Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005684.1 Kokia drynarioides strain JFW-HI SEQ_119879, 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: 10358
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--45 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43 TA T
1 TA T
46 TAAAAAAACG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3869 original size:28 final size:28
Alignment explanation
Indices: 3838--3898 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
3828 AAAATGAGAC
* *
3838 TTTGGA-TACTCGGGGGTAAAATGGTAAT
1 TTTGGACT-CTCGGGGGCAAAATGATAAT
*
3866 TTTGGACTCTTGGGGGCAAAATGATAAT
1 TTTGGACTCTCGGGGGCAAAATGATAAT
3894 TTTGG
1 TTTGG
3899 GAAAGTTTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.26, C:0.08, G:0.31, T:0.34
Consensus pattern (28 bp):
TTTGGACTCTCGGGGGCAAAATGATAAT
Found at i:4151 original size:59 final size:60
Alignment explanation
Indices: 3999--4195 Score: 183
Period size: 59 Copynumber: 3.3 Consensus size: 60
3989 ATCCGGGGGT
* * * * * *
3999 AAAATGGTAATATTT-GAAAGC-TTCGGGGTAAAAAATAGAATTTTTGGAAGTTCG-GGGATA
1 AAAATGG-AAT-TTTGGAAAACTTTCGAGGTCAAAAATGGAATTTTTGGAATTTCGAAGG-TA
*
4059 AAAATGGAATTTT-GAAAAGTTTCGAGGTCAAAAATGGAATTTTTGGAATTTCGAAGGTA
1 AAAATGGAATTTTGGAAAACTTTCGAGGTCAAAAATGGAATTTTTGGAATTTCGAAGGTA
* * *
4118 AAAATGGAATTTTGGAAACCTTTGGA-GTTAAAAATGGAA-TTTTGGAAAGTTTC-AAGGTAA
1 AAAATGGAATTTTGGAAAACTTTCGAGGTCAAAAATGGAATTTTTGG-AA-TTTCGAAGGT-A
*
4178 AAAATGGATTTTTTGGAA
1 AAAATGGA-ATTTTGGAA
4196 GTTTGGGGGT
Statistics
Matches: 118, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
58 13 0.11
59 66 0.56
60 31 0.26
61 8 0.07
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (60 bp):
AAAATGGAATTTTGGAAAACTTTCGAGGTCAAAAATGGAATTTTTGGAATTTCGAAGGTA
Found at i:4207 original size:89 final size:89
Alignment explanation
Indices: 4057--4254 Score: 238
Period size: 89 Copynumber: 2.2 Consensus size: 89
4047 AGTTCGGGGA
* * *
4057 TAAAAATGGAATTTTGAAAAGTTTCGAGGTCAAAAATGGAATTTTTGGAATTTCGAAGGTAAAAA
1 TAAAAATGGAATTTTGGAAAGTTTCAAGGTAAAAAATGGAATTTTTGGAATTTCGAAGGT-AAAA
* **
4122 TGG-AATTTTGGAAACCTTTGGAGT
65 TGGTAAATTTCAAAACCTTTGGAGT
* **
4146 TAAAAATGGAATTTTGGAAAGTTTCAAGGTAAAAAATGGATTTTTTGGAAGTTT-GGGGGTAAAA
1 TAAAAATGGAATTTTGGAAAGTTTCAAGGTAAAAAATGGAATTTTTGGAA-TTTCGAAGGTAAAA
** *
4210 TGGTAAATTTCAAAAGTTTTGGGGT
65 TGGTAAATTTCAAAACCTTTGGAGT
*
4235 TAAAAATTGAATTTTTGGAA
1 TAAAAATGGAA-TTTTGGAA
4255 GTTCATAGGT
Statistics
Matches: 93, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
88 7 0.08
89 75 0.81
90 11 0.12
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (89 bp):
TAAAAATGGAATTTTGGAAAGTTTCAAGGTAAAAAATGGAATTTTTGGAATTTCGAAGGTAAAAT
GGTAAATTTCAAAACCTTTGGAGT
Found at i:4257 original size:30 final size:30
Alignment explanation
Indices: 3999--4257 Score: 185
Period size: 30 Copynumber: 8.7 Consensus size: 30
3989 ATCCGGGGGT
* * * *
3999 AAAATGGTAATATTTGAAAGCTTCGGGGTAA
