Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013145.1 Kokia drynarioides strain JFW-HI SEQ_128164, 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: 6621
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:3576 original size:209 final size:204
Alignment explanation
Indices: 3034--3810 Score: 814
Period size: 198 Copynumber: 3.8 Consensus size: 204
3024 NNNNNNNNNN
* * * *
3034 GCTTCCTGATGACACACCGAGAAGCAGATCGGAGCAATAAACGGTTAGCTTCCTGATGAGATACG
1 GCTTCCTGATGAGATACCGAGAAGCAGGTCGAAGCAATAAACGGTTAGCTTCCTGATGAGATACG
* *
3099 GAGAAGT-AGACCAAATTCGACTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGACGC-
66 GAGAAGTGA-ACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCA
* * * * *
3162 GATTATCTTCCTAATGAGATACTGAGAAGAATACCAAACCA-AACCCATGCTCGA-CATGAGCAA
130 G-TCATCTTCCCAATGAGATACTGAGAAGAAGACCAAA-CAGAACCCACGCTCAAGCA--AGCAA
*
3225 ATCTTCGAACCACA
191 ATCTTCGAACCCCA
* * *
3239 GC-TCTCTGATGAGATACTGAGAAGC-GTGTCGAAG---T-AA---TTAGCCTCTTGATGAGATA
1 GCTTC-CTGATGAGATACCGAGAAGCAG-GTCGAAGCAATAAACGGTTAGCTTCCTGATGAGATA
* * *
3295 CGGAGAAGTAGAA-CAAATTCGTCTTCCTGATGAGATACAAAGAAGCGAATTGAAACACACTACG
64 CGGAGAAGT-GAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACG
* * * *
3359 CAGTCATCTTCCCAATGAGATGCTAAGAAGAAGACCAAATCAGGAGGCCTACGCTCAAAGCAAGC
128 CAGTCATCTTCCCAATGAGATACTGAGAAGAAGACCAAA-CA-GA-ACCCACGCTC-AAGCAAGC
3424 AAAATCTTCGAACCCCA
189 -AAATCTTCGAACCCCA
* * *
3441 GCTTCCTGATGAGATACCGAGAAGCAGGTCGAAGCAATAAACTGTTAGCTTCCAGATGAGATACT
1 GCTTCCTGATGAGATACCGAGAAGCAGGTCGAAGCAATAAACGGTTAGCTTCCTGATGAGATACG
* * * * *
3506 GAGAAGTGAACCAAATTCGTCTTCCTGATGAGATGCAGAG-AGACGGATTGAAACAAGCGATGCG
66 GAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAG-CGAATTGAAACAAACGACGCA
* * * * * * *
3570 GTCATCTTCCCGATGAGATACTGAGAAGAAGGCCAAACCGAACCCACGCACGATG-AA-TAAACC
130 GTCATCTTCCCAATGAGATACTGAGAAGAAGACCAAACAGAACCCACGCTC-AAGCAAGCAAATC
3633 TTCGAACCCCA
194 TTCGAACCCCA
* * ** * * **
3644 GCTTCTTGATAAGATATTGAGAAGCAGGACAAAATAATAAAACGGTTAGCTTCCTGATGAGATAC
1 GCTTCCTGATGAGATACCGAGAAGCAGGTCGAAGCAAT-AAACGGTTAGCTTCCTGATGAGATAC
* * * *
3709 GGAGAAGTTGATCAAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACTACAC
65 GGAGAAG-TGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGC
* * *
3774 AGTCATTTTCCCAATGAGATACTGGGAAGAAGGCCAA
129 AGTCATCTTCCCAATGAGATACTGAGAAGAAGACCAA
3811 GTCAATGAAA
Statistics
Matches: 476, Mismatches: 71, Indels: 50
0.80 0.12 0.08
Matches are distributed among these distances:
198 106 0.22
199 2 0.00
200 2 0.00
201 12 0.03
202 45 0.09
203 50 0.11
204 33 0.07
205 106 0.22
206 13 0.03
207 2 0.00
208 6 0.01
209 99 0.21
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.20
Consensus pattern (204 bp):
GCTTCCTGATGAGATACCGAGAAGCAGGTCGAAGCAATAAACGGTTAGCTTCCTGATGAGATACG
GAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCAG
TCATCTTCCCAATGAGATACTGAGAAGAAGACCAAACAGAACCCACGCTCAAGCAAGCAAATCTT
CGAACCCCA
Found at i:4168 original size:17 final size:17
Alignment explanation
Indices: 4145--4240 Score: 122
Period size: 17 Copynumber: 5.6 Consensus size: 17
4135 TCATACTCCC
4145 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
4162 ATTAAATTT-GTTTAAA
1 TTTAAATTTATTTTAAA
4178 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
4195 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
4212 TTTAAAATTATTTTCAAA
1 TTTAAATTTATTTT-AAA
4230 TTTAAAATTTA
1 TTT-AAATTTA
4241 AAATAAAACC
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
16 14 0.21
17 41 0.62
18 5 0.08
19 6 0.09
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:4181 original size:6 final size:6
Alignment explanation
Indices: 4145--4242 Score: 73
Period size: 6 Copynumber: 17.0 Consensus size: 6
4135 TCATACTCCC
* * * *
4145 TTTAAA TTT-AT TTTAAA ATTAAA TTT--G TTTAAA TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
4189 TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA ATT-AT TTTCAAA TTTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTT-AAA
4237 TTTAAA
1 TTTAAA
4243 ATAAAACCCA
Statistics
Matches: 70, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
4 3 0.04
5 16 0.23
6 41 0.59
7 10 0.14
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:4194 original size:11 final size:11
Alignment explanation
Indices: 4178--4233 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
4168 TTTGTTTAAA
4178 TTTAAATTTAT
1 TTTAAATTTAT
*
4189 TTTAAATTTAAA
1 TTTAAATTT-AT
*
4201 TTT-AATTTAAG
1 TTTAAATTT-AT
*
4212 TTTAAAATTAT
1 TTTAAATTTAT
4223 TTTCAAATTTA
1 TTT-AAATTTA
4234 AAATTTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
11 23 0.62
12 14 0.38
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:5283 original size:21 final size:23
Alignment explanation
Indices: 5253--5296 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
5243 AGGGAAAACC
*
5253 GTTTGGATCTAG-GCTAGATCTG
1 GTTTGGATCTAGACCTAGATCTG
5275 GTTT-GATCTAGACCTAGATCTG
1 GTTTGGATCTAGACCTAGATCTG
5297 TTTTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.36
Consensus pattern (23 bp):
GTTTGGATCTAGACCTAGATCTG
Found at i:6146 original size:29 final size:29
Alignment explanation
Indices: 6071--6382 Score: 202
Period size: 29 Copynumber: 10.6 Consensus size: 29
6061 AAACTTTTTG
*
6071 AAAATTACCATTTTACCCTCGAA-CTTC-C
1 AAAATTACCATTTTACCC-CGAACCTTCTA
6099 AAAA-T-CTCATTTTGGACCCCGAACCTTCTA
1 AAAATTAC-CATTTT--ACCCCGAACCTTCTA
* * *
6129 AAAATTACCATTTTACCCCTAAACTTCCA
1 AAAATTACCATTTTACCCCGAACCTTCTA
*
6158 AAAA-T-CTCATTTTTGA-CCCGATCCTTCTA
1 AAAATTAC-CA-TTTT-ACCCCGAACCTTCTA
* *
6187 AAAATTACTATTTTACCCCCGAA-CTTCCA
