Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013407.1 Kokia drynarioides strain JFW-HI SEQ_128432, 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: 3403
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Found at i:568 original size:29 final size:28
Alignment explanation
Indices: 528--792 Score: 218
Period size: 29 Copynumber: 9.0 Consensus size: 28
518 AAGGTCCCTA
*
528 AACTATCCAAAAATTACCCTTTTACTCCCG
1 AACT-TCCAAAAATTACCATTTTAC-CCCG
558 AACTTCCAAAAA-T-CTCATTTTTGACCCCG
1 AACTTCCAAAAATTAC-CA-TTTT-ACCCCG
587 AACCTTCCAAAAATTACCATTTTACCCCCG
1 AA-CTTCCAAAAATTACCATTTTA-CCCCG
* * *
617 AACTTTCAAAAA-TCCCATTTTTGACCTCG
1 AACTTCCAAAAATTACCA-TTTT-ACCCCG
*
646 AACCTTCAAAAAATTACCATTTTACCCCCG
1 AA-CTTCCAAAAATTACCATTTTA-CCCCG
* * *
676 AACTTCCAAAAA-TCCCATTTTTTACCTCA
1 AACTTCCAAAAATTACCA--TTTTACCCCG
705 AACCTTCCAAAAATTACCATTTTACCCCCG
1 AA-CTTCCAAAAATTACCATTTTA-CCCCG
*
735 AACTTCCAAAAA-TCCCATTTTTGA-CCCG
1 AACTTCCAAAAATTACCA-TTTT-ACCCCG
* *
763 AACCTTCTAAAAATTACTATTTTACTCCCG
1 AA-CTTCCAAAAATTACCATTTTAC-CCCG
793 GATGTCCGAA
Statistics
Matches: 193, Mismatches: 19, Indels: 46
0.75 0.07 0.18
Matches are distributed among these distances:
27 1 0.01
28 21 0.11
29 85 0.44
30 74 0.38
31 11 0.06
32 1 0.01
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (28 bp):
AACTTCCAAAAATTACCATTTTACCCCG
Found at i:627 original size:59 final size:59
Alignment explanation
Indices: 533--792 Score: 405
Period size: 59 Copynumber: 4.4 Consensus size: 59
523 CCCTAAACTA
* * *
533 TCCAAAAATTACCCTTTTACTCCCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* *
592 TCCAAAAATTACCATTTTACCCCCGAACTTTCAAAAATCCCATTTTTGACCTCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* * * *
651 TCAAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCTCAAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
710 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* * *
768 TCTAAAAATTACTATTTTACTCCCG
1 TCCAAAAATTACCATTTTACCCCCG
793 GATGTCCGAA
Statistics
Matches: 185, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
58 29 0.16
59 156 0.84
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
Done.