1 AAAATGG-AATTTTTGGAAGTTTCGGGGTTA
* *
4030 AAAATAGAATTTTTGGAAG-TTCGGGGATA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTTA
* * *
4059 AAAATGGAA-TTTTGAAAAGTTTCGAGGTCA
1 AAAATGGAATTTTTG-GAAGTTTCGGGGTTA
*
4089 AAAATGGAATTTTTGGAA-TTTCGAAGG-TA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTTA
* *
4118 AAAATGGAA-TTTTGGAAACCTTT-GGAGTTA
1 AAAATGGAATTTTTGG-AA-GTTTCGGGGTTA
** *
4148 AAAATGGAA-TTTTGGAAAGTTTCAAGGTAA
1 AAAATGGAATTTTTGG-AAGTTTCGGGGTTA
* *
4178 AAAATGGATTTTTTGGAAGTTT-GGGGGT-
1 AAAATGGAATTTTTGGAAGTTTCGGGGTTA
* *** *
4206 AAAATGGTAAATTTCAAAAGTTTTGGGGTTA
1 AAAATGG-AATTTTTGGAAGTTTCGGGGTTA
*
4237 AAAATTGAATTTTTGGAAGTT
1 AAAATGGAATTTTTGGAAGTT
4258 CATAGGTCAA
Statistics
Matches: 180, Mismatches: 35, Indels: 27
0.74 0.14 0.11
Matches are distributed among these distances:
28 18 0.10
29 52 0.29
30 84 0.47
31 26 0.14
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTTA
Found at i:5429 original size:10 final size:10
Alignment explanation
Indices: 5414--5455 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
5404 TTGTTAGAAC
5414 ATTATTATTA
1 ATTATTATTA
5424 ATTATTATTA
1 ATTATTATTA
*
5434 ATTATTAAT-
1 ATTATTATTA
5443 ATTATTTATTA
1 ATTA-TTATTA
5454 AT
1 AT
5456 AGCATTAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 4 0.14
10 22 0.79
11 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTATTATTA
Found at i:5454 original size:13 final size:13
Alignment explanation
Indices: 5416--5456 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
5406 GTTAGAACAT
* *
5416 TATTATTAATTAT
1 TATTATTTATTAA
*
5429 TATTAATTATTAA
1 TATTATTTATTAA
5442 TATTATTTATTAA
1 TATTATTTATTAA
5455 TA
1 TA
5457 GCATTAAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TATTATTTATTAA
Found at i:6131 original size:16 final size:17
Alignment explanation
Indices: 6110--6144 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6100 CTGTTTTAGG
*
6110 TTTAGG-CCACTTGTAA
1 TTTAGGCCCACTTGAAA
6126 TTTAGGCCCACTTGAAA
1 TTTAGGCCCACTTGAAA
6143 TT
1 TT
6145 GTGCTTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (17 bp):
TTTAGGCCCACTTGAAA
Found at i:6231 original size:17 final size:17
Alignment explanation
Indices: 6211--6318 Score: 137
Period size: 17 Copynumber: 6.4 Consensus size: 17
6201 CATTATTTAT
* *
6211 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
6228 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
6245 TTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAA
*
6262 TTCAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
6279 TCTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
6296 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
6313 TTTAAA
1 TTTAAA
6319 AGGGGTCCGA
Statistics
Matches: 77, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
16 3 0.04
17 72 0.94
18 2 0.03
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:6237 original size:6 final size:6
Alignment explanation
Indices: 6211--6290 Score: 62