1 AAAATTACCATTTTA-CCCCGAACCTTCTA
* * *
6216 AAAA-TCCCATTTTTTTATCCTGAACCTTCTA
1 AAAATTACCA---TTTTACCCCGAACCTTCTA
** * *
6247 AAAATTACCATTTTACCCATAAACTTCCA
1 AAAATTACCATTTTACCCCGAACCTTCTA
6276 AAAA-T-CTCATTTTTGACCCCGAACCTTCTA
1 AAAATTAC-CA-TTTT-ACCCCGAACCTTCTA
** *
6306 AAAATTATTATTTTACCCCCGAA-CTTCCA
1 AAAATTACCATTTTA-CCCCGAACCTTCTA
*
6335 AAAA-TCCCATTTTTGACCCCGAACCTT-TCA
1 AAAATTACCA-TTTT-ACCCCGAACCTTCT-A
6365 AAAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
6383 TCTAACTTCC
Statistics
Matches: 220, Mismatches: 34, Indels: 59
0.70 0.11 0.19
Matches are distributed among these distances:
26 1 0.00
27 9 0.04
28 20 0.09
29 101 0.46
30 56 0.25
31 28 0.13
32 5 0.02
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCGAACCTTCTA
Found at i:6178 original size:58 final size:59
Alignment explanation
Indices: 6071--6441 Score: 466
Period size: 59 Copynumber: 6.3 Consensus size: 59
6061 AAACTTTTTG
* *
6071 AAAATTACCATTTTA-CCCTCGAACTTCC-AAAATCTCATTTTGGACCCCGAACCTTCTA
1 AAAATTACCATTTTACCCCT-GAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTA
* * *
6129 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTGA-CCCGATCCTTCTA
1 AAAATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTA
* * * * *
6187 AAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTTATCCTGAACCTTCTA
1 AAAATTACCATTTTACCCCTGAACTTCCAAAAATCCCA-TTTTTGACCCCGAACCTTCTA
* * *
6247 AAAATTACCATTTTACCCATAAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTCTA
1 AAAATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTA
** *
6306 AAAATTATTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT-TCA
1 AAAATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT-A
* ** *
6365 AAAATTACCATTTTACCCTCT-AACTTCCAAAAATCCCATTTTTGACTCTAAACCTTC-C
1 AAAATTACCATTTTACCC-CTGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTA
* *
6423 AAAACTACCATTTTGCCCC
1 AAAATTACCATTTTACCCC
6442 CGTGCATCCA
Statistics
Matches: 273, Mismatches: 33, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
57 1 0.00
58 85 0.31
59 142 0.52
60 45 0.16
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTA
Found at i:6277 original size:118 final size:116
Alignment explanation
Indices: 6071--6410 Score: 513
Period size: 118 Copynumber: 2.9 Consensus size: 116
6061 AAACTTTTTG
* * * *
6071 AAAATTACCATTTTACCCTCGAACTTCC-AAAATCTCATTTTGGACCCCGAACCTTCTAAAAATT
1 AAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATT
*
6135 ACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTGACCCGATCCTTCTA
66 ACCATTTTA-CCCTAAACTTCCAAAAATCTCATTTTTGACCCGAACCTTCTA
* * *
6187 AAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTTATCCTGAACCTTCTAAAAAT
1 AAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTTGACCCCGAACCTTCTAAAAAT
6252 TACCATTTTACCCATAAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTCTA
