Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013504.1 Corchorus capsularis cultivar CVL-1 contig13525, 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: 35884
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:1915 original size:11 final size:11
Alignment explanation
Indices: 1901--1938 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1891 ATTCATAACA
1901 AATTTATAATT
1 AATTTATAATT
1912 AATTTATAATT
1 AATTTATAATT
1923 -ATTTGATAATT
1 AATTT-ATAATT
*
1934 TATTT
1 AATTT
1939 TATATAGGAA
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:5153 original size:2 final size:2
Alignment explanation
Indices: 5146--5176 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5136 AATAAAATCC
5146 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5177 GTTCTTGCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7102 original size:2 final size:2
Alignment explanation
Indices: 7097--7130 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
7087 TTATATAAGT
*
7097 TA TA TA TA TA TA TA CA TA TA TA CTA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA T
7131 TTAGTAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:7368 original size:16 final size:16
Alignment explanation
Indices: 7349--7407 Score: 84
Period size: 16 Copynumber: 3.8 Consensus size: 16
7339 TCGGGTTGCC
7349 TCGGGTTCGGGTAATT
1 TCGGGTTCGGGTAATT
* *
7365 TCGGATTCGGTTAATT
1 TCGGGTTCGGGTAATT
*
7381 TCGGGTTCGGTTAATT
1 TCGGGTTCGGGTAATT
7397 TC-GGTTCGGGT
1 TCGGGTTCGGGT
7408 TCGGATAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
15 8 0.21
16 31 0.79
ACGTcount: A:0.12, C:0.14, G:0.34, T:0.41
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:7420 original size:21 final size:21
Alignment explanation
Indices: 7380--7421 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
7370 TTCGGTTAAT
* *
7380 TTCGGGTTCGGTTAATTTCGG
1 TTCGGGTTCGGATAAGTTCGG
*
7401 TTCGGGTTCGGATAGGTTCGG
1 TTCGGGTTCGGATAAGTTCGG
7422 GATGTTGACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.14, G:0.38, T:0.38
Consensus pattern (21 bp):
TTCGGGTTCGGATAAGTTCGG
Found at i:7774 original size:15 final size:15
Alignment explanation
Indices: 7726--7774 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
7716 GAGGAACATA
7726 TAATTATTTATATAT
1 TAATTATTTATATAT
**
7741 TAATT-TTT-TGA-GG
1 TAATTATTTAT-ATAT
7754 TAATTATTTATATAT
1 TAATTATTTATATAT
7769 TAATTA
1 TAATTA
7775 ATAGGGTGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
13 6 0.23
14 8 0.31
15 12 0.46
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (15 bp):
TAATTATTTATATAT
Found at i:10026 original size:16 final size:16
Alignment explanation
Indices: 10001--10104 Score: 113
Period size: 16 Copynumber: 6.6 Consensus size: 16
9991 GGCAATTGGG
* *
10001 CGGGATCGGGTGTTTT
1 CGGGTTCGGGTATTTT
* *
10017 CGGGTACGGGTAATTT
1 CGGGTTCGGGTATTTT
*
10033 CGGGCTCGGGT-TTTT
1 CGGGTTCGGGTATTTT
* *
10048 TGGGTTCGGTTATTTT
1 CGGGTTCGGGTATTTT
*
10064 CGGGTTCGGGT-TATGT
1 CGGGTTCGGGTAT-TTT
10080 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
10096 CGGGTTCGG
1 CGGGTTCGG
10105 ACTCGGATTT
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
15 12 0.17
16 58 0.82
17 1 0.01
ACGTcount: A:0.07, C:0.13, G:0.40, T:0.39
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:10074 original size:47 final size:48
Alignment explanation
Indices: 10013--10104 Score: 132
Period size: 47 Copynumber: 1.9 Consensus size: 48
10003 GGATCGGGTG
* *
10013 TTTTCGGGTACGGGTAATTTCGGGCTCGGGT-TTTTTGGGTTCGGTTA
1 TTTTCGGGTACGGGTAATGTCGGGCTCGGGTATTTTCGGGTTCGGTTA
* * *
10060 TTTTCGGGTTCGGGTTATGTCGGGTTCGGGTATTTTCGGGTTCGG
1 TTTTCGGGTACGGGTAATGTCGGGCTCGGGTATTTTCGGGTTCGG
