Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013087.1 Kokia drynarioides strain JFW-HI SEQ_128105, 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: 43145
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 30 characters in sequence are not A, C, G, or T
Found at i:6885 original size:30 final size:30
Alignment explanation
Indices: 6847--7061 Score: 137
Period size: 29 Copynumber: 7.3 Consensus size: 30
6837 CAAACATTCG
*
6847 AGGG-TAAAATGGTAATTTTTGGTAGGTTC
1 AGGGTTAAAATGGTAATTTTTGGAAGGTTC
*
6876 AGGGTTAAAAATAGG--ATTTTTGGAA-GTTT
1 AGGGTT-AAAAT-GGTAATTTTTGGAAGGTTC
* * *
6905 AGGGGTAAAATGGTAA-TTTTAGAAGGTTT
1 AGGGTTAAAATGGTAATTTTTGGAAGGTTC
* * * *
6934 GGGGTCAAAAAT-G-AGATTTTT-GAAAGTTT
1 AGGGT-TAAAATGGTA-ATTTTTGGAAGGTTC
* * *
6963 GGGGGTGAAATGGTAATTTTTGGAAGGTTC
1 AGGGTTAAAATGGTAATTTTTGGAAGGTTC
* * *
6993 GGGGTCAAAAATGG-GATTTTTGGAA-GTTC
1 AGGGT-TAAAATGGTAATTTTTGGAAGGTTC
*
7022 GAGGG-TAAAACGGTAATTTTTGGAAGGTTC
1 -AGGGTTAAAATGGTAATTTTTGGAAGGTTC
* *
7052 GGGGTCAAAA
1 AGGGTTAAAA
7062 ATGGGATTTC
Statistics
Matches: 146, Mismatches: 23, Indels: 33
0.72 0.11 0.16
Matches are distributed among these distances:
27 2 0.01
28 23 0.16
29 57 0.39
30 51 0.35
31 11 0.08
32 2 0.01
ACGTcount: A:0.31, C:0.04, G:0.33, T:0.33
Consensus pattern (30 bp):
AGGGTTAAAATGGTAATTTTTGGAAGGTTC
Found at i:6908 original size:29 final size:28
Alignment explanation
Indices: 6877--7070 Score: 119
Period size: 30 Copynumber: 6.6 Consensus size: 28
6867 GGTAGGTTCA
6877 GGGTTAAAAATAGGATTTTTGGAAGTTTAG
1 GGGTTAAAAAT-GGATTTTTGGAAGTTT-G
* *
6907 GGG-T-AAAATGGTAATTTTAGAAGGTTTG
1 GGGTTAAAAATGG-ATTTTTGGAA-GTTTG
* *
6935 GGGTCAAAAATGAGATTTTTGAAAGTTTG
1 GGGTTAAAAATG-GATTTTTGGAAGTTTG
* * *
6964 GGGGT-GAAATGGTAATTTTTGGAAGGTTCG
1 GGGTTAAAAATGG--ATTTTTGGAA-GTTTG
* *
6994 GGGTCAAAAATGGGATTTTTGGAAGTTCG
1 GGGTTAAAAAT-GGATTTTTGGAAGTTTG
* *
7023 AGGG-T-AAAACGGTAATTTTTGGAAGGTTCG
1 -GGGTTAAAAATGG--ATTTTTGGAA-GTTTG
*
7053 GGGTCAAAAATGGGATTT
1 GGGTTAAAAAT-GGATTT
7071 CTGAACAATC
Statistics
Matches: 129, Mismatches: 18, Indels: 34
0.71 0.10 0.19
Matches are distributed among these distances:
27 5 0.04
28 26 0.20
29 40 0.31
30 45 0.35
31 9 0.07
32 4 0.03
ACGTcount: A:0.30, C:0.04, G:0.33, T:0.33
Consensus pattern (28 bp):
GGGTTAAAAATGGATTTTTGGAAGTTTG
Found at i:6914 original size:59 final size:59
Alignment explanation
Indices: 6848--7070 Score: 315
Period size: 59 Copynumber: 3.8 Consensus size: 59
6838 AAACATTCGA
* * * *
6848 GGGTAAAATGGTAATTTTTGGTAGGTTCAGGGTTAAAAATAGGATTTTTGGAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTAG
* * * * *
6907 GGGTAAAATGGTAA-TTTTAGAAGGTTTGGGGTCAAAAATGAGATTTTTGAAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTAG
* *
6965 GGGTGAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG-TTCG
1 GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTAG
*
7023 AGGGTAAAACGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTT
1 -GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTT
7071 CTGAACAATC
Statistics
Matches: 145, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
58 51 0.35
59 94 0.65
ACGTcount: A:0.30, C:0.04, G:0.33, T:0.34
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTAG
Found at i:8994 original size:11 final size:11
Alignment explanation
Indices: 8964--9011 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
8954 TTTAAATTCG
8964 AAAATAAATTT
1 AAAATAAATTT
*
8975 AAAATTAAAATT
1 AAAA-TAAATTT
8987 AAAATAAATTT
1 AAAATAAATTT
* *
8998 AAATTTAATTT
1 AAAATAAATTT
9009 AAA
1 AAA
9012 TTTTTAACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAATAAATTT
Found at i:9011 original size:17 final size:17
Alignment explanation
Indices: 8937--9045 Score: 69
Period size: 17 Copynumber: 6.4 Consensus size: 17
8927 TGGACCTTAT
*
8937 TTTAAATTTATAA-TAA
1 TTTAAATTTAAAATTAA
* *
8953 TTTTAAATTCGAAAATAAA
1 -TTTAAATT-TAAAATTAA
*
8972 TTTAAAATTAAAATTAA
1 TTTAAATTTAAAATTAA
** *
8989 AATAAATTTAAATTTAA
1 TTTAAATTTAAAATTAA
** **
9006 TTTAAATTTTTAACAAA
1 TTTAAATTTAAAATTAA
*
9023 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATTAA
9040 TTTAAA
1 TTTAAA
9046 GGAGAGTTTT
Statistics
Matches: 68, Mismatches: 20, Indels: 7
0.72 0.21 0.07
Matches are distributed among these distances:
16 3 0.04
17 51 0.75
18 12 0.18
19 2 0.03
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATTAA
Found at i:9013 original size:6 final size:6
Alignment explanation
Indices: 8968--9014 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
8958 AATTCGAAAA
* * *
8968 TAAATT TAAAAT TAAAAT TAAA-A TAAATT TAAATT T-AATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
9014 T
1 T
9015 TTAACAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
5 9 0.25
6 27 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:14341 original size:35 final size:35
Alignment explanation
Indices: 14295--14364 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
14285 AGCTCGGAGG
14295 CTGGCAAGTGCCCGACCCCTTAAAATAAAAACTTT
1 CTGGCAAGTGCCCGACCCCTTAAAATAAAAACTTT
14330 CTGGCAAGTGCCCGACCCCTTAAAATAAAAACTTT
1 CTGGCAAGTGCCCGACCCCTTAAAATAAAAACTTT
14365 TTCATTTAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (35 bp):
CTGGCAAGTGCCCGACCCCTTAAAATAAAAACTTT
Found at i:16423 original size:29 final size:29
Alignment explanation
Indices: 16380--16529 Score: 128
Period size: 29 Copynumber: 5.1 Consensus size: 29
16370 CTAATCTAAG
*
16380 TTCACTTTTTATACTCATATATTTTTTTA
1 TTCACTTTTTCTACTCATATATTTTTTTA
16409 TTCACTTTTTCTACTCATATATTTTTTTA
1 TTCACTTTTTCTACTCATATATTTTTTTA
* * * * ** * *
16438 -T---TTTTCCATATGTGTAAATAACTAATCTAA
1 TTCACTTTTTC-TA-CT-CATAT-A-TTTTTTTA
*
16468 GTTCACTTTTTATACTCATATATTTTTTTA
1 -TTCACTTTTTCTACTCATATATTTTTTTA
16498 TTCACTTTTTCTACTCATATATTTTTTTA
1 TTCACTTTTTCTACTCATATATTTTTTTA
16527 TTC
1 TTC
16530 TTTTTGAAAA
Statistics
Matches: 92, Mismatches: 19, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
25 5 0.05
26 2 0.02
27 1 0.01
28 4 0.04
29 60 0.65
30 8 0.09
31 1 0.01
32 4 0.04
33 1 0.01
34 2 0.02
35 4 0.04
ACGTcount: A:0.25, C:0.15, G:0.02, T:0.58
Consensus pattern (29 bp):
TTCACTTTTTCTACTCATATATTTTTTTA
Found at i:16497 original size:89 final size:89
Alignment explanation
Indices: 16349--16528 Score: 360
Period size: 89 Copynumber: 2.0 Consensus size: 89
16339 GAAAAGTTAT
16349 TTTTTCCATATGTGTAAATAACTAATCTAAGTTCACTTTTTATACTCATATATTTTTTTATTCAC
1 TTTTTCCATATGTGTAAATAACTAATCTAAGTTCACTTTTTATACTCATATATTTTTTTATTCAC
16414 TTTTTCTACTCATATATTTTTTTA
66 TTTTTCTACTCATATATTTTTTTA
16438 TTTTTCCATATGTGTAAATAACTAATCTAAGTTCACTTTTTATACTCATATATTTTTTTATTCAC
1 TTTTTCCATATGTGTAAATAACTAATCTAAGTTCACTTTTTATACTCATATATTTTTTTATTCAC
16503 TTTTTCTACTCATATATTTTTTTA
66 TTTTTCTACTCATATATTTTTTTA
16527 TT
1 TT
16529 CTTTTTGAAA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 91 1.00
ACGTcount: A:0.27, C:0.14, G:0.03, T:0.56
Consensus pattern (89 bp):
TTTTTCCATATGTGTAAATAACTAATCTAAGTTCACTTTTTATACTCATATATTTTTTTATTCAC
TTTTTCTACTCATATATTTTTTTA
Found at i:26573 original size:2 final size:2
Alignment explanation
Indices: 26568--26593 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26558 TAAAAAAATG
26568 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
26594 CCTATGGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31039 original size:22 final size:22
