Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013004.1 Kokia drynarioides strain JFW-HI SEQ_128022, 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, 634
Length: 1058
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.36
Found at i:257 original size:29 final size:28
Alignment explanation
Indices: 225--670 Score: 300
Period size: 29 Copynumber: 15.3 Consensus size: 28
215 GTCCCTAAAC
225 CTTCCAAAAATTACCATTTTACCCTCGAA
1 CTTCCAAAAATTACCATTTTACCC-CGAA
*
254 CTTCCAAAAA-TCCCATTTTTTACCCCGAA
1 CTTCCAAAAATTACCA--TTTTACCCCGAA
*
283 TCTTCCAAAAATTACTATTTTACCCTCGAA
1 -CTTCCAAAAATTACCATTTTACCC-CGAA
* **
313 CTTCCAAAAA-TCCCATTTTTGACCCTAAA
1 CTTCCAAAAATTACCA-TTTT-ACCCCGAA
*
342 TCTTCC-AAAATTACTATTTTACCCCGAA
1 -CTTCCAAAAATTACCATTTTACCCCGAA
*
370 CTTCCAAAAA-TCCCATTTTCGACCCCGAA
1 CTTCCAAAAATTACCATTTT--ACCCCGAA
* *
399 TCTTCCAAAAATTACTATTTTACCCCTAAA
1 -CTTCCAAAAATTACCATTTTACCCC-GAA
* *
429 CTTCCAAAAATCA-CATTTTTGATCCCCAAA
1 CTTCCAAAAATTACCA-TTTT-A-CCCCGAA
* * * *
459 CTCCCAAAAA--CCCAGTTTTTGATCTCGAA
1 CTTCCAAAAATTACCA--TTTT-ACCCCGAA
* *
488 CCTTCC-AAAATTACTATTTTACCCCTAAA
1 -CTTCCAAAAATTACCATTTTACCCC-GAA
*
517 CTTCCAAAAA-TCCCATTTTTAACCCCGAA
1 CTTCCAAAAATTACCA-TTTT-ACCCCGAA
** *
546 CCTTCTTAAAATTACCATTTTACCCCCAAA
1 -CTTCCAAAAATTACCATTTTA-CCCCGAA
* * **
576 CTTCCAATAA-TCCCATTTTTTACCTTGAA
1 CTTCCAAAAATTACCA--TTTTACCCCGAA
* * *
605 TCTTCCAAAAATTACTATTTTTCCTCGAA
1 -CTTCCAAAAATTACCATTTTACCCCGAA
* *
634 TTTCCAAAAATTACAATTTTACCCTCGAA
1 CTTCCAAAAATTACCATTTTACCC-CGAA
663 CTTCCAAA
1 CTTCCAAA
671 GATCCTATTT
Statistics
Matches: 329, Mismatches: 53, Indels: 70
0.73 0.12 0.15
Matches are distributed among these distances:
27 12 0.04
28 53 0.16
29 134 0.41
30 107 0.33
31 23 0.07
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.33
Consensus pattern (28 bp):
CTTCCAAAAATTACCATTTTACCCCGAA
Found at i:317 original size:59 final size:59
Alignment explanation
Indices: 225--682 Score: 354
Period size: 59 Copynumber: 7.8 Consensus size: 59
215 GTCCCTAAAC
*
225 CTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAAT
1 CTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAAT
* **
284 CTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCTAAAT
1 CTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAAT
**
343 CTTCC-AAAATTACTATTTTACCC-CGAACTTCCAAAAATCCCATTTTCGACCCCGAAT
1 CTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAAT
* * * *
400 CTTCCAAAAATTACTATTTTACCC-CTAAACTTCCAAAAATCACATTTTTGATCCCC-AAA
1 CTTCCAAAAATTACTATTTTACCCTC-GAACTTCCAAAAATCCCATTTTTTA-CCCCGAAT
* ** * * ** * * *
459 CTCCCAAAAACCCAGT-TTTTGA-TCTCGAACCTTCC-AAAATTAC-TATTTTACCCCTAAA
1 CTTCCAAAAA-TTACTATTTT-ACCCTCGAA-CTTCCAAAAATCCCATTTTTTACCCCGAAT
* * * * * * *
517 CTTCCAAAAA-TCCCATTTTTAACCC-CGAACCTTCTTAAAATTACCA--TTTTACCCCCAAA
1 CTTCCAAAAATTACTA-TTTT-ACCCTCGAA-CTTC-CAAAAATCCCATTTTTTACCCCGAAT
* ** * * ** *
576 CTTCCAATAATCCCATTTTTTA-CCTTGAATCTTCCAAAAATTAC-TATTTTT-CCTCGAAT
1 CTTCCAAAAATTAC-TATTTTACCCTCGAA-CTTCCAAAAATCCCAT-TTTTTACCCCGAAT
* * *
635 -TTCCAAAAATTACAATTTTACCCTCGAACTTCCAAAGATCCTATTTTT
1 CTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTT
