26 7 0.17
27 4 0.10
28 16 0.38
29 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (28 bp):
TTTTTATTTATATTTAAAATTATAAATG
Found at i:29898 original size:16 final size:16
Alignment explanation
Indices: 29877--29910 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29867 ATACGTTTAA
*
29877 AGTCCTTATACTTTTT
1 AGTCCTTATAATTTTT
*
29893 AGTCCTTTTAATTTTT
1 AGTCCTTATAATTTTT
29909 AG
1 AG
29911 ATTTAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.56
Consensus pattern (16 bp):
AGTCCTTATAATTTTT
Found at i:36698 original size:16 final size:18
Alignment explanation
Indices: 36639--36706 Score: 61
Period size: 17 Copynumber: 3.8 Consensus size: 18
36629 AATTTTTTTT
36639 ATTATTTATTTATTTTATA
1 ATTATTTA-TTATTTTATA
*
36658 ATTGATTTATT-TTTAATA
1 ATT-ATTTATTATTTTATA
36676 A-TATTTTATTATTTTAT-
1 ATTA-TTTATTATTTTATA
* *
36693 ATTTTTTATAATTT
1 ATTATTTATTATTT
36707 AATTATACTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
16 1 0.02
17 17 0.41
18 13 0.32
19 5 0.12
20 5 0.12
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (18 bp):
ATTATTTATTATTTTATA
Found at i:36701 original size:45 final size:46
Alignment explanation
Indices: 36635--36731 Score: 121
Period size: 45 Copynumber: 2.1 Consensus size: 46
36625 AGTTAATTTT
*
36635 TTTTATTATTTATTTATTTTATAA-TTGATT-TA-TTTTTAATAATA
1 TTTTATTATTTATTTATTTTATAATTTAATTATACTTTTTAAT-ATA
*
36679 TTTTATTATTTTATATT-TTTTATAATTTAATTATACTTTTTAATATT
1 TTTTATTA-TTTAT-TTATTTTATAATTTAATTATACTTTTTAATATA
36726 TTTTAT
1 TTTTAT
36732 GTGAATAGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
44 8 0.17
45 13 0.28
46 7 0.15
47 10 0.22
48 8 0.17
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (46 bp):
TTTTATTATTTATTTATTTTATAATTTAATTATACTTTTTAATATA
Found at i:36707 original size:16 final size:15
Alignment explanation
Indices: 36632--36707 Score: 59
Period size: 16 Copynumber: 5.0 Consensus size: 15
36622 AATAGTTAAT
*
36632 TTTTTTTATTATTTA
1 TTTTTTTATAATTTA
*
36647 TTTATTTTATAATTGA
1 TTT-TTTTATAATTTA
*
36663 TTTATTTT-TAATAATA
1 TTT-TTTTATAAT-TTA
*
36679 TTTTATTAT--TTTA
1 TTTTTTTATAATTTA
36692 TATTTTTTATAATTTA
1 T-TTTTTTATAATTTA
36708 ATTATACTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
13 3 0.06
14 8 0.17
15 10 0.21
16 27 0.56
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (15 bp):
TTTTTTTATAATTTA
Found at i:37666 original size:7 final size:7
Alignment explanation
Indices: 37651--37681 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
37641 AACATAGTGA
*
37651 ATTTCGT
1 ATTTAGT
37658 ATTTAGT
1 ATTTAGT
37665 ATTTAGT
1 ATTTAGT
37672 ATTTAGT
1 ATTTAGT
37679 ATT
1 ATT
37682 ATACCACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.58
Consensus pattern (7 bp):
ATTTAGT
Found at i:38465 original size:18 final size:18
Alignment explanation
Indices: 38442--38502 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
38432 GGGAGCTTAA
38442 CTCAATTCCAATCGTCAC
1 CTCAATTCCAATCGTCAC
*
38460 CTCAATTCTAATCGTCAC
1 CTCAATTCCAATCGTCAC
*
38478 C-CTAATACCAATCG-CAAC
1 CTC-AATTCCAATCGTC-AC
38496 CTCAATT
1 CTCAATT
38503 TCCACCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 2 0.06
18 33 0.92
19 1 0.03
ACGTcount: A:0.31, C:0.36, G:0.05, T:0.28
Consensus pattern (18 bp):
CTCAATTCCAATCGTCAC
Found at i:54688 original size:26 final size:28
Alignment explanation
Indices: 54634--54696 Score: 85
Period size: 26 Copynumber: 2.3 Consensus size: 28
54624 CTTTTTTCAA
* *
54634 AATAATATGAAAAAATATTATTTAGCGG
1 AATAATATGAAAAAATATTAATCAGCGG
*
54662 AATAATAT-AAAAAAT-TTAATCATCGG
1 AATAATATGAAAAAATATTAATCAGCGG
54688 AATAATATG
1 AATAATATG
54697 GGTTGTGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.52
27 7 0.23
28 8 0.26
ACGTcount: A:0.52, C:0.05, G:0.11, T:0.32
Consensus pattern (28 bp):
AATAATATGAAAAAATATTAATCAGCGG
Found at i:58642 original size:16 final size:17
Alignment explanation
Indices: 58607--58643 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
58597 CACATAATAT
58607 AATAAACGTATTTAAAA
1 AATAAACGTATTTAAAA
58624 AATAAAC-T-TTTATAAA
1 AATAAACGTATTTA-AAA
58640 AATA
1 AATA
58644 TTTTGTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.21
16 8 0.42
17 7 0.37