Period size: 6 Copynumber: 14.0 Consensus size: 6
6201 CATTATTTAT
* * *
6211 TTTAAA TTTATAA --TAAT TTTAAA TTTAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
6257 -TTAAA TTCAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
6291 ACAAATTTAA
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
4 1 0.02
5 15 0.26
6 40 0.69
7 2 0.03
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:6244 original size:11 final size:11
Alignment explanation
Indices: 6230--6284 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
6220 ATAATAATTT
6230 TAAATTTAAAA
1 TAAATTTAAAA
*
6241 TAAATTTAAACT
1 TAAATTTAAA-A
*
6253 TAAA-TTAAAT
1 TAAATTTAAAA
6263 TCAAATTTAAAA
1 T-AAATTTAAAA
*
6275 TAAATCTAAA
1 TAAATTTAAA
6285 TTTAAAACAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
10 2 0.05
11 26 0.68
12 10 0.26
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.36
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:6284 original size:23 final size:23
Alignment explanation
Indices: 6242--6286 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
6232 AATTTAAAAT
*
6242 AAATTTAAACTTAAATTAAATTC
1 AAATTTAAACATAAATTAAATTC
6265 AAATTTAAA-ATAAATCTAAATT
1 AAATTTAAACATAAAT-TAAATT
6287 TAAAACAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATTTAAACATAAATTAAATTC
Found at i:7099 original size:15 final size:16
Alignment explanation
Indices: 7079--7112 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
7069 ATAAAGTTAT
*
7079 AATAAA-ATATTAAAA
1 AATAAATATATAAAAA
7094 AATAAATATATAAAAA
1 AATAAATATATAAAAA
7110 AAT
1 AAT
7113 GAACACATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAAATATATAAAAA
Found at i:7710 original size:34 final size:34
Alignment explanation
Indices: 7666--7748 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
7656 TCTGGACCCA
* ** * * *
7666 ATAAACTTAAATTTATTTTAAAATTGAGTTTATT
1 ATAAATTTAAATTTAGCTGAAAATTAAATTTATT
*
7700 ATAAATTTAAATTTAGCTGAAATTTAAATTTATT
1 ATAAATTTAAATTTAGCTGAAAATTAAATTTATT
*
7734 ATAAATTTAATTTTA
1 ATAAATTTAAATTTA
7749 AATGTCCAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (34 bp):
ATAAATTTAAATTTAGCTGAAAATTAAATTTATT
Found at i:7714 original size:17 final size:17
Alignment explanation
Indices: 7666--7748 Score: 78
Period size: 17 Copynumber: 4.9 Consensus size: 17
7656 TCTGGACCCA
*
7666 ATAAACTTAAATTTATT
1 ATAAATTTAAATTTATT
* * * *
7683 TTAAAATTGAGTTTATT
1 ATAAATTTAAATTTATT
*
7700 ATAAATTTAAATTTAGCT
1 ATAAATTTAAATTTA-TT
*
7718 -GAAATTTAAATTTATT
1 ATAAATTTAAATTTATT
*
7734 ATAAATTTAATTTTA
1 ATAAATTTAAATTTA
7749 AATGTCCAAA
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
16 1 0.02
17 49 0.96
18 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (17 bp):
ATAAATTTAAATTTATT
Found at i:8483 original size:29 final size:30
Alignment explanation
Indices: 8432--8488 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
8422 GTTTTTTTTT
8432 ATAATAAATGTTTAAATAATAATAATAATA
