Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011656.1 Kokia drynarioides strain JFW-HI SEQ_126648, 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: 36485
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Found at i:2637 original size:380 final size:381
Alignment explanation
Indices: 1933--2700 Score: 1243
Period size: 380 Copynumber: 2.0 Consensus size: 381
1923 GAGTGTGGTG
** * * *
1933 GGTACAAAACTCGAAACCATCCTTACCCTACGATCCGTAAGACTGAAATTATCTCTATTCCATTA
1 GGTACAAAACTCGAAACCATCCCCACCCTACGATCCGTAAGACTAAAATCATCTCTATTCCATCA
** * *
1998 CCCATGTGAGTCCCTAGACCCACCTAACCTTTGCTATATTTGCACTGCGACCCATTTCATATAAA
66 CCCACCTGAGTCCCTAGACCCACCTAACCTTTGCTATATCTGCACTACGACCCATTTCATATAAA
* *
2063 TATATTTATAAATAGGGTAAATTACACAAACAATCACTCAACTTTGGGTTGGCTGACAAAACAGT
131 TATATTTATAAATAGGGTAAATTACACAAACAATCACTCAACTTTAGGCTGGCTGACAAAACAGT
*
2128 CACATTGATTTCATTTCAATCACTCAACTTTGAAAAAGTGACAAAGTAATCACTAACGTTATCAA
196 CACATTGATTTCATTTCAATCACTCAACTTTGAAAAAGTGACAAAGTAATCACTAAAGTTATCAA
*
2193 AAAGTGACAAAATAGTCACTGATTAACAATTCTCGTTAAGAGCTTAACGAGACCGCTTATGTGAC
261 AAAGTGACAAAATAGTCACTGATTAACAATTCTCGTTAAGAGCTTAACGAGACCGCTAATGTGAC
*
2258 AAGTTAACTAGCTAATATGACTAGTTAACTTGCCACGTGGATGAAGTCAGGTAAAA
326 AAGTTAACTAGCTAATATGACTAGTTAACTTGCCACGTAGATGAAGTCAGGTAAAA
*
2314 GGTACAAAACTCGAAACCATCCCCGCCCTACGATCCGTAAGACTAAAATCATCTCTATTCCATCA
1 GGTACAAAACTCGAAACCATCCCCACCCTACGATCCGTAAGACTAAAATCATCTCTATTCCATCA
** * * *
2379 CCCACCTGAGTCCCTAGACTTACCTAATCTTTGCTATATCTGCCCTACGATCCATTTCATAT-AA
66 CCCACCTGAGTCCCTAGACCCACCTAACCTTTGCTATATCTGCACTACGACCCATTTCATATAAA
* * *
2443 TATATTTATAAGTAGGGTAAATTACACCAACAATCACTCAACTTTAGGCTGGCTGATAAAACAGT
131 TATATTTATAAATAGGGTAAATTACACAAACAATCACTCAACTTTAGGCTGGCTGACAAAACAGT
* * * *
2508 CACCTTGGTTTCATTTCAGTCACTCAACTTTGAAAAATTGACAAAGTAATCACTAAAGTTATCAA
196 CACATTGATTTCATTTCAATCACTCAACTTTGAAAAAGTGACAAAGTAATCACTAAAGTTATCAA
* * *
2573 AAAGTGACAAAATAGTCACTGATTAACAATTTTCGTTAGGGGCTTAACGAGACCGCTAATGTGAC
261 AAAGTGACAAAATAGTCACTGATTAACAATTCTCGTTAAGAGCTTAACGAGACCGCTAATGTGAC
*
2638 AAGTTAACTAGCTGATATGACTAGTTAACTTGCCACGTAGATGAAGTCAGGTAAAA
326 AAGTTAACTAGCTAATATGACTAGTTAACTTGCCACGTAGATGAAGTCAGGTAAAA
2694 GGT-CAAA
1 GGTACAAA
2701 CATTCGAGGG
Statistics
Matches: 356, Mismatches: 31, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
379 4 0.01
380 240 0.67
381 112 0.31
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (381 bp):
GGTACAAAACTCGAAACCATCCCCACCCTACGATCCGTAAGACTAAAATCATCTCTATTCCATCA
CCCACCTGAGTCCCTAGACCCACCTAACCTTTGCTATATCTGCACTACGACCCATTTCATATAAA
TATATTTATAAATAGGGTAAATTACACAAACAATCACTCAACTTTAGGCTGGCTGACAAAACAGT
CACATTGATTTCATTTCAATCACTCAACTTTGAAAAAGTGACAAAGTAATCACTAAAGTTATCAA
AAAGTGACAAAATAGTCACTGATTAACAATTCTCGTTAAGAGCTTAACGAGACCGCTAATGTGAC
AAGTTAACTAGCTAATATGACTAGTTAACTTGCCACGTAGATGAAGTCAGGTAAAA
Found at i:4447 original size:24 final size:24
Alignment explanation
Indices: 4387--4447 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
4377 CTCATTGCGT
* * *
4387 TTTACGCTCGCCAGCTTTCATACG
1 TTTACGCTCGTCAGCTTGCACACG
*
4411 TTTACGCTTGTCAGCTTGCACACG
1 TTTACGCTCGTCAGCTTGCACACG
4435 TTTACGCTCGTCA
1 TTTACGCTCGTCA
4448 ATTATATATG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.34
Consensus pattern (24 bp):
TTTACGCTCGTCAGCTTGCACACG
Found at i:4741 original size:21 final size:21
Alignment explanation
Indices: 4717--4770 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
4707 TAGTGTAGAA
*
4717 TTCTATTGATACAAGTGATAG-
1 TTCTATTGATACAAGTCAT-GC
* *
4738 TTCTACTGACACAAGTCATGC
1 TTCTATTGATACAAGTCATGC
*
4759 TTCTGTTGATAC
1 TTCTATTGATAC
4771 CAAAAACTCC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.37
