Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011784.1 Corchorus capsularis cultivar CVL-1 contig11805, 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: 51038
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:26 original size:2 final size:2
Alignment explanation
Indices: 15--47 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5 ATTTTATAAT
15 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48 AGCCATACTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:33172 original size:21 final size:21
Alignment explanation
Indices: 33146--33189 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
33136 CAAAAGGGGA
*
33146 TTGCTAAATACCGCCCTATTT
1 TTGCTAAATACCGCCCCATTT
**
33167 TTGCTATTTACCGCCCCATTT
1 TTGCTAAATACCGCCCCATTT
33188 TT
1 TT
33190 TTACACTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.30, G:0.09, T:0.43
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCATTT
Found at i:33301 original size:21 final size:21
Alignment explanation
Indices: 33277--33316 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
33267 GCCCTCGATA
* *
33277 AATTTTTTTTAAAATAATAAT
1 AATTTTTTTAAAAAAAATAAT
33298 AATTTTTTTAAAAAAAATA
1 AATTTTTTTAAAAAAAATA
33317 GCCTAGCCGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTTTTTTAAAAAAAATAAT
Found at i:33462 original size:42 final size:42
Alignment explanation
Indices: 33415--33498 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
33405 TCAAAAATTG
* * * *
33415 CATTTTTCTTAATTCGTCATCAAAATACGGCATGTTATTGTT
1 CATTTTTCTTAAATCGTCATCAAAATACAGCACGTTAATGTT
33457 CATTTTTCTTAAATCGTCATCAAAATACAGCACGTTAATGTT
1 CATTTTTCTTAAATCGTCATCAAAATACAGCACGTTAATGTT
33499 ATTCTACGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.42
Consensus pattern (42 bp):
CATTTTTCTTAAATCGTCATCAAAATACAGCACGTTAATGTT
Found at i:35016 original size:41 final size:42
Alignment explanation
Indices: 34954--35037 Score: 152
Period size: 41 Copynumber: 2.0 Consensus size: 42
34944 CGTGCGGCTG
34954 TTTTATTTTATAAATTCTTTTAAG-AAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
*
34995 TTTTATTTTATAAATTTTTTTAAGAAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
35037 T
1 T
35038 GATATTTTGT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 23 0.56
42 18 0.44
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.48
Consensus pattern (42 bp):
TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
Found at i:35044 original size:42 final size:41
Alignment explanation
Indices: 34957--35045 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 41
34947 GCGGCTGTTT
**
34957 TATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATTT
1 TATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATGA
*
34998 TATTTTATAAATTTTTTTAAGAAAAATTCAGTTAAGAAATGA
1 TATTTTATAAATTCTTTTAAG-AAAATTCAGTTAAGAAATGA
35040 TATTTT
1 TATTTT
35046 GTTGTGAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 20 0.45
42 24 0.55
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (41 bp):
TATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATGA
Found at i:35364 original size:11 final size:11
Alignment explanation
Indices: 35350--35387 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
35340 ATACATAACA
35350 AATTTATAATT
1 AATTTATAATT
35361 AATTTATAATT
1 AATTTATAATT
35372 -ATTTGATAATT
1 AATTT-ATAATT
*
35383 TATTT
1 AATTT
35388 CATATTGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:38479 original size:56 final size:57
Alignment explanation
Indices: 38399--38535 Score: 161
Period size: 56 Copynumber: 2.4 Consensus size: 57
38389 GCCATTATCA
* * * * * * *
38399 CCCTACTAAATATGAAACCATATGATTATGA-ACCTACTGATTATGTAACTATATGG-
1 CCCTACTGAATATGCAACTATATGATTATGACA-CAAATGAATATGCAACTATATGGC
* *
38455 CCCTACTGAATGTGCAACTTTATGATTATGACACAAATGAATATGCAACTATATGGC
1 CCCTACTGAATATGCAACTATATGATTATGACACAAATGAATATGCAACTATATGGC
*
38512 CCCTACTGGATATGCAACTATATG
1 CCCTACTGAATATGCAACTATATG
38536 TCCCCTACTG
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
56 45 0.67
57 22 0.33
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.31
Consensus pattern (57 bp):
CCCTACTGAATATGCAACTATATGATTATGACACAAATGAATATGCAACTATATGGC
Found at i:38524 original size:26 final size:26
Alignment explanation
Indices: 38492--38592 Score: 130
Period size: 26 Copynumber: 3.7 Consensus size: 26
38482 ATGACACAAA
38492 TGAATATGCAACTATATGGCCCCTAC
1 TGAATATGCAACTATATGGCCCCTAC
* *
38518 TGGATATGCAACTATATGTCCCCTAC
1 TGAATATGCAACTATATGGCCCCTAC
*
38544 TGAATATGCAACTATATGATTATGGCCCTAC
1 TGAATATGCAACTATATG-----GCCCCTAC
38575 TGAATATGCAACTATATG
1 TGAATATGCAACTATATG
38593 ATGGCGCAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
26 41 0.63
31 24 0.37
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.31
Consensus pattern (26 bp):
TGAATATGCAACTATATGGCCCCTAC
Found at i:38554 original size:83 final size:82
Alignment explanation
Indices: 38431--38592 Score: 227
Period size: 83 Copynumber: 2.0 Consensus size: 82
38421 TGATTATGAA
* * * *
38431 CCTACTGATTATGTAACTATATGGCCCTACTGAATGTGCAACTTTATGATTATGACACAAATGAA
1 CCTACTGATTATGCAACTATATGCCCCTACTGAATATGCAACTATATGATTATGACACAAATGAA
38496 TATGCAACTATATGGCC
66 TATGCAACTATATGGCC
* * * *
38513 CCTACTGGA-TATGCAACTATATGTCCCCTACTGAATATGCAACTATATGATTATGGCCCTACTG
1 CCTACT-GATTATGCAACTATATG-CCCCTACTGAATATGCAACTATATGATTATGACACAAATG
38577 AATATGCAACTATATG
64 AATATGCAACTATATG
38593 ATGGCGCAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
82 19 0.27
83 51 0.73
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31
Consensus pattern (82 bp):
CCTACTGATTATGCAACTATATGCCCCTACTGAATATGCAACTATATGATTATGACACAAATGAA
TATGCAACTATATGGCC
Found at i:38576 original size:31 final size:31
Alignment explanation
Indices: 38450--38594 Score: 139
Period size: 31 Copynumber: 5.0 Consensus size: 31
38440 TATGTAACTA
* * *
38450 TATGGCCCTACTGAATGTGCAACTTTATGAT
1 TATGCCCCTACTGAATATGCAACTATATGAT
* * * *
38481 TATGACACAAATGAATATGCAACTATATG--
1 TATGCCCCTACTGAATATGCAACTATATGAT
*
38510 ---GCCCCTACTGGATATGCAACTATATG--
1 TATGCCCCTACTGAATATGCAACTATATGAT
38536 --T-CCCCTACTGAATATGCAACTATATGAT
1 TATGCCCCTACTGAATATGCAACTATATGAT
*
38564 TATGGCCCTACTGAATATGCAACTATATGAT
1 TATGCCCCTACTGAATATGCAACTATATGAT
38595 GGCGCAATAA
Statistics
Matches: 95, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
26 45 0.47
30 1 0.01
31 49 0.52
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (31 bp):
TATGCCCCTACTGAATATGCAACTATATGAT
Done.