Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000917.1 Kokia drynarioides strain JFW-HI SEQ_112061, 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: 10127
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Found at i:574 original size:197 final size:202
Alignment explanation
Indices: 233--996 Score: 1088
Period size: 208 Copynumber: 3.7 Consensus size: 202
223 CTTGTTTTGG
* * * *
233 TTCGCTTCTCTATACCTCATCAGGAAGACAAATTTGGTTCACTTCTCAGTATCTCATCAGTAAGC
1 TTCGCTTCTCCATATCTCATCAGGAAGACAAATTTGGTACACTTCTCAGTATCTCATCAGGAAGC
* * *
298 TAACCTTTTATTGCTTCAACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTTG
66 TAACCTTTTATTGCTTCAACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTG
* * *
363 CTCATTTTGAGCCTCGTTTGGGTTTGATTTGGTCTTCTTCTCAATATC-T-T-G-T-CCGCATCA
131 CTCGTTTCGAGCCTCGTTTGGGTTTGATTTGGTCTTCTTCTCAGTATCTTGTAGATACCGCATCA
423 TTTTTAA
196 TTTTTAA
*
430 TTCGCTTCTCCATATCTCATCAGGAAGACAAATTTGGTACACTTCTCAGTATCTCTTCAGGAAGC
1 TTCGCTTCTCCATATCTCATCAGGAAGACAAATTTGGTACACTTCTCAGTATCTCATCAGGAAGC
* * *
495 TAACCTTTTATTGCTTCAACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTTG
66 TAACCTTTTATTGCTTCAACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTG
*
560 CTCGTTTCGAGCCTCTTTTGGGTTTGATTTGGTCTTCTTCTCAGTATCTTGTCCGGAAGATAACC
131 CTCGTTTCGAGCCTCGTTTGGGTTTGATTTGGTCTTCTTCTCAGTATCTTGT-----AGAT-ACC
*
625 GCATCGTTTTTAA
190 GCATCATTTTTAA
* * *
638 TTCGCTTCTCCGTATCTCATCAGGAAGACGAATTTGGTACACTTCTCAATATCTCATCAGGAAGC
1 TTCGCTTCTCCATATCTCATCAGGAAGACAAATTTGGTACACTTCTCAGTATCTCATCAGGAAGC
* *
703 TAACCTTTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAGGAAGCGGGGGTTCGAAGATTTTG
66 TAACCTTTTATTGCTTCAACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTG
* * *
768 CTTGTTTTGAGCCTCTTTTGGGTTTGATTTGGTCTTCTTCTCAGTATCTTGTCCGGTAGATGACC
131 CTCGTTTCGAGCCTCGTTTGGGTTTGATTTGGTCTTCTTCTCAGTATC-T-T---GTAGAT-ACC
833 GCATCATTTTTAA
190 GCATCATTTTTAA
* * * * *
846 TTCGCTTCTTCGTATCTCATCAGGAAAACGAACTTGGTACACTTCTCAGTATCTCATCAGGAAGC
1 TTCGCTTCTCCATATCTCATCAGGAAGACAAATTTGGTACACTTCTCAGTATCTCATCAGGAAGC
* **
911 TAACCTTTTATTACTTTGACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTG
66 TAACCTTTTATTGCTTCAACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTG
*
976 CTTGTTTCGAGCCTCGTTTGG
131 CTCGTTTCGAGCCTCGTTTGG
997 ATCTTCTTCT
Statistics
Matches: 519, Mismatches: 32, Indels: 21
0.91 0.06 0.04
Matches are distributed among these distances:
197 169 0.33
198 1 0.00
199 1 0.00
205 1 0.00
206 1 0.00
208 342 0.66
209 1 0.00
210 1 0.00
213 2 0.00
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (202 bp):
TTCGCTTCTCCATATCTCATCAGGAAGACAAATTTGGTACACTTCTCAGTATCTCATCAGGAAGC
TAACCTTTTATTGCTTCAACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTG
