Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010638.1 Corchorus capsularis cultivar CVL-1 contig10659, 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: 19020
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:226 original size:30 final size:30
Alignment explanation
Indices: 181--246 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
171 AAAGGATCGA
* *
181 ATGGCTGGTTATGGCCGGATGGCCCGTGCG
1 ATGGCCGGTTATGGCCGGATGGCCCGCGCG
* *
211 ATGGCCGGTTGTGGCCGGATGGCTCGCGCG
1 ATGGCCGGTTATGGCCGGATGGCCCGCGCG
241 ATGGCC
1 ATGGCC
247 CGTGCGGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.09, C:0.26, G:0.44, T:0.21
Consensus pattern (30 bp):
ATGGCCGGTTATGGCCGGATGGCCCGCGCG
Found at i:2178 original size:33 final size:33
Alignment explanation
Indices: 2136--2240 Score: 174
Period size: 33 Copynumber: 3.2 Consensus size: 33
2126 TTCTCGTCAC
* **
2136 CCAAAACAGAATTATTTTCAATATTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
2169 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
2202 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
2235 TCAAAA
1 CCAAAA
2241 TAGATTCCTT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.29
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:2331 original size:33 final size:33
Alignment explanation
Indices: 2270--2373 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 33
2260 ATTAGCATCC
* *
2270 AAAATAGATTTAGTA-CATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
* * *
2302 AAAACAGATTTAGTGTCATTGCAAACAACACTC
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
** *
2335 AAATTAGGTTTAGTATCATCGCAAACAACA-TCT
1 AAAACAGATTTAGTATCATCGCAAACAACACT-T
2368 AAAACA
1 AAAACA
2374 CTCTTTGCAA
Statistics
Matches: 57, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
32 14 0.25
33 43 0.75
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.25
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCGCAAACAACACTT
Found at i:5620 original size:15 final size:15
Alignment explanation
Indices: 5581--5632 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
5571 AGTAAACACT
* *
5581 TTCGGTGCCATCACC
1 TTCGGTGCCGTCATC
*
5596 TTGGGTGCCGTCATC
1 TTCGGTGCCGTCATC
*
5611 TTCGGTGCCGCCATC
1 TTCGGTGCCGTCATC
*
5626 TTTGGTG
1 TTCGGTG
5633 TCGTTGATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.08, C:0.31, G:0.29, T:0.33
Consensus pattern (15 bp):
TTCGGTGCCGTCATC
Found at i:5716 original size:45 final size:45
Alignment explanation
Indices: 5607--5721 Score: 151
Period size: 45 Copynumber: 2.6 Consensus size: 45
5597 TGGGTGCCGT
5607 CATCTTCGGTGCCGCCATCTTTGGTGTCGTTGATTTCGATGCCAC
1 CATCTTCGGTGCCGCCATCTTTGGTGTCGTTGATTTCGATGCCAC
* *** * * *
5652 CATCTTGGGTGCTATCATCTTTGGTG-CTGTTGATTTTGGTGTCAC
1 CATCTTCGGTGCCGCCATCTTTGGTGTC-GTTGATTTCGATGCCAC
5697 CATCTTCGGTGCCGCCATCTTTGGT
1 CATCTTCGGTGCCGCCATCTTTGGT
5722 ACCATCCATT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 1 0.02
45 57 0.98
ACGTcount: A:0.10, C:0.25, G:0.25, T:0.39
Consensus pattern (45 bp):
CATCTTCGGTGCCGCCATCTTTGGTGTCGTTGATTTCGATGCCAC
Found at i:5720 original size:30 final size:31
Alignment explanation
Indices: 5606--5721 Score: 96
Period size: 30 Copynumber: 3.8 Consensus size: 31
5596 TTGGGTGCCG
*
5606 TCATCTTCGGTGCCGCCATCTTTGGTGTCGT
1 TCATCTTCGGTGCCGCCATCTTTGGTGTCGA
* * * * *
5637 TGAT-TTCGATGCCACCATCTTGGGTG-CTA
1 TCATCTTCGGTGCCGCCATCTTTGGTGTCGA
* * **
5666 TCATCTTTGGTGCTGTTGAT-TTTGGTGTC-A
1 TCATCTTCGGTGCCG-CCATCTTTGGTGTCGA
*
5696 CCATCTTCGGTGCCGCCATCTTTGGT
1 TCATCTTCGGTGCCGCCATCTTTGGT
5722 ACCATCCATT
Statistics
Matches: 62, Mismatches: 19, Indels: 9
