Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010045.1 Kokia drynarioides strain JFW-HI SEQ_124813, 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: 3762
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.30
Warning! 166 characters in sequence are not A, C, G, or T
Found at i:1341 original size:59 final size:59
Alignment explanation
Indices: 1249--1786 Score: 778
Period size: 59 Copynumber: 9.2 Consensus size: 59
1239 GTCCCTAAAC
* *
1249 CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
*
1308 CTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
* * *
1367 CTTCCAAAAATTACCATTTTA-CCCCGAACTTCCATAAATCTCATTTTTGACCCCGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
*
1425 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
* *
1484 ATTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTTACCCCGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTTGACCCCGAAT
* * * *
1544 CTTCCAAAAACTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGATCCCGAAC
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
* * *
1603 CTTCC-AAAATTACTATTTTACCCCTGAACTTCCAAAAATCCCATTTTTAACCCCGAAC
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
** * * * * **
1661 CTTCTTAAAATTACCATTTTACCGCCAAACTTCCAACAATCCCATTTTTGACCTTGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
* * **
1720 CTTCCAAAAATTACTA-TTTACCCTCGAACTTCCAAAAATCCTATTTTTGATTCCGAA-
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
1777 CATTCCAAAA
1 C-TTCCAAAA
1787 CTACCATTCT
Statistics
Matches: 428, Mismatches: 47, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
57 1 0.00
58 146 0.34
59 227 0.53
60 54 0.13
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (59 bp):
CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
Found at i:1456 original size:117 final size:117
Alignment explanation
Indices: 1249--1786 Score: 767
Period size: 117 Copynumber: 4.6 Consensus size: 117
1239 GTCCCTAAAC
* *
1249 CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAATCTTCCA
1 CTTCCAAAAATTACTATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAATCTTCCA
* *
1314 AAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
65 AAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAT
* * *
1367 CTTCCAAAAATTACCATTTTACCCCGAACTTCCATAAATCTCATTTTTGACCCCGAATCTTCCAA
1 CTTCCAAAAATTACTATTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAATCTTCCAA
* *
1432 AAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAT
66 AAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAT
* *
1484 ATTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTTACCCCGAATCTTCC
1 CTTCCAAAAATTACTATTTTA-CCCCGAACTTCCAAAAATCCCA-TTTTTGACCCCGAATCTTCC
* * *
1549 AAAAACTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGATCCCGAAC
64 AAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAT
* * **
1603 CTTCC-AAAATTACTATTTTACCCCTGAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCTT
1 CTTCCAAAAATTACTATTTTACCCC-GAACTTCCAAAAATCCCATTTTTGACCCCGAATCTTCCA
* * * **
1667 AAAATTACCATTTTACCGCCAAACTTCCAACAATCCCATTTTTGACCTTGAAT
65 AAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAT
* **
1720 CTTCCAAAAATTACTA-TTTACCCTCGAACTTCCAAAAATCCTATTTTTGATTCCGAA-CATTCC
1 CTTCCAAAAATTACTATTTTACCC-CGAACTTCCAAAAATCCCATTTTTGACCCCGAATC-TTCC
1783 AAAA
64 AAAA
1787 CTACCATTCT
Statistics
Matches: 380, Mismatches: 34, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
116 1 0.00
117 222 0.58
118 85 0.22
119 72 0.19
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (117 bp):
CTTCCAAAAATTACTATTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAATCTTCCAA
AAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAT
Done.