Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001389.1 Corchorus capsularis cultivar CVL-1 contig01389, 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: 7539
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Found at i:2646 original size:31 final size:31
Alignment explanation
Indices: 2581--2679 Score: 123
Period size: 31 Copynumber: 3.3 Consensus size: 31
2571 ACACATTTTG
* * *
2581 CCCCCTGAAC-TT-CAAATTACGACAATTTG
1 CCCCATGAACTTTCCAAATTAGGACAATTTA
* *
2610 TCCCATGAA-TTTCCAAATTCAGGATAATTTA
1 CCCCATGAACTTTCCAAATT-AGGACAATTTA
2641 CCCCATGAACTTTCCAAATTAGGACAATTTA
1 CCCCATGAACTTTCCAAATTAGGACAATTTA
2672 CCCCATGA
1 CCCCATGA
2680 TGTGTGGGGC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
29 9 0.15
30 6 0.10
31 34 0.58
32 10 0.17
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.29
Consensus pattern (31 bp):
CCCCATGAACTTTCCAAATTAGGACAATTTA
Found at i:4300 original size:31 final size:31
Alignment explanation
Indices: 4241--4308 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 31
4231 AGCTTATTCT
*
4241 AAACTAATGCTACTACATTGCCAAAAAAAAA
1 AAACTAATGCTACTACATTGACAAAAAAAAA
*
4272 AAACTAATGCTACTACGTTGATGCAAAAAAAGAA
1 AAACTAATGCTACTACATTGA--CAAAAAAA-AA
4306 AAA
1 AAA
4309 AAAAAAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 19 0.59
33 8 0.25
34 5 0.16
ACGTcount: A:0.54, C:0.16, G:0.10, T:0.19
Consensus pattern (31 bp):
AAACTAATGCTACTACATTGACAAAAAAAAA
Found at i:5488 original size:12 final size:12
Alignment explanation
Indices: 5471--5495 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5461 TGAATTAATC
5471 TATTCAAAGTTT
1 TATTCAAAGTTT
5483 TATTCAAAGTTT
1 TATTCAAAGTTT
5495 T
1 T
5496 CTTTGGTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TATTCAAAGTTT
Found at i:6705 original size:210 final size:210
Alignment explanation
Indices: 6343--6767 Score: 843
Period size: 210 Copynumber: 2.0 Consensus size: 210
6333 AACTACAAAA
6343 AAGTTTCCAATTTTTTAAAATTAAAATGGTAAAACTAAAATATTATAAAAATATTTAATTTAGTT
1 AAGTTTCCAATTTTTTAAAATTAAAATGGTAAAACTAAAATATTATAAAAATATTTAATTTAGTT
6408 AAATAAAAATAGAGTTTTTAGTAGAATAAAACTGTAAAATTTTAAACAATACTAATATATCTAAG
66 AAATAAAAATAGAGTTTTTAGTAGAATAAAACTGTAAAATTTTAAACAATACTAATATATCTAAG
6473 TTTTTTAATTAATCCTAAAATAGTAAAATGGTAAAAATAAAATAGATATAAAGATATTAGATTTA
131 TTTTTTAATTAATCCTAAAATAGTAAAATGGTAAAAATAAAATAGATATAAAGATATTAGATTTA
6538 ATTAAATAAAAATAG
196 ATTAAATAAAAATAG
6553 AAGTTTCCAATTTTTTAAAATTAAAATGGTAAAACTAAAATATTATAAAAATATTTAATTTAGTT
1 AAGTTTCCAATTTTTTAAAATTAAAATGGTAAAACTAAAATATTATAAAAATATTTAATTTAGTT
6618 AAATAAAAATAGAGTTTTTAGTAGAATAAAACTGTAAAATTTTAAACAATACTAATATATCTAAG
66 AAATAAAAATAGAGTTTTTAGTAGAATAAAACTGTAAAATTTTAAACAATACTAATATATCTAAG
6683 TTTTTTAATTAATCCTAAAATAGTAAAATGGTAAAAATAAAATAGATATAAAGATATTAGATTTA
131 TTTTTTAATTAATCCTAAAATAGTAAAATGGTAAAAATAAAATAGATATAAAGATATTAGATTTA
6748 ATTAAATAAAAATAG
196 ATTAAATAAAAATAG
6763 -AGTTT
1 AAGTTT
6768 TCAGTTGGGT
Statistics
Matches: 215, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
209 5 0.02
210 210 0.98
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.36
Consensus pattern (210 bp):
AAGTTTCCAATTTTTTAAAATTAAAATGGTAAAACTAAAATATTATAAAAATATTTAATTTAGTT
AAATAAAAATAGAGTTTTTAGTAGAATAAAACTGTAAAATTTTAAACAATACTAATATATCTAAG
TTTTTTAATTAATCCTAAAATAGTAAAATGGTAAAAATAAAATAGATATAAAGATATTAGATTTA
ATTAAATAAAAATAG
Done.