Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011813.1 Corchorus capsularis cultivar CVL-1 contig11834, 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: 47245
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:82 original size:2 final size:2
Alignment explanation
Indices: 77--108 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
67 TGTGTGTGTG
77 TA TA TA 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
109 ATAAAACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8897 original size:15 final size:15
Alignment explanation
Indices: 8877--8907 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
8867 AATAACTTGT
8877 GCCCATTTTGCAAAA
1 GCCCATTTTGCAAAA
8892 GCCCATTTTGCAAAA
1 GCCCATTTTGCAAAA
8907 G
1 G
8908 AGTCGCTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (15 bp):
GCCCATTTTGCAAAA
Found at i:19084 original size:15 final size:16
Alignment explanation
Indices: 19049--19086 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
19039 ATATGCTATA
19049 TATAAGAATTTAAATTT
1 TATAA-AATTTAAATTT
*
19066 TATAAAATTTCAA-TT
1 TATAAAATTTAAATTT
19081 TATAAA
1 TATAAA
19087 GCTATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 7 0.35
17 5 0.25
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (16 bp):
TATAAAATTTAAATTT
Found at i:19454 original size:2 final size:2
Alignment explanation
Indices: 19447--19479 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
19437 AACACTTCAT
19447 TA TA TA TA -A TA TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19480 TGTTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:19637 original size:45 final size:45
Alignment explanation
Indices: 19573--19664 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
19563 AAAATTCTTC
19573 TAACAAATGTGTTTTCGAAGAACCGAACTTATATTCTCATCCTTA
1 TAACAAATGTGTTTTCGAAGAACCGAACTTATATTCTCATCCTTA
*
19618 TAACAAATGTGTTTTCGAAGAATCGAACTTATATTCTCATCCTTA
1 TAACAAATGTGTTTTCGAAGAACCGAACTTATATTCTCATCCTTA
19663 TA
1 TA
19665 TCTTAAGTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (45 bp):
TAACAAATGTGTTTTCGAAGAACCGAACTTATATTCTCATCCTTA
Found at i:24909 original size:27 final size:27
Alignment explanation
Indices: 24879--24936 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
24869 AATTTGATGT
** *
24879 AGTTTGGTGTTGTTAAGGAGT-GGCAAA
1 AGTTTGGTAATGTAAAGGAGTAGG-AAA
*
24906 AGTTTTGTAATGTAAAGGAGTAGGAAA
1 AGTTTGGTAATGTAAAGGAGTAGGAAA
24933 AGTT
1 AGTT
24937 GAATAGCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.33, T:0.33
Consensus pattern (27 bp):
AGTTTGGTAATGTAAAGGAGTAGGAAA
Found at i:28281 original size:10 final size:10
Alignment explanation
Indices: 28258--28315 Score: 55
Period size: 10 Copynumber: 5.8 Consensus size: 10
28248 CAAACTGGAT
* *
28258 TATCTTTATG
1 TATCTATATA
*
28268 TATCTGTATA
1 TATCTATATA
28278 TATCATATATA
1 TATC-TATATA
*
28289 TATATATATA
1 TATCTATATA
*
28299 TATATATATA
1 TATCTATATA
28309 TAT-TATA
1 TATCTATA
28316 GGAAAAGGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
9 4 0.09
10 31 0.72
11 8 0.19
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (10 bp):
TATCTATATA
Found at i:28287 original size:2 final size:2
Alignment explanation
Indices: 28274--28315 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
28264 TATGTATCTG
28274 TA TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28316 GGAAAAGGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30190 original size:20 final size:21
Alignment explanation
Indices: 30165--30206 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
30155 TAAATAAATT
* *
30165 AAGAGAA-AAAAGAAGAAGAA
1 AAGAGAATAAAAAAAAAAGAA
30185 AAGAGAATAAAAAAAAAAGAA
1 AAGAGAATAAAAAAAAAAGAA
30206 A
1 A
30207 GAAAAGCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (21 bp):
AAGAGAATAAAAAAAAAAGAA
Found at i:38912 original size:7 final size:7
Alignment explanation
Indices: 38900--38924 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
38890 TTCTACTGAA
38900 TTCCCAT
1 TTCCCAT
38907 TTCCCAT
1 TTCCCAT
38914 TTCCCAT
1 TTCCCAT
38921 TTCC
1 TTCC
38925 ACTTTTGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.44, G:0.00, T:0.44
Consensus pattern (7 bp):
TTCCCAT
Found at i:39493 original size:11 final size:11
Alignment explanation
Indices: 39477--39502 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39467 ACGTGTGTGA
39477 TTTTTTTTCTT
1 TTTTTTTTCTT
39488 TTTTTTTTCTT
1 TTTTTTTTCTT
39499 TTTT
1 TTTT
39503 GGTGTTGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:39779 original size:2 final size:2
Alignment explanation
Indices: 39772--39803 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
39762 TTAAGCCACG
39772 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39804 GCTCTTCGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:40595 original size:36 final size:36
Alignment explanation
Indices: 40548--40619 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
40538 GAATGGAGAA
40548 AACCATTGTTGGGAGAACTTTATCCCATAGCAGGCC
1 AACCATTGTTGGGAGAACTTTATCCCATAGCAGGCC
40584 AACCATTGTTGGGAGAACTTTATCCCATAGCAGGCC
1 AACCATTGTTGGGAGAACTTTATCCCATAGCAGGCC
40620 CTCGGCTCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (36 bp):
AACCATTGTTGGGAGAACTTTATCCCATAGCAGGCC
Found at i:46806 original size:31 final size:31
Alignment explanation
Indices: 46741--46899 Score: 129
Period size: 31 Copynumber: 5.4 Consensus size: 31
46731 TTTGTGCACA
* * * ** *
46741 TGGCATGCCACGTGCCATTTTTTGAAACATG
1 TGGCGTGCCACGTGTCACTTTTTGGTACACG
* *
46772 TGGCATGCCACGGGTCACTTTTTGGTACACG
1 TGGCGTGCCACGTGTCACTTTTTGGTACACG
** *
46803 TGGCGTGATATGTGTCACTTTTTGGTACA--
1 TGGCGTGCCACGTGTCACTTTTTGGTACACG
* *
46832 T---GTGGCAC--G--ACTTTTTGGTACATG
1 TGGCGTGCCACGTGTCACTTTTTGGTACACG
*
46856 TGGCGTGCCACATGTCACTTTTTGGTACACG
1 TGGCGTGCCACGTGTCACTTTTTGGTACACG
46887 TGGCGTGCCACGT
1 TGGCGTGCCACGT
46900 CGGACACCGT
Statistics
Matches: 102, Mismatches: 17, Indels: 18
0.74 0.12 0.13
Matches are distributed among these distances:
22 13 0.13
24 2 0.02
26 4 0.04
27 6 0.06
29 2 0.02
31 75 0.74
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (31 bp):
TGGCGTGCCACGTGTCACTTTTTGGTACACG
Found at i:46850 original size:53 final size:53
Alignment explanation
Indices: 46788--46890 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
46778 GCCACGGGTC
* ** *
46788 ACTTTTTGGTACACGTGGCGTGATATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
* *
46841 ACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGC
46891 GTGCCACGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
Done.