Consensus pattern (21 bp):
TTCTATTGATACAAGTCATGC
Found at i:14129 original size:24 final size:24
Alignment explanation
Indices: 14096--14186 Score: 74
Period size: 24 Copynumber: 3.7 Consensus size: 24
14086 AATATATGCA
* *
14096 TTTACACTCACCAACTTGCACACG
1 TTTACGCTCACCAGCTTGCACACG
* * ** *
14120 TTTACGCTCATCAGTTTATATATGCG
1 TTTACGCTCACCAGCTTGCACA--CG
* *
14146 TTTACGCTCTCCAGCTTGCACATG
1 TTTACGCTCACCAGCTTGCACACG
*
14170 TTTACGCTCATCAGCTT
1 TTTACGCTCACCAGCTT
14187 ATATATGCAT
Statistics
Matches: 49, Mismatches: 16, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
24 31 0.63
26 18 0.37
ACGTcount: A:0.22, C:0.30, G:0.13, T:0.35
Consensus pattern (24 bp):
TTTACGCTCACCAGCTTGCACACG
Found at i:14148 original size:26 final size:26
Alignment explanation
Indices: 14118--14200 Score: 91
Period size: 26 Copynumber: 3.3 Consensus size: 26
14108 AACTTGCACA
*
14118 CGTTTACGCTCATCAGTTTATATATG
1 CGTTTACGCTCATCAGCTTATATATG
** *
14144 CGTTTACGCTC-TCCAGCTTGCACAT-
1 CGTTTACGCTCAT-CAGCTTATATATG
14169 -GTTTACGCTCATCAGCTTATATATG
1 CGTTTACGCTCATCAGCTTATATATG
*
14194 CATTTAC
1 CGTTTAC
14201 TCTTGCCAGC
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
24 19 0.42
25 2 0.04
26 24 0.53
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (26 bp):
CGTTTACGCTCATCAGCTTATATATG
Found at i:14164 original size:50 final size:50
Alignment explanation
Indices: 14087--14217 Score: 183
Period size: 50 Copynumber: 2.6 Consensus size: 50
14077 GGTTGTTACA
* * *
14087 ATATATGCATTTACACTCACCAACTTGCACACGTTTACGCTCATCAGTTT
1 ATATATGCATTTACACTCTCCAGCTTGCACACGTTTACGCTCATCAGCTT
* * *
14137 ATATATGCGTTTACGCTCTCCAGCTTGCACATGTTTACGCTCATCAGCTT
1 ATATATGCATTTACACTCTCCAGCTTGCACACGTTTACGCTCATCAGCTT
*
14187 ATATATGCATTTACTCT-TGCCAGCTTGCACA
1 ATATATGCATTTACACTCT-CCAGCTTGCACA
14218 TATCCAAATA
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
49 1 0.01
50 71 0.99
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.35
Consensus pattern (50 bp):
ATATATGCATTTACACTCTCCAGCTTGCACACGTTTACGCTCATCAGCTT
Found at i:15458 original size:45 final size:46
Alignment explanation
Indices: 15363--15459 Score: 110
Period size: 46 Copynumber: 2.1 Consensus size: 46
15353 TATTTTGTGT
* * *
15363 TTATTCGATTTTGATTTTGATATTAATTATATTTTTTATGTAGCGT
1 TTATTCGATTTTGATTTGGATATTAATTATATTTTTGATGTAGCGG
* *
15409 TTATTCGATTTTGA-TTGGAT-TCTAATTTTCATTTTTGATTTAG-GG
1 TTATTCGATTTTGATTTGGATAT-TAATTAT-ATTTTTGATGTAGCGG
15454 TTATTC
1 TTATTC
15460 TAATTTTGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
44 1 0.02
45 18 0.41
46 25 0.57
ACGTcount: A:0.22, C:0.06, G:0.14, T:0.58
Consensus pattern (46 bp):
TTATTCGATTTTGATTTGGATATTAATTATATTTTTGATGTAGCGG
Found at i:15601 original size:27 final size:23
Alignment explanation
Indices: 15569--15637 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 23
15559 TGTTATTGAA
15569 TTTGATTTCATTTTGTATTTACAT
1 TTTGATTTCATTTTGTATTTA-AT
*
15593 GTGTCTGATTTGATTTTGTA-TTAAT
1 -T-T-TGATTTCATTTTGTATTTAAT
*
15618 TTTGATTTCATTTTATATTT
1 TTTGATTTCATTTTGTATTT
15638 TGGTTTGGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 13 0.34
23 3 0.08
24 1 0.03
25 3 0.08
26 4 0.11
27 14 0.37
ACGTcount: A:0.20, C:0.06, G:0.12, T:0.62
Consensus pattern (23 bp):
TTTGATTTCATTTTGTATTTAAT
Found at i:15716 original size:31 final size:31
Alignment explanation
Indices: 15681--15761 Score: 119
Period size: 31 Copynumber: 2.6 Consensus size: 31
15671 TTTAGGGTTA
*
15681 ATTGTTTATTGTATTCCATGAAACCTTAAAT
1 ATTGTTTATTGTATTCCATGAAACCTTAAAG
*
15712 ATTGTTTATTGTATGT-TATGAAACCTTAAAG
1 ATTGTTTATTGTAT-TCCATGAAACCTTAAAG
*
15743 ATTGTTTATTGTATGCCAT
1 ATTGTTTATTGTATTCCAT
