Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008469.1 Corchorus capsularis cultivar CVL-1 contig08490, 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: 21547
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Found at i:343 original size:17 final size:18
Alignment explanation
Indices: 315--349 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
305 CGACACCTTT
*
315 AACCTAAAACTAGAGAAA
1 AACCTAAAACTAAAGAAA
333 AACCT-AAACTAAAGAAA
1 AACCTAAAACTAAAGAAA
350 GGTAGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.63, C:0.17, G:0.09, T:0.11
Consensus pattern (18 bp):
AACCTAAAACTAAAGAAA
Found at i:3437 original size:33 final size:32
Alignment explanation
Indices: 3354--3493 Score: 111
Period size: 33 Copynumber: 4.2 Consensus size: 32
3344 AAAGGATCAT
* **
3354 GTGGCCGGTTGTGGCCGGGCATGGCCGA-GTCAA
1 GTGGCCGG-TGTGGCCGGGCATCGCC-ATGTCGC
* * *
3387 GTGTCCGGGTGTAGCCGGGCATGGCCATGTCGC
1 GTGGCC-GGTGTGGCCGGGCATCGCCATGTCGC
* *
3420 GTGGCCGGTGATGGCCGGGCATCTCCATGTTGC
1 GTGGCCGGTG-TGGCCGGGCATCGCCATGTCGC
* * * * *
3453 ATGGCCGGTGTTGCGCGAGCATCTCCAAGTCGC
1 GTGGCCGGTGTGGC-CGGGCATCGCCATGTCGC
3486 GTGGCCGG
1 GTGGCCGG
3494 ATCTCCAAGT
Statistics
Matches: 88, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
32 8 0.09
33 78 0.89
34 2 0.02
ACGTcount: A:0.11, C:0.27, G:0.41, T:0.21
Consensus pattern (32 bp):
GTGGCCGGTGTGGCCGGGCATCGCCATGTCGC
Found at i:3499 original size:21 final size:21
Alignment explanation
Indices: 3473--3514 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3463 TTGCGCGAGC
*
3473 ATCTCCAAGTCGCGTGGCCGG
1 ATCTCCAAGTCGCATGGCCGG
3494 ATCTCCAAGTCGCATGGCCGG
1 ATCTCCAAGTCGCATGGCCGG
3515 TCACTTGTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.33, G:0.31, T:0.19
Consensus pattern (21 bp):
ATCTCCAAGTCGCATGGCCGG
Found at i:5324 original size:33 final size:33
Alignment explanation
Indices: 5247--5395 Score: 187
Period size: 33 Copynumber: 4.6 Consensus size: 33
5237 TTTTCGTCAC
* *
5247 CCAAAACAGATTTATTTTCAATGC--T-ATCTA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
* * *
5277 CCAAAACAGGATTATTTTCAATGTTAGGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
* *
5310 CCAAAATAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
*
5343 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
* *
5376 CCAAAACAGATTTGTTTTCA
1 CCAAAACAGAATTATTTTCA
5396 TCACAATTAG
Statistics
Matches: 102, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
30 21 0.21
33 81 0.79
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (33 bp):
CCAAAACAGAATTATTTTCAATGCTATGATCAA
Found at i:5448 original size:33 final size:33
Alignment explanation
Indices: 5411--5475 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
5401 ATTAGCATCG
5411 AAAACAGATTTAATTTCATCACAAACAACACTT
1 AAAACAGATTTAATTTCATCACAAACAACACTT
* **
5444 AAAACAGATTTAGTTTCATTGCAAACAACACT
1 AAAACAGATTTAATTTCATCACAAACAACACT
5476 CAGATTAGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.28
Consensus pattern (33 bp):
AAAACAGATTTAATTTCATCACAAACAACACTT
Found at i:7990 original size:33 final size:32
Alignment explanation
Indices: 7909--8048 Score: 113
Period size: 33 Copynumber: 4.2 Consensus size: 32
7899 AAAGGATCAT
* * **
7909 GTGGCCGGTTGTTGCCGGGCATGGCCGA-GTCAA
1 GTGGCCGG-TGTGGCCGGGCATCGCC-ATGTCGC
* *
7942 GTGTCCGGGTGTGGCCGGGCATGGCCATGTCGC
1 GTGGCC-GGTGTGGCCGGGCATCGCCATGTCGC
* *
7975 GTGGCCGGTGATGGCCGGGCATCTCCATGTTGC
1 GTGGCCGGTG-TGGCCGGGCATCGCCATGTCGC
* * *
8008 ATGGCCGGTGTTGTG-CGGGCATCTCCAAGTCGC
1 GTGGCCGGTG-TG-GCCGGGCATCGCCATGTCGC
8041 GTGGCCGG
1 GTGGCCGG
8049 ATCTCCAAGT
Statistics
Matches: 90, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
32 5 0.06
33 82 0.91
34 3 0.03
ACGTcount: A:0.09, C:0.26, G:0.42, T:0.22
Consensus pattern (32 bp):
GTGGCCGGTGTGGCCGGGCATCGCCATGTCGC
Found at i:8054 original size:21 final size:21
Alignment explanation
Indices: 8028--8069 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
8018 TTGTGCGGGC
*
8028 ATCTCCAAGTCGCGTGGCCGG
1 ATCTCCAAGTCGCATGGCCGG
8049 ATCTCCAAGTCGCATGGCCGG
1 ATCTCCAAGTCGCATGGCCGG
8070 TCACTTGTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.33, G:0.31, T:0.19
Consensus pattern (21 bp):
ATCTCCAAGTCGCATGGCCGG
Done.