CTCGTTTCGAGCCTCGTTTGGGTTTGATTTGGTCTTCTTCTCAGTATCTTGTAGATACCGCATCA
TTTTTAA
Found at i:5159 original size:87 final size:87
Alignment explanation
Indices: 5013--5189 Score: 354
Period size: 87 Copynumber: 2.0 Consensus size: 87
5003 ATTCCAATCT
5013 TCACCTCTTTCTTTTCATCTTCGTGCCCCAGATTTATAACTTCCATTGGGTCCGAATGAGGCAGG
1 TCACCTCTTTCTTTTCATCTTCGTGCCCCAGATTTATAACTTCCATTGGGTCCGAATGAGGCAGG
5078 ATCTGTTTTTCTTCCTGTTCCA
66 ATCTGTTTTTCTTCCTGTTCCA
5100 TCACCTCTTTCTTTTCATCTTCGTGCCCCAGATTTATAACTTCCATTGGGTCCGAATGAGGCAGG
1 TCACCTCTTTCTTTTCATCTTCGTGCCCCAGATTTATAACTTCCATTGGGTCCGAATGAGGCAGG
5165 ATCTGTTTTTCTTCCTGTTCCA
66 ATCTGTTTTTCTTCCTGTTCCA
5187 TCA
1 TCA
5190 TTTTTAAAAG
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 90 1.00
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.40
Consensus pattern (87 bp):
TCACCTCTTTCTTTTCATCTTCGTGCCCCAGATTTATAACTTCCATTGGGTCCGAATGAGGCAGG
ATCTGTTTTTCTTCCTGTTCCA
Found at i:6082 original size:6 final size:6
Alignment explanation
Indices: 6066--6149 Score: 54
Period size: 6 Copynumber: 14.5 Consensus size: 6
6056 TTTTTTTTAA
* *
6066 TAAATTT TAAATT TAAATT TATAA-- TAAATT TAAATT TAAA-C CAAATT
1 TAAA-TT TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT TAAATT
* * *
6113 TAAATT TAGAA-- TAAACT TAATTT TAAA-A TAAATT TAA
1 TAAATT TA-AATT TAAATT TAAATT TAAATT TAAATT TAA
6150 GCTGATTGGG
Statistics
Matches: 60, Mismatches: 9, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
4 4 0.07
5 11 0.18
6 37 0.62
7 8 0.13
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:6095 original size:17 final size:16
Alignment explanation
Indices: 6073--6149 Score: 91
Period size: 17 Copynumber: 4.6 Consensus size: 16
6063 TAATAAATTT
6073 TAAATTTAAATTTATAA
1 TAAATTTAAATTTA-AA
6090 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
*
6106 CCAAATTTAAATTTAGAA
1 -TAAATTTAAATTTA-AA
* *
6124 TAAACTTAATTTTAAAA
1 TAAATTTAAATTT-AAA
6141 TAAATTTAA
1 TAAATTTAA
6150 GCTGATTGGG
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
16 2 0.04
17 47 0.90
18 3 0.06
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:6114 original size:34 final size:34
Alignment explanation
Indices: 6074--6149 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
6064 AATAAATTTT
* * *
6074 AAATTTAAATTTATAATAAATTTAAATTTAAACC
1 AAATTTAAATTTAGAATAAACTTAAATTTAAAAC
* *
6108 AAATTTAAATTTAGAATAAACTTAATTTTAAAAT
1 AAATTTAAATTTAGAATAAACTTAAATTTAAAAC
6142 AAATTTAA
1 AAATTTAA
6150 GCTGATTGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (34 bp):
AAATTTAAATTTAGAATAAACTTAAATTTAAAAC
Found at i:7267 original size:29 final size:29
Alignment explanation
Indices: 7230--7607 Score: 246
Period size: 29 Copynumber: 12.8 Consensus size: 29
7220 GAGGTCCCTA
*
7230 AACTATCCAAAAATTACCATTTTACCCTTG
1 AACT-TCCAAAAATTACCATTTTACCCTCG