15762 TTAGAGAGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
31 43 0.98
32 1 0.02
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.47
Consensus pattern (31 bp):
ATTGTTTATTGTATTCCATGAAACCTTAAAG
Found at i:17520 original size:61 final size:59
Alignment explanation
Indices: 17410--17525 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 59
17400 ATCACTTTAA
** * * *
17410 TATTAAATTAATCTAATAATTATCAAGATAAATATTATATTAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATAATTATCAACATAAACATTAAATTAAATTTAATATTAAATCT
*
17469 TATTAAATTAATAGAATATTTATCTACACATAAACATTAAATTAAATTTAATATTAA
1 TATTAAATTAATAGAATAATTATC-A-ACATAAACATTAAATTAAATTTAATATTAA
17526 TATAATCACT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 21 0.43
60 1 0.02
61 27 0.55
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (59 bp):
TATTAAATTAATAGAATAATTATCAACATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:17551 original size:20 final size:18
Alignment explanation
Indices: 17504--17552 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
17494 ACACATAAAC
17504 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
17521 ATT-AATATAATCACTTTAAT
1 ATTAAAT-TAAT-A-TTTAAT
17541 ATTAAATTAATA
1 ATTAAATTAATA
17553 AAATACTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.11
17 6 0.22
19 2 0.07
20 13 0.48
21 3 0.11
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:17564 original size:25 final size:26
Alignment explanation
Indices: 17516--17576 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
17506 TAAATTAAAT
*
17516 TTAATATTAATATAATCACTTTAATA
1 TTAATATTAATAAAATCACTTTAATA
*
17542 TTAA-ATTAATAAAAT-ACTGTTAAGA
1 TTAATATTAATAAAATCACT-TTAATA
*
17567 TCAATATTAA
1 TTAATATTAA
17577 ATTAAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 3 0.10
25 18 0.60
26 9 0.30
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (26 bp):
TTAATATTAATAAAATCACTTTAATA
Found at i:19045 original size:27 final size:27
Alignment explanation
Indices: 19008--19066 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
18998 TACAAAGTTT
19008 ACTAA-ACTAAACTAACTTTCTAACCA
1 ACTAACACTAAACTAACTTTCTAACCA
19034 ACTAACACTAAACTAACTTTCTAACCA
1 ACTAACACTAAACTAACTTTCTAACCA
19061 ACTAAC
1 ACTAAC
19067 CATATTTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 5 0.16
27 27 0.84
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (27 bp):
ACTAACACTAAACTAACTTTCTAACCA
Found at i:26111 original size:29 final size:30
Alignment explanation
Indices: 26074--26136 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
26064 ATTTATGTAT
* * *
26074 AATTATATACAT-GAATTTTGATTTTATTC
1 AATTATATACATAAAATTTTGATTTGATCC
* *
26103 AATTTTATATATAAAATTTTGATTTGATCC
1 AATTATATACATAAAATTTTGATTTGATCC
26133 AATT
1 AATT
26137 CTTGTAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (30 bp):
AATTATATACATAAAATTTTGATTTGATCC
Found at i:26213 original size:29 final size:29
Alignment explanation
Indices: 26176--26231 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
26166 TAACATCCGT
* * *
26176 TTATGTTTATATATTACAATAATAAATAA
1 TTATATTTATATAATACAAAAATAAATAA
*
26205 TTATATTTATATAATATAAAAATAAAT
1 TTATATTTATATAATACAAAAATAAAT
26232 TAACGTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (29 bp):
TTATATTTATATAATACAAAAATAAATAA
Found at i:35905 original size:17 final size:18
Alignment explanation
Indices: 35871--35906 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
35861 TGAATTTCTA
35871 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
35889 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
35906 T
1 T
35907 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Done.