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (17 bp):
AATAAACGTATTTAAAA
Found at i:61560 original size:31 final size:31
Alignment explanation
Indices: 61525--61583 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
61515 ATATCAAAAT
*
61525 TAAAATATAGAAATTAAAATTCAAATTTTAG
1 TAAAATATAGAAATTAAAATTAAAATTTTAG
**
61556 TAAAATATAGGGATTAAAATTAAAATTT
1 TAAAATATAGAAATTAAAATTAAAATTT
61584 AACAATTCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36
Consensus pattern (31 bp):
TAAAATATAGAAATTAAAATTAAAATTTTAG
Found at i:62784 original size:29 final size:30
Alignment explanation
Indices: 62722--62801 Score: 108
Period size: 29 Copynumber: 2.6 Consensus size: 30
62712 ATACCAAAAT
* *
62722 TATACATGAATTATGGTTTAATGTGTAACTG
1 TATACATGAATTTTGATTT-ATGTGTAACTG
*
62753 TATACATGAATTTTGATTT-TGTGTAATTG
1 TATACATGAATTTTGATTTATGTGTAACTG
62782 TATACATGAAATTTTGATTT
1 TATACATG-AATTTTGATTT
62802 GATTCAATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 17 0.38
30 11 0.24
31 17 0.38
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.47
Consensus pattern (30 bp):
TATACATGAATTTTGATTTATGTGTAACTG
Found at i:63770 original size:14 final size:14
Alignment explanation
Indices: 63748--63790 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
63738 GAAATATGAA
*
63748 TAATAAAATTTAGCT
1 TAAT-AAATTTAACT
63763 TAATAAATTTAACT
1 TAATAAATTTAACT
*
63777 GAATAAATTTAACT
1 TAATAAATTTAACT
63791 GCTAAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 22 0.85
15 4 0.15
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (14 bp):
TAATAAATTTAACT
Found at i:63798 original size:13 final size:14
Alignment explanation
Indices: 63753--63791 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
63743 ATGAATAATA
* *
63753 AAATTTAGCTTAAT
1 AAATTTAACTGAAT
63767 AAATTTAACTGAAT
1 AAATTTAACTGAAT
63781 AAATTTAACTG
1 AAATTTAACTG
63792 CTAAATTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (14 bp):
AAATTTAACTGAAT
Found at i:75628 original size:2 final size:2
Alignment explanation
Indices: 75616--75655 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
75606 ACGTCCCTTG
*
75616 TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
75656 GCGGAGAAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:82581 original size:16 final size:18
Alignment explanation
Indices: 82560--82597 Score: 55
Period size: 15 Copynumber: 2.3 Consensus size: 18
82550 CTTAAAGAGA
82560 AAAAAAATA-ATA-TTGT
1 AAAAAAATATATAGTTGT
82576 -AAAAAATATATAGTTGT
1 AAAAAAATATATAGTTGT
82593 AAAAA
1 AAAAA
82598 CGCGCATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.42
16 3 0.16
17 4 0.21
18 4 0.21
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (18 bp):
AAAAAAATATATAGTTGT
Found at i:82581 original size:17 final size:17
Alignment explanation
Indices: 82559--82597 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
82549 TCTTAAAGAG
82559 AAAAAAAATAATA-TTGT
1 AAAAAAAAT-ATAGTTGT
*
82576 AAAAAATATATAGTTGT
1 AAAAAAAATATAGTTGT
82593 AAAAA
1 AAAAA
82598 CGCGCATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (17 bp):
AAAAAAAATATAGTTGT
Found at i:89686 original size:9 final size:9
Alignment explanation
Indices: 89648--89678 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
89638 GCTCTACTTA
89648 AAGAAGATG
1 AAGAAGATG
*
89657 AAGAAGAAG
1 AAGAAGATG
89666 AAGAAGATG
1 AAGAAGATG
89675 AAGA
1 AAGA
89679 TGGAGAAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.32, T:0.06
Consensus pattern (9 bp):
AAGAAGATG
Found at i:94467 original size:2 final size:2
Alignment explanation
Indices: 94460--94488 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
94450 TTGACACCAT
94460 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
94489 TGAAATGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:98728 original size:20 final size:20
Alignment explanation
Indices: 98687--98729 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
98677 TATAAAAATA
* *
98687 ATTATTTTTATTTGTTTCAT
1 ATTATTTTTAGTTATTTCAT
98707 ATTATATTTTAGTTATTT-AT
1 ATTAT-TTTTAGTTATTTCAT
98727 ATT
1 ATT
98730 TAAAATGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (20 bp):
ATTATTTTTAGTTATTTCAT
Done.