1 ATAATAAATGTTTAAATAATAATAATAATA
* * *
8462 ATAAT-AATTTTTAATTATTAATAATAA
1 ATAATAAATGTTTAAATAATAATAATAA
8489 AAAAGTATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (30 bp):
ATAATAAATGTTTAAATAATAATAATAATA
Found at i:9542 original size:29 final size:29
Alignment explanation
Indices: 9496--9681 Score: 152
Period size: 29 Copynumber: 6.3 Consensus size: 29
9486 CCCTAAATTG
*
9496 TCCAAAAATTACCATTTT-ACCCCCTAACT
1 TCCAAAAA-TACCATTTTGACCCCCGAACT
* **
9525 TCCAAAAATCCCATTTTTTGACCCCAAAACT
1 TCCAAAAATACCA--TTTTGACCCCCGAACT
* *
9556 ACCTAAAATTACCATTTT-ACCCCCGAACT
1 TCC-AAAAATACCATTTTGACCCCCGAACT
*
9585 TCAAAAAAT-CTCATTTTTGA-CCCCGAACCT
1 TCCAAAAATAC-CA-TTTTGACCCCCGAA-CT
*
9615 TCCAAAAATTACCATTTT-ACCCCCTAACT
1 TCCAAAAA-TACCATTTTGACCCCCGAACT
9644 TCCAAAAAT-CTCATTTTTGA-CCCCGATACT
1 TCCAAAAATAC-CA-TTTTGACCCCCGA-ACT
9674 TCCAAAAA
1 TCCAAAAA
9682 AAACTACCAT
Statistics
Matches: 128, Mismatches: 14, Indels: 29
0.75 0.08 0.17
Matches are distributed among these distances:
27 2 0.02
28 14 0.11
29 49 0.38
30 40 0.31
31 14 0.11
32 9 0.07
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (29 bp):
TCCAAAAATACCATTTTGACCCCCGAACT
Found at i:9622 original size:30 final size:29
Alignment explanation
Indices: 9516--9681 Score: 137
Period size: 30 Copynumber: 5.6 Consensus size: 29
9506 ACCATTTTAC
* *
9516 CCCCTAACTTCCAAAAATCCCATTTTTTGA
1 CCCCGAACTTCCAAAAATCTCA-TTTTTGA
* * *
9546 CCCCAAAACTACCTAAAAT-TACCA-TTTT-A
1 CCCC-GAACTTCCAAAAATCT--CATTTTTGA
*
9575 CCCCCGAACTTCAAAAAATCTCATTTTTGA
1 -CCCCGAACTTCCAAAAATCTCATTTTTGA
9605 CCCCGAACCTTCCAAAAAT-TACCA-TTTT-A
1 CCCCGAA-CTTCCAAAAATCT--CATTTTTGA
*
9634 CCCCCTAACTTCCAAAAATCTCATTTTTGA
1 -CCCCGAACTTCCAAAAATCTCATTTTTGA
9664 CCCCGATACTTCCAAAAA
1 CCCCGA-ACTTCCAAAAA
9682 AAACTACCAT
Statistics
Matches: 110, Mismatches: 11, Indels: 30
0.73 0.07 0.20
Matches are distributed among these distances:
28 4 0.04
29 44 0.40
30 47 0.43
31 13 0.12
32 2 0.02
ACGTcount: A:0.34, C:0.33, G:0.04, T:0.29
Consensus pattern (29 bp):
CCCCGAACTTCCAAAAATCTCATTTTTGA
Found at i:9623 original size:59 final size:58
Alignment explanation
Indices: 9496--9681 Score: 282
Period size: 59 Copynumber: 3.1 Consensus size: 58
9486 CCCTAAATTG
* *
9496 TCCAAAAATTACCATTTTACCCCCTAACTTCCAAAAATCCCATTTTTTGACCCCAAAACT
1 TCCAAAAATTACCATTTTACCCCCTAACTTCCAAAAATCTCA-TTTTTGACCCC-GAACT
* * * *
9556 ACCTAAAATTACCATTTTACCCCCGAACTTCAAAAAATCTCATTTTTGACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCCCTAACTTCCAAAAATCTCATTTTTGACCCCGAA-CT
9615 TCCAAAAATTACCATTTTACCCCCTAACTTCCAAAAATCTCATTTTTGACCCCGATACT
1 TCCAAAAATTACCATTTTACCCCCTAACTTCCAAAAATCTCATTTTTGACCCCGA-ACT
9674 TCCAAAAA
1 TCCAAAAA
9682 AAACTACCAT
Statistics
Matches: 114, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
58 2 0.02
59 74 0.65
60 38 0.33
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (58 bp):
TCCAAAAATTACCATTTTACCCCCTAACTTCCAAAAATCTCATTTTTGACCCCGAACT
Done.