65 TACCATTTTACCC-TAAACTTCCAAAAATCTCATTTTTGA-CCCGAACCTTCTA
*
6306 AAAATTATTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT-TCAAAAAT
1 AAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT-AAAAAT
* *
6370 TACCATTTTACCCTCTAACTTCCAAAAATCCCATTTTTGAC
65 TACCATTTTACCCT-AAACTTCCAAAAATCTCATTTTTGAC
6411 TCTAAACCTT
Statistics
Matches: 204, Mismatches: 14, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
116 26 0.13
117 14 0.07
118 115 0.56
119 49 0.24
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (116 bp):
AAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATT
ACCATTTTACCCTAAACTTCCAAAAATCTCATTTTTGACCCGAACCTTCTA
Found at i:6424 original size:30 final size:30
Alignment explanation
Indices: 6081--6436 Score: 192
Period size: 29 Copynumber: 12.1 Consensus size: 30
6071 AAAATTACCA
*
6081 TTTT-ACCCTCGAA-CTTCC-AAAATCTCAT
1 TTTTGACCCT-GAACCTTCCAAAAATCCCAT
* * * *
6109 TTTGGACCCCGAACCTTCTAAAAATTACCA-
1 TTTTGACCCTGAACCTTCCAAAAA-TCCCAT
* *
6139 TTTT-ACCCCT-AAACTTCCAAAAATCTCAT
1 TTTTGA-CCCTGAACCTTCCAAAAATCCCAT
* * **
6168 TTTTGACCC-GATCCTTCTAAAAATTAC-T
1 TTTTGACCCTGAACCTTCCAAAAATCCCAT
*
6196 ATTTT-ACCCCCGAA-CTTCCAAAAATCCCATT
1 -TTTTGA-CCCTGAACCTTCCAAAAATCCCA-T
* * * *
6227 TTTTTATCCTGAACCTTCTAAAAATTACCA-
1 TTTTGACCCTGAACCTTCCAAAAA-TCCCAT
* *
6257 TTTT-ACCCAT-AAACTTCCAAAAATCTCAT
1 TTTTGACCC-TGAACCTTCCAAAAATCCCAT
* * *
6286 TTTTGACCCCGAACCTTCTAAAAAT--TAT
1 TTTTGACCCTGAACCTTCCAAAAATCCCAT
* *
6314 TATTTTACCCCCGAA-CTTCCAAAAATCCCAT
1 T-TTTGA-CCCTGAACCTTCCAAAAATCCCAT
* * *
6345 TTTTGACCCCGAACCTTTCAAAAATTACCA-
1 TTTTGACCCTGAACCTTCCAAAAA-TCCCAT
*
6375 TTTT-ACCCTCTAA-CTTCCAAAAATCCCAT
1 TTTTGACCCT-GAACCTTCCAAAAATCCCAT
* * * *
6404 TTTTGACTCTAAACCTTCCAAAACTACCAT
1 TTTTGACCCTGAACCTTCCAAAAATCCCAT
6434 TTT
1 TTT
6437 GCCCCCGTGC
Statistics
Matches: 251, Mismatches: 47, Indels: 58
0.71 0.13 0.16
Matches are distributed among these distances:
28 21 0.08
29 115 0.46
30 90 0.36
31 21 0.08
32 4 0.02
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (30 bp):
TTTTGACCCTGAACCTTCCAAAAATCCCAT
Found at i:6426 original size:29 final size:30
Alignment explanation
Indices: 6329--6436 Score: 89
Period size: 30 Copynumber: 3.7 Consensus size: 30
6319 TACCCCCGAA
* * *
6329 CTTCCAAAAA-TCCCATTTTTGACCCCGAAC
1 CTTCCAAAAACTACCATTTTTGA-CTCTAAC
* * ***
6359 CTTTCAAAAATTACCATTTTACCCTCTAA-
1 CTTCCAAAAACTACCATTTTTGACTCTAAC
*
6388 CTTCCAAAAA-TCCCATTTTTGACTCTAAAC
1 CTTCCAAAAACTACCATTTTTGACTCT-AAC
6418 CTTCC-AAAACTACCATTTT
1 CTTCCAAAAACTACCATTTT
6437 GCCCCCGTGC
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
28 12 0.20
29 15 0.25
30 26 0.43
31 8 0.13
ACGTcount: A:0.32, C:0.31, G:0.03, T:0.33
Consensus pattern (30 bp):
CTTCCAAAAACTACCATTTTTGACTCTAAC
Done.