Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009030.1 Corchorus capsularis cultivar CVL-1 contig09051, 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: 24516
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:1878 original size:32 final size:32
Alignment explanation
Indices: 1837--1898 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
1827 GGGGCATTTC
*
1837 TTTATCTCACTTAGGGTTTATATATCATGTAT
1 TTTATCTCACTTAGGGTTTAGATATCATGTAT
*
1869 TTTATCTCACTTAGGGTTTAGATTTCATGT
1 TTTATCTCACTTAGGGTTTAGATATCATGT
1899 CATGTCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.50
Consensus pattern (32 bp):
TTTATCTCACTTAGGGTTTAGATATCATGTAT
Found at i:2819 original size:58 final size:59
Alignment explanation
Indices: 2726--2841 Score: 189
Period size: 58 Copynumber: 2.0 Consensus size: 59
2716 GAGGTCTTGG
* * *
2726 GTTCTAGTCTCACGGAATGTGAGTTTATTTGTAATTTATTTGTTTGTGTA-TTTGGTAA
1 GTTCTAGTCTCACGAAATGTGAGTTTATTTATAATTTATTTATTTGTGTATTTTGGTAA
*
2784 GTTCTAGTCTCATGAAATGTGAGTTTATTTATAATTTATTTATTTGTGTATTTTGGTA
1 GTTCTAGTCTCACGAAATGTGAGTTTATTTATAATTTATTTATTTGTGTATTTTGGTA
2842 TGTTTGGTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
58 46 0.87
59 7 0.13
ACGTcount: A:0.22, C:0.06, G:0.20, T:0.52
Consensus pattern (59 bp):
GTTCTAGTCTCACGAAATGTGAGTTTATTTATAATTTATTTATTTGTGTATTTTGGTAA
Found at i:4390 original size:13 final size:13
Alignment explanation
Indices: 4368--4401 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
4358 TTTAAAATAA
*
4368 ATATAAATTATAT
1 ATATATATTATAT
4381 ATATATATTATAT
1 ATATATATTATAT
4394 ATATATAT
1 ATATATAT
4402 ACATTATCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATATATATTATAT
Found at i:4396 original size:17 final size:17
Alignment explanation
Indices: 4376--4408 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4366 AAATATAAAT
*
4376 TATATATATATATTATA
1 TATATATATACATTATA
4393 TATATATATACATTAT
1 TATATATATACATTAT
4409 CAGTTTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATATATACATTATA
Found at i:5183 original size:2 final size:2
Alignment explanation
Indices: 5176--5203 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5166 TGGGTTATGC
5176 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
5204 GATCAGGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6517 original size:68 final size:68
Alignment explanation
Indices: 6439--6574 Score: 236
Period size: 68 Copynumber: 2.0 Consensus size: 68
6429 ATTACGTTTA
* *
6439 ATTGCATTGTTCTTTATAATTTTTTTATAAGTGGTAGATTAACTTGATTTAATTAATTGATTTTT
1 ATTGCATTGTTCTTTATAATTTTTTTATAAGTAGTACATTAACTTGATTTAATTAATTGATTTTT
6504 TTC
66 TTC
* *
6507 ATTGCATTGTTCTTTGTAATTTTTTTATAATTAGTACATTAACTTGATTTAATTAATTGATTTTT
1 ATTGCATTGTTCTTTATAATTTTTTTATAAGTAGTACATTAACTTGATTTAATTAATTGATTTTT
6572 TTC
66 TTC
6575 TTAAGGATTG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.26, C:0.07, G:0.10, T:0.57
Consensus pattern (68 bp):
ATTGCATTGTTCTTTATAATTTTTTTATAAGTAGTACATTAACTTGATTTAATTAATTGATTTTT
TTC
Found at i:8870 original size:13 final size:13
Alignment explanation
Indices: 8852--8877 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8842 CGACATGTAT
8852 ACACTCTCATTGA
1 ACACTCTCATTGA
8865 ACACTCTCATTGA
1 ACACTCTCATTGA
8878 GGAGATCACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (13 bp):
ACACTCTCATTGA
Found at i:11374 original size:21 final size:21
Alignment explanation
Indices: 11322--11374 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
11312 ATTATAAAGA
* * *
11322 AAACCTCTAAATATAAATAAG
1 AAACCTCCAACTACAAATAAG
11343 AAACCTCCAACTACAAATAAG
1 AAACCTCCAACTACAAATAAG
11364 AAACCTCCAAC
1 AAACCTCCAAC
11375 ATAGGTTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.53, C:0.26, G:0.04, T:0.17
Consensus pattern (21 bp):
AAACCTCCAACTACAAATAAG
Found at i:14316 original size:2 final size:2
Alignment explanation
Indices: 14311--14339 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
14301 CTTTCAAAAA
14311 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14340 GATGGTAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14434 original size:29 final size:29
Alignment explanation
Indices: 14378--14440 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
14368 TAGTCATTAA
*
14378 AATTCCATCTACCAATATACGTGGTACAT
1 AATTCCATCTACCAATAAACGTGGTACAT
* * * *
14407 AATTCCATTTACCCATAAATGTGTTACAT
1 AATTCCATCTACCAATAAACGTGGTACAT
14436 AATTC
1 AATTC
14441 TTTAGTTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (29 bp):
AATTCCATCTACCAATAAACGTGGTACAT
Found at i:15836 original size:23 final size:23
Alignment explanation
Indices: 15785--15836 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
15775 TTTAAAGTTA
* *
15785 CTAAAAAAGCTACAGTGATTATT
1 CTAAAAAAGCTAAAGTGAATATT
15808 CT-AAAAAG-TATAAGTGAATATT
1 CTAAAAAAGCTA-AAGTGAATATT
15830 CTAAAAA
1 CTAAAAA
15837 GAATATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 2 0.08
22 17 0.68
23 6 0.24
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.29
Consensus pattern (23 bp):
CTAAAAAAGCTAAAGTGAATATT
Done.