Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000726.1 Kokia drynarioides strain JFW-HI SEQ_111746, 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: 2107
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Found at i:382 original size:30 final size:29
Alignment explanation
Indices: 348--848 Score: 320
Period size: 30 Copynumber: 17.1 Consensus size: 29
338 TAAATTACTA
* *
348 TTTTACCCTCAAAATTTCCAAAAATCCCAT
1 TTTTACCC-CGAAACTTCCAAAAATCCCAT
* * * * *
378 TTTTAACCTCGAACCTTCCAAAATTACTA-
1 TTTT-ACCCCGAAACTTCCAAAAATCCCAT
407 TTTTACCCTCG-AACTTCCAAAAAATCCCAT
1 TTTTACCC-CGAAACTTCC-AAAAATCCCAT
* * *
437 TTTTGACCCCGAACCTTCTAAAAATTACCA-
1 TTTT-ACCCCGAAACTTCCAAAAA-TCCCAT
467 TTTTACCCCCG-AACTTCCAAAAATCCCAT
1 TTTTA-CCCCGAAACTTCCAAAAATCCCAT
* * * *
496 TTTTGAGCCCGAACCTTCCAAAATTACCA-
1 TTTT-ACCCCGAAACTTCCAAAAATCCCAT
*
525 TTTTACCCCCAAACTTCCAAAAATCCCAT
1 TTTTACCCCGAAACTTCCAAAAATCCCAT
* * * *
554 TTTCAACCCCGAACCTTCTAAAAATTACCA-
1 TTT-TACCCCGAAACTTCCAAAAA-TCCCAT
* *
584 TTTTACCCTCG-AATTTCCAAAAATCTCAT
1 TTTTACCC-CGAAACTTCCAAAAATCCCAT
* * *
613 TTTTGACCCTG-AACTTTCCAAAATTACCA-
1 TTTT-ACCCCGAAAC-TTCCAAAAATCCCAT
642 TTTTACCCCCG--A-TTCCAAAAATCCCAT
1 TTTTA-CCCCGAAACTTCCAAAAATCCCAT
* * * *
669 TTTTGACCCCGAACCTTCTAAAAATTACC-G
1 TTTT-ACCCCGAAACTTCCAAAAA-TCCCAT
*
699 TTTCATCCCCG-AACTTCC-AAAATCCCAT
1 TTTTA-CCCCGAAACTTCCAAAAATCCCAT
* *
727 TTTTGA-CCCTAAACTTTCCAAAAATTACCA-
1 TTTT-ACCCCGAAAC-TTCCAAAAA-TCCCAT
*
757 TTTTACCCCCAAACTTCCAAAAATCCCAT
1 TTTTACCCCGAAACTTCCAAAAATCCCAT
* * * *
786 TTTTGACCTCGAATCTTCTAAAAATTACCA-
1 TTTT-ACCCCGAAACTTCCAAAAA-TCCCAT
* *
816 TTTTACCCCCG-AACTTCTAAAAATCCTAT
1 TTTTA-CCCCGAAACTTCCAAAAATCCCAT
845 TTTT
1 TTTT
849 GATTATGAAC
Statistics
Matches: 364, Mismatches: 69, Indels: 77
0.71 0.14 0.15
Matches are distributed among these distances:
26 12 0.03
27 15 0.04
28 55 0.15
29 108 0.30
30 143 0.39
31 31 0.09
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.32
Consensus pattern (29 bp):
TTTTACCCCGAAACTTCCAAAAATCCCAT
Found at i:543 original size:58 final size:57
Alignment explanation
Indices: 339--877 Score: 625
Period size: 59 Copynumber: 9.2 Consensus size: 57
329 TTTAATCCTT
* ** * *
339 AAATTACTATTTTACCCTCAAAATTTCCAAAAATCCCATTTTTAACCTCGAACCTTCCA
1 AAATTACCATTTTACCC-CCGAACTTCCAAAAATCCCATTTTTGACC-CGAACCTTCCA
* * *
398 AAATTACTATTTTACCCTCGAACTTCCAAAAAATCCCATTTTTGACCCCGAACCTTCTAA
1 AAATTACCATTTTACCCCCGAACTTCC-AAAAATCCCATTTTTGA-CCCGAACCTTC-CA
458 AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGAGCCCGAACCTTCCA
1 AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCCGAACCTTCCA
* ** *
516 AAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTCAACCCCGAACCTTCTAA
1 AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCCGAACCTTC-CA
* * * *
575 AAATTACCATTTTACCCTCGAATTTCCAAAAATCTCATTTTTGACCCTGAACTTTCCA
1 AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCC-GAACCTTCCA
*
633 AAATTACCATTTTACCCCCG-A-TTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAA
1 AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCCGAACCTTC-CA
* * * * *
690 AAATTACCGTTTCATCCCCGAACTTCC-AAAATCCCATTTTTGACCCTAAACTTTCCAA
1 AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCC-GAACCTTCC-A
* * *
748 AAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAATCTTCTAA
1 AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACC-CGAACCTTC-CA