10105 ACTCGGATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 27 0.69
48 12 0.31
ACGTcount: A:0.07, C:0.13, G:0.38, T:0.42
Consensus pattern (48 bp):
TTTTCGGGTACGGGTAATGTCGGGCTCGGGTATTTTCGGGTTCGGTTA
Found at i:11324 original size:18 final size:18
Alignment explanation
Indices: 11303--11363 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
11293 TTAATTAGAA
*
11303 TTAATTAGTTTATTAGTT
1 TTAATTAGTTTATTAGTG
* *
11321 TTAATTACTTTTTTAGTG
1 TTAATTAGTTTATTAGTG
11339 TTAATTAGTTTATTAG-G
1 TTAATTAGTTTATTAGTG
11356 ATTAATTA
1 -TTAATTA
11364 CTGTTAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 1 0.03
18 36 0.97
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (18 bp):
TTAATTAGTTTATTAGTG
Found at i:11327 original size:10 final size:10
Alignment explanation
Indices: 11293--11349 Score: 50
Period size: 10 Copynumber: 6.1 Consensus size: 10
11283 TTAATTAAGG
**
11293 TTAATTAGAA
1 TTAATTAGTT
11303 TTAATTAG-T
1 TTAATTAGTT
11312 TT-ATTAGTT
1 TTAATTAGTT
*
11321 TTAATTACTT
1 TTAATTAGTT
*
11331 TT--TTAGTG
1 TTAATTAGTT
11339 TTAATTAGTT
1 TTAATTAGTT
11349 T
1 T
11350 ATTAGGATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
8 11 0.29
9 5 0.13
10 22 0.58
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.58
Consensus pattern (10 bp):
TTAATTAGTT
Found at i:13725 original size:50 final size:49
Alignment explanation
Indices: 13650--13747 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 49
13640 TGGCCGACTC
* *
13650 ATTTGTATTTTCATTTCTCTTATATAACATCTTATACATTTGTATTTGTG
1 ATTTGTATTTCCATTTCTCTTATATAACAT-TTAAACATTTGTATTTGTG
*
13700 ATTTGTATTTCCCTTTCT-TCTATATAACATTTAAACATTTGTATTTGT
1 ATTTGTATTTCCATTTCTCT-TATATAACATTTAAACATTTGTATTTGT
13748 AAAATGGGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
49 18 0.41
50 26 0.59
ACGTcount: A:0.24, C:0.13, G:0.07, T:0.55
Consensus pattern (49 bp):
ATTTGTATTTCCATTTCTCTTATATAACATTTAAACATTTGTATTTGTG
Found at i:15938 original size:18 final size:19
Alignment explanation
Indices: 15910--15949 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
15900 ATGCATAGAC
15910 TAATAAATAACACTAAAAA
1 TAATAAATAACACTAAAAA
* *
15929 TAAT-AATAACATTAATAA
1 TAATAAATAACACTAAAAA
15947 TAA
1 TAA
15950 ATGCTACGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (19 bp):
TAATAAATAACACTAAAAA
Found at i:23657 original size:24 final size:24
Alignment explanation
Indices: 23640--23685 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
23630 GAGCAGCAGA
*
23640 AAAAGAAAATGAGTGAGCAACAAC
1 AAAAGAAAAAGAGTGAGCAACAAC
* *
23664 AGAAGAAAAAGAGTGAGTAACA
1 AAAAGAAAAAGAGTGAGCAACA
23686 GGTTAAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.59, C:0.09, G:0.24, T:0.09
Consensus pattern (24 bp):
AAAAGAAAAAGAGTGAGCAACAAC
Found at i:30412 original size:6 final size:6
Alignment explanation
Indices: 30396--30427 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
30386 AAATCAAAGC
30396 AAATC- AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
30428 GCAAATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (6 bp):
AAATCT
Found at i:34106 original size:42 final size:42
Alignment explanation
Indices: 34059--34152 Score: 170
Period size: 42 Copynumber: 2.2 Consensus size: 42
34049 AAGCATGGCT
* *
34059 GGGCAGGCGGTGCAAGTGGTGCGGCTGTGGCTTGGTAGGGCC
1 GGGCAGGCGGTGCAAGTGGCGCGGCTGTGGCTTGGCAGGGCC
34101 GGGCAGGCGGTGCAAGTGGCGCGGCTGTGGCTTGGCAGGGCC
1 GGGCAGGCGGTGCAAGTGGCGCGGCTGTGGCTTGGCAGGGCC
34143 GGGCAGGCGG
1 GGGCAGGCGG
34153 CACGGCAAGG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.10, C:0.21, G:0.54, T:0.15
Consensus pattern (42 bp):
GGGCAGGCGGTGCAAGTGGCGCGGCTGTGGCTTGGCAGGGCC
Done.