Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004860.1 Corchorus capsularis cultivar CVL-1 contig04878, 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: 13193
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Found at i:4671 original size:31 final size:31
Alignment explanation
Indices: 4633--4713 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 31
4623 AGCATCTGAT
* *
4633 GTGGCATGCCACGTGTACCAAAAAATGTCAC
1 GTGGCATGCCACGTGTACCAAAAAAGGACAC
4664 GTGGCATGCCACGTGTA-C--AAAAGGACAC
1 GTGGCATGCCACGTGTACCAAAAAAGGACAC
*
4692 ATGGCATGCCACGTGT-CCAAAA
1 GTGGCATGCCACGTGTACCAAAA
4714 TGCCACGTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
28 24 0.55
30 3 0.07
31 17 0.39
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (31 bp):
GTGGCATGCCACGTGTACCAAAAAAGGACAC
Found at i:5643 original size:65 final size:65
Alignment explanation
Indices: 5539--5669 Score: 246
Period size: 65 Copynumber: 2.0 Consensus size: 65
5529 TTCCCACCTA
5539 AAATTAGATTCCACCAACCAAACATGGGAATGTTATTCCCTCTA-CTTAACTTACCACACTTTCC
1 AAATTAGATTCCACCAACCAAACATGGGAATGTTATTCCCTCTATC-TAACTTACCACACTTTCC
5603 C
65 C
5604 AAATTAGATTCCACCAACCAAACATGGGAATGTTATTCCCTCTATCTAACTTACCACACTTTCCC
1 AAATTAGATTCCACCAACCAAACATGGGAATGTTATTCCCTCTATCTAACTTACCACACTTTCCC
5669 A
1 A
5670 CTACATTCCA
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
65 64 0.98
66 1 0.02
ACGTcount: A:0.33, C:0.31, G:0.08, T:0.29
Consensus pattern (65 bp):
AAATTAGATTCCACCAACCAAACATGGGAATGTTATTCCCTCTATCTAACTTACCACACTTTCCC
Found at i:9801 original size:33 final size:34
Alignment explanation
Indices: 9764--9831 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 34
9754 TTTTGCCTCC
9764 AATGATCATATATGG-TCTACTTCTAGGCTAATT
1 AATGATCATATATGGTTCTACTTCTAGGCTAATT
9797 AATGATCATATATGGTTTCTACTTCTAGGCTAATT
1 AATGATCATATATGG-TTCTACTTCTAGGCTAATT
9832 GCTCAAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 15 0.45
35 18 0.55
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (34 bp):
AATGATCATATATGGTTCTACTTCTAGGCTAATT
Found at i:10548 original size:13 final size:13
Alignment explanation
Indices: 10530--10555 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10520 GTGCATGTAT
10530 AAAAAAAGAAAAG
1 AAAAAAAGAAAAG
10543 AAAAAAAGAAAAG
1 AAAAAAAGAAAAG
10556 GGTTCTATCA
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:12677 original size:22 final size:22
Alignment explanation
Indices: 12652--12720 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
12642 GAATTGTTAG
* *
12652 TAATCACAATCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
12674 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
*
12696 TAA-CATCGCTATGAAATTTTGA
1 TAATCA-CACTATGAAATTTTGA
12718 TAA
1 TAA
12721 ATCTTCTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
21 2 0.05
22 39 0.95
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:12737 original size:23 final size:23
Alignment explanation
Indices: 12709--12788 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
12699 CATCGCTATG
12709 AAATTTTGATAAATCTTCTTATA
1 AAATTTTGATAAATCTTCTTATA
* * *
12732 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCTTATA
* *
12755 AAATTTTGATAACT-TTCTTATG
1 AAATTTTGATAAATCTTCTTATA
*
12777 AAATCTTGATAA
1 AAATTTTGATAA
12789 TTACAAATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
22 16 0.33
23 32 0.67
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCTTATA
Found at i:12773 original size:45 final size:46