* * *** *
807 AAATTACCATTTTACCCCCGAACTTCTAAAAATCCTATTTTTGATTATGAACATTCCA
1 AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCCGAACCTTCCA
*
865 AAACTACCATTTT
1 AAATTACCATTTT
878 GCCACTCCGT
Statistics
Matches: 414, Mismatches: 51, Indels: 31
0.83 0.10 0.06
Matches are distributed among these distances:
56 27 0.07
57 25 0.06
58 142 0.34
59 191 0.46
60 29 0.07
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (57 bp):
AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCGAACCTTCCA
Found at i:608 original size:117 final size:116
Alignment explanation
Indices: 339--877 Score: 724
Period size: 117 Copynumber: 4.6 Consensus size: 116
329 TTTAATCCTT
* ** * *
339 AAATTACTATTTTACCCTCAAAATTTCCAAAAATCCCATTTTTAACCTCGAACCTTCCAAAATTA
1 AAATTACCATTTTACCC-CCGAACTTCCAAAAATCCCATTTTTGACC-CGAACCTTCCAAAATTA
* * *
404 CTATTTTACCCTCGAACTTCCAAAAAATCCCATTTTTGACCCCGAACCTTCTAA
64 CCATTTTACCCCCAAACTTCC-AAAAATCCCATTTTTGACCCCGAACCTTCTAA
458 AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGAGCCCGAACCTTCCAAAATTAC
1 AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCCGAACCTTCCAAAATTAC
**
523 CATTTTACCCCCAAACTTCCAAAAATCCCATTTTCAACCCCGAACCTTCTAA
65 CATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAA
* * * *
575 AAATTACCATTTTACCCTCGAATTTCCAAAAATCTCATTTTTGACCCTGAACTTTCCAAAATTAC
1 AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCC-GAACCTTCCAAAATTAC
*
640 CATTTTACCCCC-GA-TTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAA
65 CATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAA
* * * * *
690 AAATTACCGTTTCATCCCCGAACTTCC-AAAATCCCATTTTTGACCCTAAACTTTCCAAAAATTA
1 AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCC-GAACCTTCC-AAAATTA
* *
754 CCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAATCTTCTAA
64 CCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAA
* * *** * *
807 AAATTACCATTTTACCCCCGAACTTCTAAAAATCCTATTTTTGATTATGAACATTCCAAAACTAC
1 AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCCGAACCTTCCAAAATTAC
872 CATTTT
65 CATTTT
878 GCCACTCCGT
Statistics
Matches: 375, Mismatches: 38, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
114 27 0.07
115 76 0.20
116 5 0.01
117 169 0.45
118 80 0.21
119 18 0.05
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (116 bp):
AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCGAACCTTCCAAAATTACC
ATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAA
Found at i:1243 original size:96 final size:96
Alignment explanation
Indices: 1116--1306 Score: 246
Period size: 96 Copynumber: 2.0 Consensus size: 96
1106 AAACTTTAAT
* **
1116 ATCGAGGTAATATTCTTTTATTTCGAGTTCCGAAA-ATTTACGCCTTAACTCACTAGGTGCAATT
1 ATCGAGGTAATATTCTTTTATTTCGAGTTCCGAAATA-TTACGCCTTAACTCACTAGGTACAACC
*
1180 TTTCTTCAAATCGA-AGTAATCGAATACCCTTA
65 TTTCTTCAAATCGAGA-TAATCAAATACCCTTA
* * *
1212 ATCGAGGTAATGTT-TTCTTATCTTCGA-TTCCGAAATATTGCGCCTTAACTTACTAGGTACAAC
1 ATCGAGGTAATATTCTT-TTAT-TTCGAGTTCCGAAATATTACGCCTTAACTCACTAGGTACAAC
*
1275 CTTTCTTCAAATCGAGATAATCAAATATCCTT
64 CTTTCTTCAAATCGAGATAATCAAATACCCTT
1307 CTCGTAAAAG
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
95 2 0.02
96 74 0.89
97 7 0.08
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (96 bp):
ATCGAGGTAATATTCTTTTATTTCGAGTTCCGAAATATTACGCCTTAACTCACTAGGTACAACCT
TTCTTCAAATCGAGATAATCAAATACCCTTA
Done.