Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014611.1 Kokia drynarioides strain JFW-HI SEQ_129650, 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: 98610
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Warning! 132 characters in sequence are not A, C, G, or T
Found at i:12417 original size:29 final size:31
Alignment explanation
Indices: 12385--12445 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
12375 TATATTTTTA
*
12385 TTTATATTTTTAAAAGG-TTAAAT-TAATTT
1 TTTATAGTTTTAAAAGGATTAAATGTAATTT
*
12414 TTTATCGTTTTAAAAGGATTAAATGTAATTT
1 TTTATAGTTTTAAAAGGATTAAATGTAATTT
12445 T
1 T
12446 ACCGTTACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 15 0.54
30 6 0.21
31 7 0.25
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (31 bp):
TTTATAGTTTTAAAAGGATTAAATGTAATTT
Found at i:18871 original size:16 final size:17
Alignment explanation
Indices: 18850--18887 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
18840 ATTCCAATTC
18850 AAAATGATAT-AAATCT
1 AAAATGATATGAAATCT
* *
18866 AAAATGATTTGAAATTT
1 AAAATGATATGAAATCT
18883 AAAAT
1 AAAAT
18888 CGAAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (17 bp):
AAAATGATATGAAATCT
Found at i:18885 original size:17 final size:16
Alignment explanation
Indices: 18845--18887 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
18835 ATACAATTCC
*
18845 AATTCAAAATGATATA
1 AATTTAAAATGATATA
* *
18861 AATCTAAAATGATTTGA
1 AATTTAAAATGATAT-A
18878 AATTTAAAAT
1 AATTTAAAAT
18888 CGAAAATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (16 bp):
AATTTAAAATGATATA
Found at i:19654 original size:4 final size:4
Alignment explanation
Indices: 19637--19754 Score: 109
Period size: 4 Copynumber: 30.2 Consensus size: 4
19627 TTTCGGGTTC
* * * * *
19637 GTAT GTAT GCAT GTAT GTAT GTAT G--T GTAT GCAT GCAT GCAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * *
19683 GTAT GTA- -TAT GTCT GTAT GTAT GTGT GTAGT GTGT GTAT TTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA-T GTAT GTAT GTAT GTAT
*
19730 TTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT G
19755 GTGTAGGTGT
Statistics
Matches: 95, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.04
4 88 0.93
5 3 0.03
ACGTcount: A:0.22, C:0.05, G:0.26, T:0.47
Consensus pattern (4 bp):
GTAT
Found at i:19717 original size:7 final size:8
Alignment explanation
Indices: 19700--19782 Score: 60
Period size: 8 Copynumber: 10.4 Consensus size: 8
19690 TATGTCTGTA
19700 TGTATGTG
1 TGTATGTG
19708 TGTAGTGTG
1 TGTA-TGTG
* *
19717 TGTATTTA
1 TGTATGTG
* *
19725 TGTATTTA
1 TGTATGTG
*
19733 TGTATGTA
1 TGTATGTG
*
19741 TGTATGTA
1 TGTATGTG
19749 TGTATG-G
1 TGTATGTG
*
19756 TGTAGGTG
1 TGTATGTG
* *
19764 TGCACGTG
1 TGTATGTG
*
19772 TGTGTGTG
1 TGTATGTG
19780 TGT
1 TGT
19783 GTACCTTCTT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
7 5 0.08
8 50 0.79
9 8 0.13
ACGTcount: A:0.16, C:0.02, G:0.34, T:0.48
Consensus pattern (8 bp):
TGTATGTG
Found at i:22432 original size:81 final size:82
Alignment explanation
Indices: 22324--22539 Score: 229
Period size: 85 Copynumber: 2.6 Consensus size: 82
22314 CATAACCTTT
* * * * *
22324 GTAAATCCAATATTCGGATCTCAACATTT-ACAACCCTTTCTCCTATTTCAACCATAACCAATGT
1 GTAAGTCCAAGATTCGAATCTCGACATTTCACAACCCTTTCTCCTATTTCAACCAAAACCAATGT
** * *
22388 TTCATATTCATCTTTTA
66 TTCATACACAACTTTCA
*