*
7260 AACTTCCAAAAA-TCCCATTTTTGACCC-CG
1 AACTTCCAAAAATTACCA-TTTT-ACCCTCG
*
7289 AAACTTCCTAAAATTACCATTTTACCCTCG
1 -AACTTCCAAAAATTACCATTTTACCCTCG
* *
7319 AACTTCCAAAAA-TCCCATTTTTGA-CCTCAA
1 AACTTCCAAAAATTACCA-TTTT-ACCCTC-G
*
7349 AACTTCCTAAAATTACCATTTTACCC-CTG
1 AACTTCCAAAAATTACCATTTTACCCTC-G
* *
7378 AACTTCCAAAAA-TCCCATTTTAACC-CG
1 AACTTCCAAAAATTACCATTTTACCCTCG
* * * *
7405 ATCCTTCCTAAATTTACCATTTTACCCCCG
1 A-ACTTCCAAAAATTACCATTTTACCCTCG
*
7435 AACTTCCAAAAA-TCCCATTTTTGACCC-CG
1 AACTTCCAAAAATTACCA-TTTT-ACCCTCG
** **
7464 AAACTTCTTAAAATTACTGTTTTACCCTCG
1 -AACTTCCAAAAATTACCATTTTACCCTCG
* * *
7494 AACTTCC-GAAAGT-CTCATTTTTGA-CATCG
1 AACTTCCAAAAATTAC-CA-TTTT-ACCCTCG
* *
7523 AAACTTCCAAAAATTACCATTTTATCCTTG
1 -AACTTCCAAAAATTACCATTTTACCCTCG
*
7553 AACTTCC-AAAAGT-CTCATTTTTAACCC-CG
1 AACTTCCAAAAATTAC-CA-TTTT-ACCCTCG
*
7582 ACAGTTCCAAAAAATTACCATTTTAC
1 A-ACTTCC-AAAAATTACCATTTTAC
7608 TCCCGGATGT
Statistics
Matches: 273, Mismatches: 43, Indels: 64
0.72 0.11 0.17
Matches are distributed among these distances:
27 4 0.01
28 43 0.16
29 106 0.39
30 91 0.33
31 20 0.07
32 8 0.03
33 1 0.00
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATTACCATTTTACCCTCG
Found at i:7331 original size:59 final size:59
Alignment explanation
Indices: 7229--7607 Score: 476
Period size: 59 Copynumber: 6.4 Consensus size: 59
7219 GGAGGTCCCT
* *
7229 AAACTATCCAAAAATTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGACCCCG
1 AAACT-TCCTAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* *
7289 AAACTTCCTAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
1 AAACTTCCTAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
*
7348 AAACTTCCTAAAATTACCATTTTACCC-CTGAACTTCCAAAAATCCCA-TTTT-AACCCG
1 AAACTTCCTAAAATTACCATTTTACCCTC-GAACTTCCAAAAATCCCATTTTTGACCCCG
** * *
7405 ATCCTTCCTAAATTTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
1 AAACTTCCTAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* ** * * * **
7464 AAACTTCTTAAAATTACTGTTTTACCCTCGAACTTCCGAAAGTCTCATTTTTGACATCG
1 AAACTTCCTAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * * * *
7523 AAACTTCCAAAAATTACCATTTTATCCTTGAACTTCCAAAAGTCTCATTTTTAACCCCG
1 AAACTTCCTAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
7582 ACAGTTCCAAAAAATTACCATTTTAC
1 AAACTTCC-TAAAATTACCATTTTAC
7608 TCCCGGATGT
Statistics
Matches: 278, Mismatches: 36, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
57 45 0.16
58 10 0.04
59 202 0.73
60 21 0.08
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.32
Consensus pattern (59 bp):
AAACTTCCTAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:7538 original size:175 final size:176
Alignment explanation
Indices: 7243--7579 Score: 532
Period size: 175 Copynumber: 1.9 Consensus size: 176