683 GATTCCGAAC
Statistics
Matches: 322, Mismatches: 55, Indels: 46
0.76 0.13 0.11
Matches are distributed among these distances:
57 59 0.18
58 93 0.29
59 142 0.44
60 28 0.09
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (59 bp):
CTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAAT
Found at i:382 original size:116 final size:117
Alignment explanation
Indices: 216--467 Score: 384
Period size: 116 Copynumber: 2.1 Consensus size: 117
206 ACCCCGGAGG
**
216 TCCCTAAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCG
1 TCCCTAAA-CTTCC-AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTCGACCCCG
* *
281 AATCTTCCAAAAATTACTATTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTGA
64 AATCTTCCAAAAATTACTATTTTACCCCT-AAACTTCCAAAAATCACATTTTTGA
*
335 -CCCTAAATCTTCCAAAATTACTATTTTACCC-CGAACTTCCAAAAATCCCATTTTCGACCCCGA
1 TCCCTAAA-CTTCCAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTCGACCCCGA
398 ATCTTCCAAAAATTACTATTTTACCCCTAAACTTCCAAAAATCACATTTTTGA
65 ATCTTCCAAAAATTACTATTTTACCCCTAAACTTCCAAAAATCACATTTTTGA
* *
451 TCCCCAAACTCCCAAAA
1 TCCCTAAACTTCCAAAA
468 ACCCAGTTTT
Statistics
Matches: 123, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
116 84 0.68
117 27 0.22
118 12 0.10
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (117 bp):
TCCCTAAACTTCCAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTCGACCCCGAA
TCTTCCAAAAATTACTATTTTACCCCTAAACTTCCAAAAATCACATTTTTGA
Found at i:682 original size:29 final size:28
Alignment explanation
Indices: 225--701 Score: 295
Period size: 30 Copynumber: 16.3 Consensus size: 28
215 GTCCCTAAAC
*
225 CTTCCAAAAATTACCA-TTTTACCCTCGAA
1 CTTCCAAAAA-TCCCATTTTTACCC-CGAA
254 CTTCCAAAAATCCCATTTTTTACCCCGAA
1 CTTCCAAAAATCCCA-TTTTTACCCCGAA
**
283 TCTTCCAAAAATTAC-TATTTTACCCTCGAA
1 -CTTCCAAAAATCCCAT-TTTTACCC-CGAA
**
313 CTTCCAAAAATCCCATTTTTGACCCTAAA
1 CTTCCAAAAATCCCATTTTT-ACCCCGAA
* * *
342 TCTTCCAAAATTACTA-TTTTACCCCGAA
1 -CTTCCAAAAATCCCATTTTTACCCCGAA
*
370 CTTCCAAAAATCCCATTTTCGACCCCGAA
1 CTTCCAAAAATCCCATTTT-TACCCCGAA
** *
399 TCTTCCAAAAATTAC-TATTTTACCCCTAAA
1 -CTTCCAAAAATCCCAT-TTTTACCCC-GAA
* *
429 CTTCCAAAAATCACATTTTTGATCCCCAAA
1 CTTCCAAAAATCCCATTTTT-A-CCCCGAA
* * *
459 CTCCCAAAAA-CCCAGTTTTTGATCTCGAA
1 CTTCCAAAAATCCCA-TTTTT-ACCCCGAA
* * * *
488 CCTTCCAAAATTACTA-TTTTACCCCTAAA
1 -CTTCCAAAAATCCCATTTTTACCCC-GAA
517 CTTCCAAAAATCCCATTTTTAACCCCGAA
1 CTTCCAAAAATCCCATTTTT-ACCCCGAA
* * * *
546 CCTTCTTAAAATTACCA-TTTTACCCCCAAA
1 -CTTC-CAAAAATCCCATTTTTA-CCCCGAA
* **
576 CTTCCAATAATCCCATTTTTTACCTTGAA
1 CTTCCAAAAATCCCA-TTTTTACCCCGAA
* * *
605 TCTTCCAAAAATTACTATTTTT-CCTCGAA
1 -CTTCCAAAAA-TCCCATTTTTACCCCGAA
* ** *
634 TTTCCAAAAATTACAATTTTACCCTCGAA
1 CTTCCAAAAATCCCATTTTTACCC-CGAA
* * **
663 CTTCCAAAGATCCTATTTTTGATTCCGAA
1 CTTCCAAAAATCCCATTTTT-ACCCCGAA
692 CATTCCAAAA
1 C-TTCCAAAA
702 CTACCATTCT
Statistics
Matches: 348, Mismatches: 67, Indels: 65
0.73 0.14 0.14
Matches are distributed among these distances:
27 18 0.05
28 47 0.14
29 132 0.38
30 134 0.39
31 17 0.05
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (28 bp):
CTTCCAAAAATCCCATTTTTACCCCGAA
Done.