22405 GTAAGTCCAAGATTCGAATCTCGACATTTACAGCAATCCCTTTCT-CTCGTTTCAACCAAAACCA
1 GTAAGTCCAAGATTCGAATCTCGACATTT-CA-CAA-CCCTTTCTCCT-ATTTCAACCAAAACCA
22469 ATGTTTCATACACAACTTTCA
62 ATGTTTCATACACAACTTTCA
* **
22490 GTGAGTTAAAGATTCGAATCTCTGACATTTCCAACAACCCTTTTCTCCTA
1 GTAAGTCCAAGATTCGAATCTC-GACATTT-C-ACAACCC-TTTCTCCTA
22540 ATGTAAAATC
Statistics
Matches: 111, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
81 25 0.23
83 1 0.01
84 5 0.05
85 61 0.55
86 16 0.14
87 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.34
Consensus pattern (82 bp):
GTAAGTCCAAGATTCGAATCTCGACATTTCACAACCCTTTCTCCTATTTCAACCAAAACCAATGT
TTCATACACAACTTTCA
Found at i:25133 original size:136 final size:136
Alignment explanation
Indices: 24983--25255 Score: 537
Period size: 136 Copynumber: 2.0 Consensus size: 136
24973 AATTGGTTTA
*
24983 AATATTTTGCTCAAACCCGACCATGATAAAAATGCTAAAACCTAGATTATGCCTGACCTGTCCGT
1 AATATTTTGCTCAAACCCGACCATGATAAAAATGCTAAAACCTAGACTATGCCTGACCTGTCCGT
25048 ATTAAATTTTATATAAAAAAATTTAAAATAAACATTTCACGACAAAGTGAAAATAAATTAAAAAA
66 ATTAAATTTTATATAAAAAAATTTAAAATAAACATTTCACGACAAAGTGAAAATAAATTAAAAAA
25113 GTCTCT
131 GTCTCT
25119 AATATTTTGCTCAAACCCGACCATGATAAAAATGCTAAAACCTAGACTATGCCTGACCTGTCCGT
1 AATATTTTGCTCAAACCCGACCATGATAAAAATGCTAAAACCTAGACTATGCCTGACCTGTCCGT
25184 ATTAAATTTTATATAAAAAAATTTAAAATAAACATTTCACGACAAAGTGAAAATAAATTAAAAAA
66 ATTAAATTTTATATAAAAAAATTTAAAATAAACATTTCACGACAAAGTGAAAATAAATTAAAAAA
25249 GTCTCT
131 GTCTCT
25255 A
1 A
25256 TACTTAAATA
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 136 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (136 bp):
AATATTTTGCTCAAACCCGACCATGATAAAAATGCTAAAACCTAGACTATGCCTGACCTGTCCGT
ATTAAATTTTATATAAAAAAATTTAAAATAAACATTTCACGACAAAGTGAAAATAAATTAAAAAA
GTCTCT
Found at i:29109 original size:25 final size:24
Alignment explanation
Indices: 29081--29142 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
29071 TACTATTTTG
29081 AAATATAATA-ATTTTATTTTTAGAT
1 AAATATAATATATTTTA-TTTTA-AT
*
29106 AAATTTAA-ATATTTTATTTTAAT
1 AAATATAATATATTTTATTTTAAT
*
29129 AAA-ATAATTTATTT
1 AAATATAATATATTT
29143 GGAAAAACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
22 3 0.09
23 10 0.31
24 6 0.19
25 13 0.41
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
AAATATAATATATTTTATTTTAAT
Found at i:35759 original size:1 final size:1
Alignment explanation
Indices: 35753--35778 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
35743 NNNNNNNNNN
35753 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
35779 CTAAATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:37030 original size:13 final size:13
Alignment explanation
Indices: 37014--37062 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
37004 AAACATGAAC
37014 CTCGAACCCAAAT
1 CTCGAACCCAAAT
* *
37027 CTCGAACCCTGAAC
1 CTCGAACCC-AAAT
* *
37041 CTCGAATCTAAAT
1 CTCGAACCCAAAT
37054 CTCGAACCC
1 CTCGAACCC
37063 TAATTCAAGC
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
13 18 0.67
14 9 0.33
ACGTcount: A:0.33, C:0.39, G:0.10, T:0.18
Consensus pattern (13 bp):
CTCGAACCCAAAT
Found at i:37053 original size:27 final size:27
Alignment explanation
Indices: 37009--37063 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
36999 ACCACAAACA
37009 TGAACCTCGAACCCAAATCTCGAACCC
1 TGAACCTCGAACCCAAATCTCGAACCC
* *
37036 TGAACCTCGAATCTAAATCTCGAACCC
