Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014536.1 Corchorus capsularis cultivar CVL-1 contig14557, 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: 68002
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:13196 original size:2 final size:2
Alignment explanation
Indices: 13189--13222 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
13179 ACATTGAATG
13189 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13223 TCACTAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16792 original size:60 final size:60
Alignment explanation
Indices: 16699--16814 Score: 187
Period size: 60 Copynumber: 1.9 Consensus size: 60
16689 TTTGCATTTT
* * * *
16699 GAGTGTAATTATCTACTCCCTCTGTCCTAAATTAACTGATTTTTTTTGGGATGAATATGC
1 GAGTGTAATGATCTACTCCCTCTGTCCCAAATTAACTGACTCTTTTTGGGATGAATATGC
*
16759 GAGTGTAATGATCTACTCCCTCTGTCCCAAATTATCTGACTCTTTTTGGGATGAAT
1 GAGTGTAATGATCTACTCCCTCTGTCCCAAATTAACTGACTCTTTTTGGGATGAAT
16815 GTTTATCCCA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (60 bp):
GAGTGTAATGATCTACTCCCTCTGTCCCAAATTAACTGACTCTTTTTGGGATGAATATGC
Found at i:17325 original size:2 final size:2
Alignment explanation
Indices: 17318--17343 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17308 ACCCCTAGAA
17318 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
17344 GTGCTTATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26878 original size:11 final size:11
Alignment explanation
Indices: 26858--26891 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
26848 TGATTACTAT
26858 ATAA-TAATTA
1 ATAATTAATTA
*
26868 TTAATTAATTA
1 ATAATTAATTA
26879 ATAATTAATTA
1 ATAATTAATTA
26890 AT
1 AT
26892 CATACTAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 3 0.14
11 18 0.86
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATAATTAATTA
Found at i:26885 original size:15 final size:15
Alignment explanation
Indices: 26862--26891 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26852 TACTATATAA
*
26862 TAATTATTAATTAAT
1 TAATAATTAATTAAT
26877 TAATAATTAATTAAT
1 TAATAATTAATTAAT
26892 CATACTAGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATAATTAATTAAT
Found at i:27822 original size:14 final size:14
Alignment explanation
Indices: 27802--27839 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
27792 TAATTCTTTT
27802 GGATTTTTCCCAC-
1 GGATTTTTCCCACA
27815 GAGATTTTTCCCACA
1 G-GATTTTTCCCACA
27830 GGATTTTTCC
1 GGATTTTTCC
27840 TTTTGGTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.18, C:0.26, G:0.16, T:0.39
Consensus pattern (14 bp):
GGATTTTTCCCACA
Found at i:30012 original size:14 final size:14
Alignment explanation
Indices: 29989--30026 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
29979 TGTCCTTTTC
*
29989 TTTCTCTTTTTATA
1 TTTCTTTTTTTATA
30003 TTTCTTTTTTTTATA
1 TTTC-TTTTTTTATA
30018 TTTCTTTTT
1 TTTCTTTTT
30027 ATAAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTCTTTTTTTATA
Found at i:30015 original size:15 final size:15
Alignment explanation
Indices: 29995--30026 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
29985 TTTCTTTCTC
29995 TTTTTATATTTCTTT
1 TTTTTATATTTCTTT
30010 TTTTTATATTTCTTT
1 TTTTTATATTTCTTT
30025 TT
1 TT
30027 ATAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTATATTTCTTT
Found at i:30754 original size:1 final size:1
Alignment explanation
Indices: 30743--30796 Score: 81
Period size: 1 Copynumber: 54.0 Consensus size: 1
30733 CAAATTGAAG
* * *
30743 TTTTTTGTTTTTTGTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
30797 CTGGTTCTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (1 bp):
T
Found at i:34103 original size:28 final size:28
Alignment explanation
Indices: 34063--34118 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
34053 CTGTCCACTT
34063 CTATTAGGGGAAAAGTTGACAGATAATA
1 CTATTAGGGGAAAAGTTGACAGATAATA
34091 CTATTAGGGGAAAAGTTGACAGATAATA
1 CTATTAGGGGAAAAGTTGACAGATAATA
34119 TGGGACGAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.07, G:0.25, T:0.25
Consensus pattern (28 bp):
CTATTAGGGGAAAAGTTGACAGATAATA
Found at i:45542 original size:42 final size:42
Alignment explanation
Indices: 45483--45564 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
45473 CTGCAAGAGT
45483 AGACTTCCGATCAAGCCGCCGAGCAGCACCAAGCTCAGCCGC
1 AGACTTCCGATCAAGCCGCCGAGCAGCACCAAGCTCAGCCGC
*
45525 AGACTTCCGATCAAGCCGCCGAGCAGCGCCAAGCTCAGCC
1 AGACTTCCGATCAAGCCGCCGAGCAGCACCAAGCTCAGCC
45565 CCAGCCCCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.26, C:0.40, G:0.24, T:0.10
Consensus pattern (42 bp):
AGACTTCCGATCAAGCCGCCGAGCAGCACCAAGCTCAGCCGC
Found at i:47300 original size:7 final size:7
Alignment explanation
Indices: 47288--47313 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
47278 TGTTCTACAA
47288 ATATACT
1 ATATACT
47295 ATATACT
1 ATATACT
47302 ATATACT
1 ATATACT
47309 ATATA
1 ATATA
47314 ATTATTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATACT
Found at i:51577 original size:17 final size:16
Alignment explanation
Indices: 51555--51592 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
51545 ATATGTATTG
51555 TATATATACACAAATTA
1 TATATATACACAAA-TA
*
51572 TATATATACACACATA
1 TATATATACACAAATA
51588 TATAT
1 TATAT
51593 GTATTAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (16 bp):
TATATATACACAAATA
Found at i:67972 original size:2 final size:2
Alignment explanation
Indices: 67965--67999 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
67955 AGAGGATTGC
67965 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
68000 CTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.