Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008143.1 Corchorus capsularis cultivar CVL-1 contig08164, 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: 37079
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:4710 original size:21 final size:21
Alignment explanation
Indices: 4685--4724 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4675 TTTTTGCGTT
*
4685 TTTTCTATAAAAAAAATTGTG
1 TTTTCCATAAAAAAAATTGTG
*
4706 TTTTCCCTAAAAAAAATTG
1 TTTTCCATAAAAAAAATTG
4725 CTTTTTGCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.40
Consensus pattern (21 bp):
TTTTCCATAAAAAAAATTGTG
Found at i:9143 original size:18 final size:17
Alignment explanation
Indices: 9116--9151 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
9106 TTTCTCTTCA
9116 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
9133 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
9151 T
1 T
9152 TTAGGTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:10124 original size:15 final size:15
Alignment explanation
Indices: 10101--10155 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
10091 GATCACACAA
*
10101 CATGATTGTTCGCAC
1 CATGGTTGTTCGCAC
*
10116 CATGGTTGTTTGCAC
1 CATGGTTGTTCGCAC
* *
10131 CATTGTGGTTCGCAC
1 CATGGTTGTTCGCAC
*
10146 CATTGTTGTT
1 CATGGTTGTT
10156 TGTGCCATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.40
Consensus pattern (15 bp):
CATGGTTGTTCGCAC
Found at i:10142 original size:30 final size:30
Alignment explanation
Indices: 10108--10203 Score: 102
Period size: 30 Copynumber: 3.2 Consensus size: 30
10098 CAACATGATT
*
10108 GTTCGCACCATGGTTGTTTGCACCATTGTG
1 GTTCGCACCATTGTTGTTTGCACCATTGTG
** *
10138 GTTCGCACCATTGTTGTTTGTGCCATTATG
1 GTTCGCACCATTGTTGTTTGCACCATTGTG
* * * * * *
10168 ATTTGCACCGTTGTGGTTCGCACCATTGTT
1 GTTCGCACCATTGTTGTTTGCACCATTGTG
10198 GTTCGC
1 GTTCGC
10204 GCCGTTATGG
Statistics
Matches: 51, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.12, C:0.23, G:0.25, T:0.40
Consensus pattern (30 bp):
GTTCGCACCATTGTTGTTTGCACCATTGTG
Found at i:10173 original size:45 final size:45
Alignment explanation
Indices: 10124--10219 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 45
10114 ACCATGGTTG
* *
10124 TTTGCACCATTGTGGTTCGCACCATTGTTGTTTGTGCCATTATGA
1 TTTGCACCATTGTGGTTCGCACCATTGTTGTTCGCGCCATTATGA
* * *
10169 TTTGCACCGTTGTGGTTCGCACCATTGTTGTTCGCGCCGTTATGG
1 TTTGCACCATTGTGGTTCGCACCATTGTTGTTCGCGCCATTATGA
10214 TTTGCA
1 TTTGCA
10220 ACCACCCTAG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.12, C:0.22, G:0.25, T:0.41
Consensus pattern (45 bp):
TTTGCACCATTGTGGTTCGCACCATTGTTGTTCGCGCCATTATGA
Found at i:10190 original size:15 final size:15
Alignment explanation
Indices: 10108--10203 Score: 84
Period size: 15 Copynumber: 6.4 Consensus size: 15
10098 CAACATGATT
* *
10108 GTTCGCACCATGGTT
1 GTTCGCACCATTGTG
*
10123 GTTTGCACCATTGTG
1 GTTCGCACCATTGTG
*
10138 GTTCGCACCATTGTT
1 GTTCGCACCATTGTG
* ** *
10153 GTTTGTGCCATTATG
1 GTTCGCACCATTGTG
* * *
10168 ATTTGCACCGTTGTG
1 GTTCGCACCATTGTG
*
10183 GTTCGCACCATTGTT
1 GTTCGCACCATTGTG
10198 GTTCGC
1 GTTCGC
10204 GCCGTTATGG
Statistics
Matches: 62, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 62 1.00
ACGTcount: A:0.12, C:0.23, G:0.25, T:0.40
Consensus pattern (15 bp):
GTTCGCACCATTGTG
Found at i:10868 original size:15 final size:14
Alignment explanation
Indices: 10847--10881 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
10837 AAAGAAAACT
*
10847 AAAAAAGAAAGGGA
1 AAAAAAGAAAAGGA
10861 AGAAAAAGAAAAGGA
1 A-AAAAAGAAAAGGA
10876 AAAAAA
1 AAAAAA
10882 CGTAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAGGA
Found at i:13348 original size:15 final size:15
Alignment explanation
Indices: 13325--13354 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13315 GAAATCCTAA
*
13325 AAAATAAAGAAAAAT
1 AAAACAAAGAAAAAT
13340 AAAACAAAGAAAAAT
1 AAAACAAAGAAAAAT
13355 TAAGGATTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (15 bp):
AAAACAAAGAAAAAT
Found at i:16805 original size:33 final size:35
Alignment explanation
Indices: 16735--16814 Score: 137
Period size: 35 Copynumber: 2.3 Consensus size: 35
16725 TTTAAATCGC
*
16735 AAACTTTTTTTTTTAGAAAAAACGGAAAAAAGGAA
1 AAACTTTTTTTTTTAGAAAAAACGGAAAAAAGCAA
16770 AAACTTTTTTTTTTAGAAAAAACGG-AAAAA-CAA
1 AAACTTTTTTTTTTAGAAAAAACGGAAAAAAGCAA
16803 AAACTTTTTTTT
1 AAACTTTTTTTT
16815 AGAGCAGATT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 14 0.32
34 5 0.11
35 25 0.57
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.35
Consensus pattern (35 bp):
AAACTTTTTTTTTTAGAAAAAACGGAAAAAAGCAA
Found at i:18274 original size:11 final size:10
Alignment explanation
Indices: 18256--18289 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
18246 CATTTGTTTC
18256 AAATCTTCAA
1 AAATCTTCAA
18266 AATATCTTCAA
1 AA-ATCTTCAA
18277 GAAATCTTCAA
1 -AAATCTTCAA
18288 AA
1 AA
18290 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:20092 original size:31 final size:31
Alignment explanation
Indices: 20023--20124 Score: 123
Period size: 31 Copynumber: 3.3 Consensus size: 31
20013 TCCTTTTGTG
* * **
20023 CACGTGGCATGCCACGTGCCATTTTTTGAAA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
*
20054 CATGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* * *
20085 CACGTGGCGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
*
20116 CATGTGGCA
1 CACGTGGCA
20125 CGACTTTTTG
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (31 bp):
CACGTGGCATGCCACGTGTCACTTTTTGGTA
Found at i:20176 original size:53 final size:53
Alignment explanation
Indices: 20074--20176 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 53
20064 GCCACGTGTC
** * *
20074 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGATACACGTGGCACG
* * * *
20127 ACTTTTTGGTACATGTGGTGTGCCACATGTCACTTTTTGATATACGTGGC
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGATACACGTGGC
20177 GTGCCACGTC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.38
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGATACACGTGGCACG
Found at i:33005 original size:10 final size:10
Alignment explanation
Indices: 32992--33016 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
32982 TATATTCAGC
32992 CCATATAAGT
1 CCATATAAGT
33002 CCATATAAGT
1 CCATATAAGT
33012 CCATA
1 CCATA
33017 ATTGAAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (10 bp):
CCATATAAGT
Done.