1 TGAACCTCGAACCCAAATCTCGAACCC
37063 T
1 T
37064 AATTCAAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.36, G:0.11, T:0.20
Consensus pattern (27 bp):
TGAACCTCGAACCCAAATCTCGAACCC
Found at i:41412 original size:30 final size:30
Alignment explanation
Indices: 41354--41412 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
41344 TAACGAAATG
* **
41354 AAAGTTTAAATATTAATTTAATCCAAAAAA
1 AAAGTTTAAATATTAAATTAATAAAAAAAA
41384 AAAGTTTAAATACTTAAATTAA-AAAAAAA
1 AAAGTTTAAATA-TTAAATTAATAAAAAAA
41413 TAATTTGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (30 bp):
AAAGTTTAAATATTAAATTAATAAAAAAAA
Found at i:50991 original size:77 final size:77
Alignment explanation
Indices: 50864--51008 Score: 236
Period size: 77 Copynumber: 1.9 Consensus size: 77
50854 ATTATTTTGG
* * *
50864 GTTTAAATCTTACAATTCATGAATCTTATTCCGATTTATTCTAACTTAAATCCGCATATAATTAA
1 GTTTAAATCTTACAATTCAAGAATCTTATTCAGATTTATTCTAACTTAAATCCCCATATAATTAA
50929 GATAGATTTAAA
66 GATAGATTTAAA
* * *
50941 GTTTAAGTCTTACAATTCAAGAATTTTATTCAGATTTATTCTAACTTAAATCCCCGTATAATTAA
1 GTTTAAATCTTACAATTCAAGAATCTTATTCAGATTTATTCTAACTTAAATCCCCATATAATTAA
51006 GAT
66 GAT
51009 TATCATGATA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 62 1.00
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (77 bp):
GTTTAAATCTTACAATTCAAGAATCTTATTCAGATTTATTCTAACTTAAATCCCCATATAATTAA
GATAGATTTAAA
Found at i:58489 original size:2 final size:2
Alignment explanation
Indices: 58482--58509 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
58472 GACAATTACA
58482 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
58510 ATGTTAGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:70574 original size:16 final size:16
Alignment explanation
Indices: 70538--70576 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
70528 TATTTTTATG
70538 TTTTTATTAAAATTTA
1 TTTTTATTAAAATTTA
* **
70554 ATTTTATTAATTTTTA
1 TTTTTATTAAAATTTA
70570 TTTTTAT
1 TTTTTAT
70577 ATTTTATGTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTATTAAAATTTA
Found at i:83385 original size:30 final size:29
Alignment explanation
Indices: 83337--83393 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
83327 TACTTTGGTC
83337 ACTTAACTTTTAAAAGTTACAAATTAGTT
1 ACTTAACTTTTAAAAGTTACAAATTAGTT
* *
83366 ACTTAACTTTTCGAAAGTTACATATTAG
1 ACTTAACTTTT-AAAAGTTACAAATTAG
83394 ATATTAGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (29 bp):
ACTTAACTTTTAAAAGTTACAAATTAGTT
Found at i:89021 original size:23 final size:23
Alignment explanation
Indices: 88948--89119 Score: 190
Period size: 23 Copynumber: 7.5 Consensus size: 23
88938 TATACGGAAC
* *
88948 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
88970 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
88991 GGGCAACAGAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
89017 AAACAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
89040 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
89063 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
89086 GATCAGAGGGCACA-AAACGTGCT
1 AAACAGAGAGCACACAAA-GTGCT
89109 AAACAGAGAGC
1 AAACAGAGAGC
89120 GCACTAGTGT
Statistics
Matches: 130, Mismatches: 13, Indels: 13
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.13
22 3 0.02
23 91 0.70
25 13 0.10
26 6 0.05
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Done.