Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007678.1 Corchorus capsularis cultivar CVL-1 contig07699, 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: 5963
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Found at i:3345 original size:30 final size:30
Alignment explanation
Indices: 3287--3345 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
3277 TGTCTTCAAG
*
3287 TCCATAATAAGTCCTTGGCGCATAATTCCT
1 TCCATAATAAGTCCTTGGCGCACAATTCCT
* *
3317 TCCATGATAAG-CCTTGGGCGCACCATTCC
1 TCCATAATAAGTCCTT-GGCGCACAATTCC
3346 CTCCCCCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.29
Consensus pattern (30 bp):
TCCATAATAAGTCCTTGGCGCACAATTCCT
Found at i:3732 original size:33 final size:33
Alignment explanation
Indices: 3688--3773 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
3678 TTCTTTTCAC
* *
3688 CCAAAACAGAATTATTTTCAATGTTATGATCAA
1 CCAAAATAGAATTATTTTCAATGCTATGATCAA
*
3721 CCAAAATAGAATTATTTGCAATGCTATGATCAA
1 CCAAAATAGAATTATTTTCAATGCTATGATCAA
* *
3754 CCAAAATAGATTTGTTTTCA
1 CCAAAATAGAATTATTTTCA
3774 TCACAATTAG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (33 bp):
CCAAAATAGAATTATTTTCAATGCTATGATCAA
Found at i:3831 original size:33 final size:33
Alignment explanation
Indices: 3756--3891 Score: 116
Period size: 33 Copynumber: 4.1 Consensus size: 33
3746 ATGATCAACC
** *
3756 AAAATAGATTT-GTTTTCATCACAATTAGCATCC-
1 AAAATAGATTTAG-TTTCATCACAAACAACA-CCT
*
3789 AAAACAGATTTAGTTTCATCACAAACAACACCT
1 AAAATAGATTTAGTTTCATCACAAACAACACCT
* **
3822 AAAATAGATTTAGTGTCATTGCAAACAACA-CT
1 AAAATAGATTTAGTTTCATCACAAACAACACCT
* * * * *
3854 CAAATCAGGTTTAGTATCATCGCAAACAACATCT
1 AAAAT-AGATTTAGTTTCATCACAAACAACACCT
3888 AAAA
1 AAAA
3892 CACTCTTTAC
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
32 8 0.09
33 72 0.84
34 6 0.07
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.28
Consensus pattern (33 bp):
AAAATAGATTTAGTTTCATCACAAACAACACCT
Found at i:5255 original size:10 final size:9
Alignment explanation
Indices: 5238--5264 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
5228 TAACAGCACA
5238 GATTTTTTT
1 GATTTTTTT
5247 GATTTTTTT
1 GATTTTTTT
5256 GATTTTTTT
1 GATTTTTTT
5265 CAATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (9 bp):
GATTTTTTT
Found at i:5388 original size:10 final size:10
Alignment explanation
Indices: 5373--5407 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
5363 CTGGTCGAAA
5373 TTTTTTTTA-
1 TTTTTTTTAT
5382 TTTTTTTTAT
1 TTTTTTTTAT
5392 TTTTTTTTAT
1 TTTTTTTTAT
5402 ATTTTT
1 -TTTTT
5408 CGATATAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.38
10 10 0.42
11 5 0.21
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:5407 original size:9 final size:9
Alignment explanation
Indices: 5372--5398 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
5362 TCTGGTCGAA
5372 ATTTTTTTT
1 ATTTTTTTT
5381 ATTTTTTTT
1 ATTTTTTTT
5390 ATTTTTTTT
1 ATTTTTTTT
5399 TATATTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
ATTTTTTTT
Done.