Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006033.1 Kokia drynarioides strain JFW-HI SEQ_120488, 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: 2620
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Found at i:882 original size:7 final size:7
Alignment explanation
Indices: 870--895 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
860 AATAAATAAA
870 TAAATTT
1 TAAATTT
877 TAAATTT
1 TAAATTT
884 TAAATTT
1 TAAATTT
891 TAAAT
1 TAAAT
896 GTCCAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TAAATTT
Found at i:2514 original size:30 final size:30
Alignment explanation
Indices: 2489--2620 Score: 178
Period size: 30 Copynumber: 4.5 Consensus size: 30
2479 TAAACTATCC
*
2489 AAAAATCACATTTTGACCCTCAAACTTCTT
1 AAAAATTACATTTTGACCCTCAAACTTCTT
* *
2519 AAAAATTATATTTTTACCCTCAAACTTCTT
1 AAAAATTACATTTTGACCCTCAAACTTCTT
* * *
2549 GAAAATTACATTTTTACCCTCAAACTTCTC
1 AAAAATTACATTTTGACCCTCAAACTTCTT
* *
2579 AAAAATTACATTTTG-CCCTTAAACTGC-T
1 AAAAATTACATTTTGACCCTCAAACTTCTT
2607 AAAAATTACATTTT
1 AAAAATTACATTTT
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
28 14 0.15
29 10 0.11
30 67 0.74
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCTCAAACTTCTT
Done.