Alignment explanation
Indices: 12687--12788 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 46
12677 TCACACTATG
* * *
12687 AAATTGTGAT-AACATCGCTATGAAATTTTGATAAATCTTCTTATA
1 AAATTTTGATAAACATCCCTATAAAATTTTGATAAATCTTCTTATA
* * *
12732 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACT-TTCTTATG
1 AAATTTTGATAAACATCCCTATAAAATTTTGATAAATCTTCTTATA
*
12777 AAATCTTGATAA
1 AAATTTTGATAA
12789 TTACAAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
45 27 0.55
46 22 0.45
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (46 bp):
AAATTTTGATAAACATCCCTATAAAATTTTGATAAATCTTCTTATA
Found at i:12822 original size:60 final size:61
Alignment explanation
Indices: 12732--12850 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 61
12722 TCTTCTTATA
*
12732 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTCTTATGAAATCTTGATAATTAC
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTATTATGAAATCTTGATAATTAC
* ** * *
12793 AAATTTTGAT-AACCTCCCTATGATTTTTTGATAACTTTATTATGAAATTTTGTTAATT
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTATTATGAAATCTTGATAATT
12851 TCCCTATGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
60 42 0.81
61 10 0.19
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (61 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTATTATGAAATCTTGATAATTAC
Found at i:12843 original size:22 final size:22
Alignment explanation
Indices: 12663--12957 Score: 153
Period size: 22 Copynumber: 13.6 Consensus size: 22
12653 AATCACAATC
**
12663 TGAAATTTTGATAA-TCACACTA
1 TGAAATTTTGATAACTTTC-CTA
* *
12685 TGAAATTGTGATAAC-ATCGCTA
1 TGAAATTTTGATAACTTTC-CTA
* *
12707 TGAAATTTTGATAAATCTTCTTA
1 TGAAATTTTGATAACT-TTCCTA
* * *
12730 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AACTTTCCTA
* *
12753 TAAAATTTTGATAACTTTCTTA
1 TGAAATTTTGATAACTTTCCTA
*
12775 TGAAATCTTGATAA---T--TA
1 TGAAATTTTGATAACTTTCCTA
* * *
12792 -CAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACTTTCCTA
** **
12813 TGATTTTTTGATAACTTTATTA
1 TGAAATTTTGATAACTTTCCTA
*
12835 TGAAATTTTGTTAA-TTTCCCTA
1 TGAAATTTTGATAACTTT-CCTA
* * *
12857 TGAAATTTTGATCTAC-ATACTA
1 TGAAATTTTGAT-AACTTTCCTA
* *
12879 TGAAATTTTGATAA-TTCTCTTG
1 TGAAATTTTGATAACTT-TCCTA
* ***
12901 TGAAATTTTGAAAACTAAACTA
1 TGAAATTTTGATAACTTTCCTA
* * * *
12923 TGAATTTTTCATAACCTTCATA
1 TGAAATTTTGATAACTTTCCTA
12945 TGAAATTTTGATA
1 TGAAATTTTGATA
12958 TCCTCCCTGA
Statistics
Matches: 199, Mismatches: 58, Indels: 32
0.69 0.20 0.11
Matches are distributed among these distances:
16 11 0.06
17 2 0.01
19 1 0.01
21 6 0.03
22 143 0.72
23 32 0.16
24 4 0.02
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACTTTCCTA
Found at i:13001 original size:19 final size:20
Alignment explanation
Indices: 12945--12995 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
12935 AACCTTCATA
12945 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
12965 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
12984 TGAAATTTTGAT
1 TGAAATTTTGAT
12996 TACTCCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:13135 original size:22 final size:22
Alignment explanation
Indices: 13103--13154 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
13093 TCTCATTTTG
*
13103 AAAA-TTTGATAAGCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
13124 AAAATTTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
13146 AAAATTTTG
1 AAAATTTTG
13155 TTGACCCCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTTTAT
Done.