Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013955.1 Corchorus capsularis cultivar CVL-1 contig13976, 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: 17181
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:4999 original size:21 final size:21
Alignment explanation
Indices: 4975--5041 Score: 89
Period size: 21 Copynumber: 3.1 Consensus size: 21
4965 GCCTAATTTA
*
4975 ATTCTATTTTCTAAATTACTT
1 ATTCTAATTTCTAAATTACTT
*
4996 ATTCTAATATCTAAATTACTTT
1 ATTCTAATTTCTAAATTAC-TT
*
5018 AATTCTAATTTCTAAATCACTT
1 -ATTCTAATTTCTAAATTACTT
5040 AT
1 AT
5042 ATTTGAAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.47
22 4 0.10
23 17 0.43
ACGTcount: A:0.34, C:0.15, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTCTAATTTCTAAATTACTT
Found at i:5026 original size:23 final size:23
Alignment explanation
Indices: 4971--5039 Score: 97
Period size: 23 Copynumber: 3.1 Consensus size: 23
4961 TTAAGCCTAA
*
4971 TTTAATTCTATTTTCTAAATTAC
1 TTTAATTCTAATTTCTAAATTAC
*
4994 -TT-ATTCTAATATCTAAATTAC
1 TTTAATTCTAATTTCTAAATTAC
*
5015 TTTAATTCTAATTTCTAAATCAC
1 TTTAATTCTAATTTCTAAATTAC
5038 TT
1 TT
5040 ATATTTGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.43
22 4 0.10
23 19 0.47
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAATTCTAATTTCTAAATTAC
Found at i:5457 original size:7 final size:6
Alignment explanation
Indices: 5446--5475 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5436 TTTCGCTTTC
*
5446 CTTTTT CTTTTT CTTTTT CTTTTT ATTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
5476 TTATATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (6 bp):
CTTTTT
Found at i:6245 original size:14 final size:16
Alignment explanation
Indices: 6220--6253 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
6210 AACAACTAAG
6220 AAAGCAAACAGATTA-
1 AAAGCAAACAGATTAT
6235 AAAGC-AACAGATTAT
1 AAAGCAAACAGATTAT
6250 AAAG
1 AAAG
6254 AAAGTAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (16 bp):
AAAGCAAACAGATTAT
Found at i:6790 original size:33 final size:33
Alignment explanation
Indices: 6722--6791 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
6712 GCTGTGCCAC
* **
6722 GGCATGCCGTCCCAGGAGGGAGGTAATGTTTAT
1 GGCATGCCGCCCCAGGAGGGAGGTAATGTCCAT
*
6755 GGCATGCCGCCCCAGGAGGGCGGCT-ATGTCCAT
1 GGCATGCCGCCCCAGGAGGGAGG-TAATGTCCAT
6788 GGCA
1 GGCA
6792 GGTCGCCCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.19, C:0.26, G:0.37, T:0.19
Consensus pattern (33 bp):
GGCATGCCGCCCCAGGAGGGAGGTAATGTCCAT
Found at i:6939 original size:31 final size:32
Alignment explanation
Indices: 6871--6942 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 32
6861 CCGCCCCAAG
* **
6871 AGGGCGGTATACCATGGCTCATGCCGCCTTCC
1 AGGGCGGCATACCATGGCTCATGCCGCCCCCC
* *
6903 TGGGCGGCATACCGTGG-TCATGCCGCCCCCC
1 AGGGCGGCATACCATGGCTCATGCCGCCCCCC
6934 AGGGCGGCA
1 AGGGCGGCA
6943 CGGTCATCAG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 20 0.59
32 14 0.41
ACGTcount: A:0.14, C:0.36, G:0.33, T:0.17
Consensus pattern (32 bp):
AGGGCGGCATACCATGGCTCATGCCGCCCCCC
Found at i:7148 original size:21 final size:21
Alignment explanation
Indices: 7123--7166 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
7113 CAAAAGTGTA
* *
7123 AAAAAAGGGGCGGTTTTTAGC
1 AAAAAAGGGGCGCTGTTTAGC
*
7144 AAAAAATGGGCGCTGTTTAGC
1 AAAAAAGGGGCGCTGTTTAGC
7165 AA
1 AA
7167 TACCCAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.30, T:0.23
Consensus pattern (21 bp):
AAAAAAGGGGCGCTGTTTAGC
Found at i:12886 original size:33 final size:33
Alignment explanation
Indices: 12838--12917 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
12828 GCCGGGGATG
* *
12838 ACCGGGCAGGAGGCGCGGTAATGGCCT-GGCTCA
1 ACCGGGCAGGTGGCGCGGCAA-GGCCTGGGCTCA
* *
12871 ACCGGGCATGTGGCGCGGCAAGGGCTGGGCTCA
1 ACCGGGCAGGTGGCGCGGCAAGGCCTGGGCTCA
*
12904 TCCGGGCAGGTGGC
1 ACCGGGCAGGTGGC
12918 TCGGGTGGCC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
32 4 0.10
33 36 0.90
ACGTcount: A:0.15, C:0.28, G:0.45, T:0.12
Consensus pattern (33 bp):
ACCGGGCAGGTGGCGCGGCAAGGCCTGGGCTCA
Done.