0.69 0.21 0.10
Matches are distributed among these distances:
29 6 0.10
30 50 0.81
31 6 0.10
ACGTcount: A:0.10, C:0.25, G:0.25, T:0.40
Consensus pattern (31 bp):
TCATCTTCGGTGCCGCCATCTTTGGTGTCGA
Found at i:6909 original size:18 final size:18
Alignment explanation
Indices: 6886--7030 Score: 98
Period size: 18 Copynumber: 8.1 Consensus size: 18
6876 TGTTGAACAA
*
6886 GTGCGGCAACTTGGTGTG
1 GTGCGGCCACTTGGTGTG
* *
6904 GTGCGGCCACTAGGTGCG
1 GTGCGGCCACTTGGTGTG
* * * *
6922 GTGTGACCATTTGGTATG
1 GTGCGGCCACTTGGTGTG
6940 GTGCGGCCA-TTGGGTGTG
1 GTGCGGCCACTT-GGTGTG
* * * *
6958 GTGCGACCATTTGGTATT
1 GTGCGGCCACTTGGTGTG
*
6976 GTGCAGCCA-TTGGGTGTG
1 GTGCGGCCACTT-GGTGTG
* * *
6994 GTGCGACCATTTGGTATG
1 GTGCGGCCACTTGGTGTG
*
7012 GTGCAGCCA-TTGGGTGTG
1 GTGCGGCCACTT-GGTGTG
7030 G
1 G
7031 CGCCATTTGC
Statistics
Matches: 97, Mismatches: 25, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
17 6 0.06
18 87 0.90
19 4 0.04
ACGTcount: A:0.12, C:0.17, G:0.41, T:0.30
Consensus pattern (18 bp):
GTGCGGCCACTTGGTGTG
Found at i:6936 original size:36 final size:36
Alignment explanation
Indices: 6896--7030 Score: 198
Period size: 36 Copynumber: 3.8 Consensus size: 36
6886 GTGCGGCAAC
* * * * * *
6896 TTGGTGTGGTGCGGCCACTAGGTGCGGTGTGACCAT
1 TTGGTATGGTGCAGCCATTGGGTGTGGTGCGACCAT
*
6932 TTGGTATGGTGCGGCCATTGGGTGTGGTGCGACCAT
1 TTGGTATGGTGCAGCCATTGGGTGTGGTGCGACCAT
*
6968 TTGGTATTGTGCAGCCATTGGGTGTGGTGCGACCAT
1 TTGGTATGGTGCAGCCATTGGGTGTGGTGCGACCAT
7004 TTGGTATGGTGCAGCCATTGGGTGTGG
1 TTGGTATGGTGCAGCCATTGGGTGTGG
7031 CGCCATTTGC
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 91 1.00
ACGTcount: A:0.12, C:0.16, G:0.41, T:0.31
Consensus pattern (36 bp):
TTGGTATGGTGCAGCCATTGGGTGTGGTGCGACCAT
Found at i:10139 original size:20 final size:21
Alignment explanation
Indices: 10114--10159 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
10104 TATTTTTTCT
10114 CTCTCGC-CTC-GCTTCTCTG
1 CTCTCGCACTCAGCTTCTCTG
*
10133 CCTCTCGCACTCATCTTCTCTG
1 -CTCTCGCACTCAGCTTCTCTG
10155 CTCTC
1 CTCTC
10160 CTCCCTCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 8 0.35
22 8 0.35
ACGTcount: A:0.04, C:0.48, G:0.11, T:0.37
Consensus pattern (21 bp):
CTCTCGCACTCAGCTTCTCTG
Found at i:11797 original size:22 final size:23
Alignment explanation
Indices: 11763--11812 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
11753 GATGATACTA
*
11763 CTCG-TGAACTACTCGGGCTCGG
1 CTCGATGAACTACTCGAGCTCGG
*
11785 CTCGATGAA-TACTCGAGTTCGG
1 CTCGATGAACTACTCGAGCTCGG
11807 CTCGAT
1 CTCGAT
11813 TTTTCTCGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (23 bp):
CTCGATGAACTACTCGAGCTCGG
Found at i:15530 original size:3 final size:3
Alignment explanation
Indices: 15522--15592 Score: 133
Period size: 3 Copynumber: 23.7 Consensus size: 3
15512 GAACCAAATA
*
15522 AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
15570 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
15593 AGAACTGACT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17638 original size:40 final size:40
Alignment explanation
Indices: 17557--17651 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 40
17547 TCAAAAGCAA
* * *
17557 TACATGGAACACCAAATTTACCCTTGGCGACTACATAAAAT
1 TACA-GGAAAACCAAATTTACCCTTGCCAACTACATAAAAT
* * * *
17598 TACGGGAAAACCAAATTTACCCTTGCCAACTCCTTCAAAT
1 TACAGGAAAACCAAATTTACCCTTGCCAACTACATAAAAT
*
17638 TACATGAAAACCAA
1 TACAGGAAAACCAA
17652 TGGTGGAGGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 42 0.93
41 3 0.07
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (40 bp):
TACAGGAAAACCAAATTTACCCTTGCCAACTACATAAAAT
Done.