Alignment explanation
Indices: 31008--31081 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
30998 ACTGGGGAAA
31008 CAGAAGCACACACAATGCTAAT
1 CAGAAGCACACACAATGCTAAT
* *
31030 CAGAACCACACACACTGCTAAAT
1 CAGAAGCACACACAATGCT-AAT
* * *
31053 -AGAAGCACACATAGTGCTAAA
1 CAGAAGCACACACAATGCTAAT
31074 CAGTAAGC
1 CAG-AAGC
31082 GCGTTAGCGT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.05
22 34 0.79
23 7 0.16
ACGTcount: A:0.45, C:0.27, G:0.15, T:0.14
Consensus pattern (22 bp):
CAGAAGCACACACAATGCTAAT
Found at i:32965 original size:2 final size:2
Alignment explanation
Indices: 32958--32982 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32948 ATCTCGAAAG
32958 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
32983 CACAATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40233 original size:20 final size:20
Alignment explanation
Indices: 40210--40254 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
40200 AATTCATTAT
40210 TAAAATAATAA-ATTTATAAA
1 TAAAATAATAATA-TTATAAA
40230 TAAAATAATAATATTATAAA
1 TAAAATAATAATATTATAAA
40250 TAAAA
1 TAAAA
40255 CAATTTAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAATAATAATATTATAAA
Found at i:41487 original size:13 final size:14
Alignment explanation
Indices: 41471--41505 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
41461 ATGTCATTTG
41471 TTTATTTTTC-TTA
1 TTTATTTTTCGTTA
41484 TTTA-TTTTCGTTA
1 TTTATTTTTCGTTA
41497 TTTATTTTT
1 TTTATTTTT
41506 ATCTCATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 11 0.55
14 4 0.20
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTATTTTTCGTTA
Found at i:42298 original size:26 final size:25
Alignment explanation
Indices: 42262--42311 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
42252 GTGATTATTA
42262 TATATAAAATT-TTAATATATATAAAG
1 TATATAAAATTATTAA-ATAT-TAAAG
42288 TATATAAAATTATTAAATATTAAA
1 TATATAAAATTATTAAATATTAAA
42312 TTGAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.17
26 15 0.65
27 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
TATATAAAATTATTAAATATTAAAG
Found at i:42300 original size:41 final size:39
Alignment explanation
Indices: 42255--42332 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 39
42245 AACTCCCGTG
* **
42255 ATTATTATATATAAAATTTTAATATATATAAAGTATATAAA
1 ATTATTAAATATAAAATTGAAATA-ATATAAA-TATATAAA
*
42296 ATTATTAAATATTAAATTGAAATAATATAAATATATA
1 ATTATTAAATATAAAATTGAAATAATATAAATATATA
42333 TATTTTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 6 0.18
40 7 0.21
41 20 0.61
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (39 bp):
ATTATTAAATATAAAATTGAAATAATATAAATATATAAA
Found at i:42320 original size:26 final size:26
Alignment explanation
Indices: 42265--42320 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
42255 ATTATTATAT
*
42265 ATAAAATTTTAATATATATAAAGTAT
1 ATAAAATTTTAATATATATAAAGTAA
*
42291 ATAAAATTATTAA-ATAT-TAAATTGAA
1 ATAAAATT-TTAATATATATAAAGT-AA
42317 ATAA
1 ATAA
42321 TATAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 5 0.19
26 17 0.65
27 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (26 bp):
ATAAAATTTTAATATATATAAAGTAA
Found at i:42651 original size:23 final size:21
Alignment explanation
Indices: 42611--42658 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
42601 TGAGAGTTTT
*
42611 ATATATTTTTTAATATATGTTAA
1 ATATATTTTTTAACATA--TTAA
42634 ATAT-TTTTTTCAACATATTAA
1 ATATATTTTTT-AACATATTAA
42655 ATAT
1 ATAT
42659 CTTATTCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 8 0.35
22 6 0.26
23 9 0.39
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (21 bp):
ATATATTTTTTAACATATTAA
Done.