Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015266.1 Corchorus capsularis cultivar CVL-1 contig15287, 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: 18062
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Found at i:268 original size:27 final size:27
Alignment explanation
Indices: 238--306 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
228 GGTGATTCTT
*
238 AAAAATGACTAAAATGCCCCTGAGTGC
1 AAAAATGACCAAAATGCCCCTGAGTGC
*
265 AAAAATGACCAAAATGCCCCTGGGTGC
1 AAAAATGACCAAAATGCCCCTGAGTGC
292 AAAAATGACCAAAAT
1 AAAAATGACCAAAAT
307 ACCCTGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.16
Consensus pattern (27 bp):
AAAAATGACCAAAATGCCCCTGAGTGC
Found at i:3322 original size:28 final size:28
Alignment explanation
Indices: 3282--3336 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
3272 GTTTTCCTCT
3282 TCCAATGAGTTAACAGGCTAAAAAAAAC
1 TCCAATGAGTTAACAGGCTAAAAAAAAC
3310 TCCAATGAGTTAACAGGCTAAAAAAAA
1 TCCAATGAGTTAACAGGCTAAAAAAAA
3337 GCACATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.51, C:0.16, G:0.15, T:0.18
Consensus pattern (28 bp):
TCCAATGAGTTAACAGGCTAAAAAAAAC
Found at i:10590 original size:110 final size:111
Alignment explanation
Indices: 10439--10655 Score: 373
Period size: 110 Copynumber: 2.0 Consensus size: 111
10429 ATCAAAATGG
** * * *
10439 TACCAAAAGTTCAATCAATTATTCATGTAACGGTTGATCTGAAAGAATCAATTGGAAACTATGGG
1 TACCAAAAGTTCAATCAATTAAGCATGTAACGGTTGATCTGAAAGAATCAATTAGAAACTAAGAG
*
10504 AATAAATTTATAAAGTTAGGTTTAACCAAAAAATTTTATAAAGTGT
66 AATAAATTTATAAAGTTAGGTTTAACCAAAAAAATTTATAAAGTGT
10550 TACCAAAAGTTCAATCAA-TAAGCATGTAACGGTTGATCTGAAAGAATCAATTAGAAACTAAGAG
1 TACCAAAAGTTCAATCAATTAAGCATGTAACGGTTGATCTGAAAGAATCAATTAGAAACTAAGAG
10614 AATAAATTTATAAAGTTAGGTTTAACCAAAAAAATTTATAAA
66 AATAAATTTATAAAGTTAGGTTTAACCAAAAAAATTTATAAA
10656 CTTAGGTTAC
Statistics
Matches: 100, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
110 82 0.82
111 18 0.18
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.30
Consensus pattern (111 bp):
TACCAAAAGTTCAATCAATTAAGCATGTAACGGTTGATCTGAAAGAATCAATTAGAAACTAAGAG
AATAAATTTATAAAGTTAGGTTTAACCAAAAAAATTTATAAAGTGT
Found at i:13886 original size:2 final size:2
Alignment explanation
Indices: 13879--13918 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
13869 GAACTACAAA
*
13879 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13919 GCTAAGACCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:15534 original size:99 final size:99
Alignment explanation
Indices: 15363--15559 Score: 385
Period size: 99 Copynumber: 2.0 Consensus size: 99
15353 ACACTCTAGA
*
15363 CATTTAAAAAGGTATCTAATTATGGATATGTTTGATGTATACATTTTAAACTTTGGGCTTCCTCT
1 CATTTAAAAAGGTATCTAATTATGGAAATGTTTGATGTATACATTTTAAACTTTGGGCTTCCTCT
15428 GAAGAAATCAAATATTTCTCAAGCTGCAATACAT
66 GAAGAAATCAAATATTTCTCAAGCTGCAATACAT
15462 CATTTAAAAAGGTATCTAATTATGGAAATGTTTGATGTATACATTTTAAACTTTGGGCTTCCTCT
1 CATTTAAAAAGGTATCTAATTATGGAAATGTTTGATGTATACATTTTAAACTTTGGGCTTCCTCT
15527 GAAGAAATCAAATATTTCTCAAGCTGCAATACA
66 GAAGAAATCAAATATTTCTCAAGCTGCAATACA
15560 AATTATCATT
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (99 bp):
CATTTAAAAAGGTATCTAATTATGGAAATGTTTGATGTATACATTTTAAACTTTGGGCTTCCTCT
GAAGAAATCAAATATTTCTCAAGCTGCAATACAT
Found at i:17135 original size:73 final size:73
Alignment explanation
Indices: 17016--17158 Score: 259
Period size: 73 Copynumber: 2.0 Consensus size: 73
17006 CGGACTAATC
* *
17016 CGGATTCGACCCACGTCGCGCACCTGGTTATGGTGGATGAGTCTCCCAACAGGGGCAGTTGCGTA
1 CGGATTCGACCCACGTCGCGCACCTGGTTATGGTGGATGAGTCTCCCAACAGGGACAGTTGCATA
17081 CACAAGGT
66 CACAAGGT
*
17089 CGGATTCGACCCACGTCGCGCACCTGGTTATGGTGGGTGAGTCTCCCAACAGGGACAGTTGCATA
1 CGGATTCGACCCACGTCGCGCACCTGGTTATGGTGGATGAGTCTCCCAACAGGGACAGTTGCATA
17154 CACAA
66 CACAA
17159 AGTCTCGAAC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 67 1.00
ACGTcount: A:0.22, C:0.28, G:0.30, T:0.20
Consensus pattern (73 bp):
CGGATTCGACCCACGTCGCGCACCTGGTTATGGTGGATGAGTCTCCCAACAGGGACAGTTGCATA
CACAAGGT
Found at i:17875 original size:3 final size:3
Alignment explanation
Indices: 17867--17916 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
17857 ATATAATATA
* *
17867 ATT ATT ATT ATT ATT ATT ATT AAT ATA ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17915 AT
1 AT
17917 ATATATAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:17929 original size:6 final size:6
Alignment explanation
Indices: 17858--17931 Score: 50
Period size: 6 Copynumber: 13.0 Consensus size: 6
17848 TTTTATACTA
* * * *
17858 TATAA- TATAAT TATTAT TATTAT TATTA- T-TAA- TATAAT TATTAT
1 TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT
* *
17902 TATTAT TATTAT TAT-AT ATATAAT TATAAT
1 TATAAT TATAAT TATAAT -TATAAT TATAAT
17932 AATATGCTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
4 3 0.05
5 11 0.18
6 45 0.74
7 2 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (6 bp):
TATAAT
Found at i:17934 original size:9 final size:9
Alignment explanation
Indices: 17863--17931 Score: 68
Period size: 9 Copynumber: 7.7 Consensus size: 9
17853 TACTATATAA
17863 TATAATTAT
1 TATAATTAT
*
17872 TATTATTAT
1 TATAATTAT
* *
17881 TATTATTAA
1 TATAATTAT
17890 TATAATTAT
1 TATAATTAT
*
17899 TATTATTAT
1 TATAATTAT
*
17908 TATTATTA-
1 TATAATTAT
*
17916 TATATATAAT
1 TATA-ATTAT
17926 TATAAT
1 TATAAT
17932 AATATGCTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
8 3 0.06
9 44 0.86
10 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TATAATTAT
Done.