Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015343.1 Corchorus capsularis cultivar CVL-1 contig15364, 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: 29799
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:2535 original size:29 final size:30
Alignment explanation
Indices: 2468--2539 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
2458 TAATAAATCT
2468 AATCCTTATTCTTCATTTCCTGCCAAAAAA
1 AATCCTTATTCTTCATTTCCTGCCAAAAAA
2498 AATCCTTATTCTTCATTTCCTGCC-AAAAA
1 AATCCTTATTCTTCATTTCCTGCCAAAAAA
*
2527 AATCATTATTCTT
1 AATCCTTATTCTT
2540 TATTCAATCT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 17 0.41
30 24 0.59
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.40
Consensus pattern (30 bp):
AATCCTTATTCTTCATTTCCTGCCAAAAAA
Found at i:9691 original size:31 final size:31
Alignment explanation
Indices: 9656--9716 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
9646 TGTCACTTTT
9656 CCTTAAGTTTATAGGGGCTGCTACTTTGCAC
1 CCTTAAGTTTATAGGGGCTGCTACTTTGCAC
9687 CCTTAAGTTTATAGGGGCTGCTACTTTGCA
1 CCTTAAGTTTATAGGGGCTGCTACTTTGCA
9717 TCCAATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (31 bp):
CCTTAAGTTTATAGGGGCTGCTACTTTGCAC
Found at i:9855 original size:30 final size:31
Alignment explanation
Indices: 9819--9889 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
9809 ACGGCATCCG
* **
9819 ACGTGGCATGCCATATGTC-TTTTTTTTTAC
1 ACGTGGCATGCCACATGTCATTTTTTGGTAC
*
9849 ACGTGGCGTGCCACATGTCATTTTTTGGTAC
1 ACGTGGCATGCCACATGTCATTTTTTGGTAC
9880 ACGTGGCATG
1 ACGTGGCATG
9890 TCACGTCGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 17 0.49
31 18 0.51
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (31 bp):
ACGTGGCATGCCACATGTCATTTTTTGGTAC
Found at i:11389 original size:14 final size:14
Alignment explanation
Indices: 11370--11409 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
11360 GCCGAGTTGG
*
11370 ATTTGGGTTCGGTT
1 ATTTGGGTTAGGTT
11384 ATTTGGGTTAGGTT
1 ATTTGGGTTAGGTT
11398 AGTTTCGGGTTA
1 A-TTT-GGGTTA
11410 AGGAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.61
15 3 0.13
16 6 0.26
ACGTcount: A:0.12, C:0.05, G:0.35, T:0.47
Consensus pattern (14 bp):
ATTTGGGTTAGGTT
Found at i:11902 original size:17 final size:17
Alignment explanation
Indices: 11880--11966 Score: 156
Period size: 17 Copynumber: 5.1 Consensus size: 17
11870 TTAATTCAAA
11880 CATATTAGGTCACGTGC
1 CATATTAGGTCACGTGC
11897 CATATTAGGTCACGTGC
1 CATATTAGGTCACGTGC
*
11914 CATATTAAGTCACGTGC
1 CATATTAGGTCACGTGC
11931 CATATTAGGTCACGTGC
1 CATATTAGGTCACGTGC
*
11948 CATATTAAGTCACGTGC
1 CATATTAGGTCACGTGC
11965 CA
1 CA
11967 CGTGCAAGGC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 67 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (17 bp):
CATATTAGGTCACGTGC
Found at i:12230 original size:2 final size:2
Alignment explanation
Indices: 12184--12213 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12174 TCCAAAATAC
*
12184 AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12214 TATCTTACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12719 original size:23 final size:24
Alignment explanation
Indices: 12682--12728 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
12672 GATTTACAAG
* *
12682 AAGAGATTTGAAAGCCAGGGGCTT
1 AAGAGATTTGAAAGCAAGGAGCTT
12706 AAGAGA-TTGAAAGCAAGGAGCTT
1 AAGAGATTTGAAAGCAAGGAGCTT
12729 GATTGTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.38, C:0.11, G:0.32, T:0.19
Consensus pattern (24 bp):
AAGAGATTTGAAAGCAAGGAGCTT
Found at i:16181 original size:15 final size:15
Alignment explanation
Indices: 16161--16197 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
16151 GAAGTTGACT
16161 AATTGATCAGATTCA
1 AATTGATCAGATTCA
16176 AATTGATCAGATTCA
1 AATTGATCAGATTCA
16191 AATTGAT
1 AATTGAT
16198 GCTGATGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.35
Consensus pattern (15 bp):
AATTGATCAGATTCA
Found at i:19694 original size:25 final size:25
Alignment explanation
Indices: 19660--19710 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
19650 GAATAATCAT
19660 CAATGAATGTGATCATGTATTGATA
1 CAATGAATGTGATCATGTATTGATA
19685 CAATGAATGTGATCATGTATTGATA
1 CAATGAATGTGATCATGTATTGATA
19710 C
1 C
19711 CCACTTACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (25 bp):
CAATGAATGTGATCATGTATTGATA
Found at i:24508 original size:72 final size:72
Alignment explanation
Indices: 24432--24598 Score: 289
Period size: 72 Copynumber: 2.3 Consensus size: 72
24422 TGAACAATTT
* *
24432 CCAATCTCCTTGGGTATTTCCCCAACTAAGGCATTATGAGATAACCACAATTCTTTCAAGTTTCC
1 CCAATTTCCTTGGGAATTTCCCCAACTAAGGCATTATGAGATAACCACAATTCTTTCAAGTTTCC
24497 AAGCAGC
66 AAGCAGC
*
24504 CCAATTTCCTTGGGAATTTCCCCAATTAAGGCATTATGAGATAACCACAATTCTTTCAAGTTTCC
1 CCAATTTCCTTGGGAATTTCCCCAACTAAGGCATTATGAGATAACCACAATTCTTTCAAGTTTCC
24569 AAGCAGC
66 AAGCAGC
* *
24576 CCAATTTCCCTGGGGATTTCCCC
1 CCAATTTCCTTGGGAATTTCCCC
24599 TCCAAGTCGG
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 90 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (72 bp):
CCAATTTCCTTGGGAATTTCCCCAACTAAGGCATTATGAGATAACCACAATTCTTTCAAGTTTCC
AAGCAGC
Done.