Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013327.1 Corchorus capsularis cultivar CVL-1 contig13348, 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: 7842
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Found at i:493 original size:2 final size:2
Alignment explanation
Indices: 486--520 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
476 TTGAACAAGA
486 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
521 GATAGTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1236 original size:9 final size:9
Alignment explanation
Indices: 1219--1250 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1209 GTTATGGGCT
*
1219 TATGGCTTA
1 TATGACTTA
1228 TATGACTTA
1 TATGACTTA
1237 TATGACTTA
1 TATGACTTA
1246 TATGA
1 TATGA
1251 GTAAAAGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (9 bp):
TATGACTTA
Found at i:7476 original size:7 final size:7
Alignment explanation
Indices: 7464--7842 Score: 599
Period size: 7 Copynumber: 55.9 Consensus size: 7
7454 ATATCAAAGA
7464 AGGGTTT
1 AGGGTTT
7471 AGGG-TT
1 AGGGTTT
7477 AGGGTTT
1 AGGGTTT
7484 AGGGTTT
1 AGGGTTT
*
7491 -GGGGTT
1 AGGGTTT
*
7497 AGGGGTT
1 AGGGTTT
7504 AGGGTTT
1 AGGGTTT
7511 A-GGTTT
1 AGGGTTT
7517 AGGGTTT
1 AGGGTTT
7524 AGGGGTTT
1 A-GGGTTT
7532 AGGGGTTT
1 A-GGGTTT
7540 AGGG-TT
1 AGGGTTT
7546 AGGGTTT
1 AGGGTTT
7553 AGGGTTT
1 AGGGTTT
7560 AGGGTTT
1 AGGGTTT
7567 AGGGGTTT
1 A-GGGTTT
7575 AGGG-TT
1 AGGGTTT
*
7581 AGGGGTT
1 AGGGTTT
7588 AGGGTTT
1 AGGGTTT
7595 AGGG-TT
1 AGGGTTT
7601 AGGGTTT
1 AGGGTTT
7608 AGGGTTT
1 AGGGTTT
7615 AGGG-TT
1 AGGGTTT
7621 AGGG-TT
1 AGGGTTT
7627 AGGGTTT
1 AGGGTTT
7634 AGGG-TT
1 AGGGTTT
7640 AGGG-TT
1 AGGGTTT
7646 AGGGTTT
1 AGGGTTT
7653 AGGGTTT
1 AGGGTTT
7660 AGGGTTT
1 AGGGTTT
7667 AGGGTTT
1 AGGGTTT
7674 AGGGTTT
1 AGGGTTT
7681 AGGG-TT
1 AGGGTTT
7687 AGGG-TT
1 AGGGTTT
7693 AGGGTTT
1 AGGGTTT
7700 AGGGTTT
1 AGGGTTT
7707 AGGG-TT
1 AGGGTTT
7713 AGGG-TT
1 AGGGTTT
7719 AGGGTTT
1 AGGGTTT
7726 AGGGTTT
1 AGGGTTT
7733 AGGGTTT
1 AGGGTTT
7740 AGGGTTT
1 AGGGTTT
7747 AGGGTTT
1 AGGGTTT
7754 AGGGTTT
1 AGGGTTT
7761 AGGG-TT
1 AGGGTTT
7767 AGGGTTT
1 AGGGTTT
7774 AGGGTTT
1 AGGGTTT
7781 AGGGTTT
1 AGGGTTT
7788 AGGGTTT
1 AGGGTTT
7795 AGGGTTT
1 AGGGTTT
7802 AGGGTTT
1 AGGGTTT
7809 AGGGTTT
1 AGGGTTT
7816 AGGGTTT
1 AGGGTTT
7823 AGGGTTT
1 AGGGTTT
7830 AGGGTTT
1 AGGGTTT
7837 AGGGTT
1 AGGGTT
Statistics
Matches: 356, Mismatches: 3, Indels: 26
0.92 0.01 0.07
Matches are distributed among these distances:
6 89 0.25
7 245 0.69
8 22 0.06
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.40
Consensus pattern (7 bp):
AGGGTTT
Done.