Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010092.1 Kokia drynarioides strain JFW-HI SEQ_124873, 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, 672
Length: 1121
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.35
Found at i:158 original size:29 final size:29
Alignment explanation
Indices: 115--738 Score: 472
Period size: 29 Copynumber: 21.5 Consensus size: 29
105 GGAGGTCCTT
115 GAACTTTCCAAAAATCACCATTTTACCCCC
1 GAAC-TTCCAAAAATCACCATTTTACCCCC
145 GAACTTCCAAAAATC-CCATTTTTGA-CCCC
1 GAACTTCCAAAAATCACCA-TTTT-ACCCCC
* *
174 AAACTTTCC-AAAATTACCATTTTACCCCC
1 GAAC-TTCCAAAAATCACCATTTTACCCCC
* *
203 AAACTTCCAAAAATC-CCATTTT-----T
1 GAACTTCCAAAAATCACCATTTTACCCCC
* * *
226 G-AC-CCCAAAAATTACCATTTTACCCTC
1 GAACTTCCAAAAATCACCATTTTACCCCC
253 GAACTTCCAAAAATC-CCATTTTTGA-CCCC
1 GAACTTCCAAAAATCACCA-TTTT-ACCCCC
* * *
282 GAACCTTCTAAAAATTACCATTTTACCCTC
1 GAA-CTTCCAAAAATCACCATTTTACCCCC
*
312 GAACTTCCAAAAATC-TCATTTTTGA-CCCC
1 GAACTTCCAAAAATCACCA-TTTT-ACCCCC
* * ** *
341 GAACATTCTAAAAATTACCATTTTGTCCTC
1 GAAC-TTCCAAAAATCACCATTTTACCCCC
371 GAACTTCCAAAAATC-CCATTTTTGA-CCCC
1 GAACTTCCAAAAATCACCA-TTTT-ACCCCC
* *
400 GAACTTCCAAAAATTACCATTTTACCCCA
1 GAACTTCCAAAAATCACCATTTTACCCCC
*
429 AAACTTCCAAAAATC-CCATTTTTGA-CCCC
1 GAACTTCCAAAAATCACCA-TTTT-ACCCCC
* * * *
458 TAACCTTCTAAAAATTACCATTTTATCCCC
1 GAA-CTTCCAAAAATCACCATTTTACCCCC
488 GAACTTCCAAAAATC-CCATTTTTGA-CCCC
1 GAACTTCCAAAAATCACCA-TTTT-ACCCCC
* * *
517 AAACTTTCCAAAAATTACCATTTTACCCTC
1 GAAC-TTCCAAAAATCACCATTTTACCCCC
* * *
547 AAACTTCCAAAAATC-CCATTTTTAACCTCG
1 GAACTTCCAAAAATCACCA-TTTT-ACCCCC
* * * *
577 GATCTTCTAAAAATTACCATTTTACCCCT
1 GAACTTCCAAAAATCACCATTTTACCCCC
*
606 GAACTTCCAAAAATC-CCATTTTTTA-CCTC
1 GAACTTCCAAAAATCACCA--TTTTACCCCC
* *
635 GAATCTTCTAAAAATTACCATTTTACCCCC
1 GAA-CTTCCAAAAATCACCATTTTACCCCC
*
665 GAACTTCCAAAAATC-CCATTTTTGA-CCTC
1 GAACTTCCAAAAATCACCA-TTTT-ACCCCC
* * *
694 GAATCTTCTAAAAATTACCATTTTACCCTC
1 GAA-CTTCCAAAAATCACCATTTTACCCCC
724 GAACTTCCAAAAATC
1 GAACTTCCAAAAATC
739 CTATTTTTGA
Statistics
Matches: 477, Mismatches: 66, Indels: 103
0.74 0.10 0.16
Matches are distributed among these distances:
21 8 0.02
22 9 0.02
27 1 0.00
28 41 0.09
29 237 0.50
30 161 0.34
31 20 0.04
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (29 bp):
GAACTTCCAAAAATCACCATTTTACCCCC
Found at i:300 original size:59 final size:59
Alignment explanation
Indices: 232--748 Score: 781
Period size: 59 Copynumber: 8.8 Consensus size: 59
222 TTTTGACCCC
232 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
* *
291 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCGAACATTCT
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
** *
350 AAAAATTACCATTTTGTCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAA-CTTCC
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
* *
408 AAAAATTACCATTTTACCC-CAAAACTTCCAAAAATCCCATTTTTGACCCCTAACCTTCT
1 AAAAATTACCATTTTACCCTC-GAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
* * *
467 AAAAATTACCATTTTATCCC-CGAACTTCCAAAAATCCCATTTTTGACCCCAAACTTTCC
1 AAAAATTACCATTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
* * * * *
526 AAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCTCGGATCTTCT
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
* * *
585 AAAAATTACCATTTTACCC-CTGAACTTCCAAAAATCCCATTTTTTACCTCGAATCTTCT
1 AAAAATTACCATTTTACCCTC-GAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
* * *
644 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAATCTTCT
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
*
703 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCTATTTTTGA
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
749 TTCTGAACAT
Statistics
Matches: 422, Mismatches: 30, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
57 1 0.00
58 54 0.13
59 362 0.86
60 5 0.01
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.32
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
Done.