7233 TATCCAAAAA
**
7243 TTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCTAAAATTACCA
1 TTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCTAAAATTACCA
* *
7308 TTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCAAAACTTCCTAAAATTACCATTTTAC
66 TTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACATCAAAACTTCCAAAAATTACCATTTTAC
7373 CCCTGAACTTCCAAAAATCCCA-TTTTAACCCGATCCTTCCTAAAT
131 CCCTGAACTTCCAAAAATCCCATTTTTAACCCGATCCTTCCTAAAT
* **
7418 TTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCTTAAAATTACTG
1 TTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCTAAAATTACCA
* * * * *
7483 TTTTACCCTCGAACTTCCGAAAGTCTCATTTTTGACATCGAAACTTCCAAAAATTACCATTTTAT
66 TTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACATCAAAACTTCCAAAAATTACCATTTTAC
* * *
7548 CCTTGAACTTCCAAAAGTCTCATTTTTAACCC
131 CCCTGAACTTCCAAAAATCCCATTTTTAACCC
7580 CGACAGTTCC
Statistics
Matches: 146, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
175 137 0.94
176 9 0.06
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (176 bp):
TTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCTAAAATTACCA
TTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACATCAAAACTTCCAAAAATTACCATTTTAC
CCCTGAACTTCCAAAAATCCCATTTTTAACCCGATCCTTCCTAAAT
Found at i:8087 original size:96 final size:96
Alignment explanation
Indices: 7974--8147 Score: 235
Period size: 96 Copynumber: 1.8 Consensus size: 96
7964 CAATATCCTT
* * **
7974 TTATTTCGAGTTTTGAAA-ATTTGTGCCTTAACTTACTAGGTGCAATTTTTCCTCAAATCAAAAT
1 TTATTTCGAGTTCTGAAATA-TTGCGCCTTAACTTACTAGGTGCAACCTTTCCTCAAATCAAAAT
*
8038 AATCGAATACCCTTAATCGAGGCAATGTTTCC
65 AATCAAATACCCTTAATCGAGGCAATGTTTCC
* * *
8070 TTATCTTCGA-TTCTGAAATATTGCGCCTTAACTTCCTAGGTGCAACCTTTCTTCAAATCAAGAT
1 TTAT-TTCGAGTTCTGAAATATTGCGCCTTAACTTACTAGGTGCAACCTTTCCTCAAATCAAAAT
*
8134 AATCAAATATCCTT
65 AATCAAATACCCTT
8148 TTCCCAAAGA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
96 61 0.91
97 6 0.09
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (96 bp):
TTATTTCGAGTTCTGAAATATTGCGCCTTAACTTACTAGGTGCAACCTTTCCTCAAATCAAAATA
ATCAAATACCCTTAATCGAGGCAATGTTTCC
Found at i:9602 original size:65 final size:65
Alignment explanation
Indices: 9498--9627 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
9488 GTCTCCATCC
9498 CCACAAATTCTCTTATTTTACCTTATATCTCATTTCTTTAATAAAAATTTGATTCACACAATTCT
1 CCACAAATTCTCTTATTTTACCTTATATCTCATTTCTTTAATAAAAATTTGATTCACACAATTCT
9563 CCACAAATTCTCTTATTTTACCTTATATCTCATTTCTTTAATAAAAATTTGATTCACACAATTCT
1 CCACAAATTCTCTTATTTTACCTTATATCTCATTTCTTTAATAAAAATTTGATTCACACAATTCT
9628 TACACTATTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.32, C:0.22, G:0.02, T:0.45
Consensus pattern (65 bp):
CCACAAATTCTCTTATTTTACCTTATATCTCATTTCTTTAATAAAAATTTGATTCACACAATTCT
Done.