Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007814.1 Corchorus capsularis cultivar CVL-1 contig07835, 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: 6980
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Found at i:4913 original size:47 final size:48
Alignment explanation
Indices: 4859--4961 Score: 127
Period size: 47 Copynumber: 2.2 Consensus size: 48
4849 CAGGCAGTTT
* * * ** *
4859 TCTCGGGTCATTCGGGTTTCGGGTCATTTGGGT-TCGGCTTATTCGGG
1 TCTCGGGTCATACGGGTTCCGGATCATTCCGGTATCGGCTCATTCGGG
*
4906 TCTCGGGTCATACGGGTTCCGGATCATTCCGGTATCGGGTCATTCGGG
1 TCTCGGGTCATACGGGTTCCGGATCATTCCGGTATCGGCTCATTCGGG
*
4954 TCCCGGGT
1 TCTCGGGT
4962 TGGGCGGGTT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
47 28 0.60
48 19 0.40
ACGTcount: A:0.09, C:0.23, G:0.35, T:0.33
Consensus pattern (48 bp):
TCTCGGGTCATACGGGTTCCGGATCATTCCGGTATCGGCTCATTCGGG
Found at i:4960 original size:16 final size:16
Alignment explanation
Indices: 4859--4961 Score: 102
Period size: 16 Copynumber: 6.5 Consensus size: 16
4849 CAGGCAGTTT
4859 TCTCGGGTCATTCGGG
1 TCTCGGGTCATTCGGG
* *
4875 TTTCGGGTCATTTGGG
1 TCTCGGGTCATTCGGG
* *
4891 T-TCGGCTTATTCGGG
1 TCTCGGGTCATTCGGG
*
4906 TCTCGGGTCATACGGG
1 TCTCGGGTCATTCGGG
* *
4922 T-TCCGGATCATTCCGG
1 TCT-CGGGTCATTCGGG
*
4938 TATCGGGTCATTCGGG
1 TCTCGGGTCATTCGGG
*
4954 TCCCGGGT
1 TCTCGGGT
4962 TGGGCGGGTT
Statistics
Matches: 69, Mismatches: 15, Indels: 6
0.77 0.17 0.07
Matches are distributed among these distances:
15 13 0.19
16 55 0.80
17 1 0.01
ACGTcount: A:0.09, C:0.23, G:0.35, T:0.33
Consensus pattern (16 bp):
TCTCGGGTCATTCGGG
Found at i:5233 original size:42 final size:42
Alignment explanation
Indices: 5186--5270 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
5176 TATATATTAA
* *
5186 TTTTGAATATTAAATACATAATTGATTATTAGATGAGGTATG
1 TTTTGAATATTAAATACATAATTAATTATCAGATGAGGTATG
* *
5228 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTATG
1 TTTTGAATATTAAATACATAATTAATTATCAGATGAGGTATG
5270 T
1 T
5271 GTCAACATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.42
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCAGATGAGGTATG
Found at i:5753 original size:16 final size:16
Alignment explanation
Indices: 5700--5802 Score: 91
Period size: 16 Copynumber: 6.5 Consensus size: 16
5690 CAGGCACTTT
*
5700 TTTCGGGTAATTTGGG
1 TTTCGGGTAATTCGGG
* * *
5716 TTTCGAGTCA-TCTGG
1 TTTCGGGTAATTCGGG
* *
5731 ATTCGGGTTATTCGGG
1 TTTCGGGTAATTCGGG
* *
5747 TTTCGGGTTATACGGG
1 TTTCGGGTAATTCGGG
* * *
5763 TTTCGGGTCATTTGGA
1 TTTCGGGTAATTCGGG
*
5779 TCTCGGGTAATTCGGG
1 TTTCGGGTAATTCGGG
5795 TTTCGGGT
1 TTTCGGGT
5803 CTACCGGGTC
Statistics
Matches: 67, Mismatches: 19, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
15 10 0.15
16 57 0.85
ACGTcount: A:0.12, C:0.14, G:0.35, T:0.40
Consensus pattern (16 bp):
TTTCGGGTAATTCGGG
Found at i:5753 original size:47 final size:48
Alignment explanation
Indices: 5700--5802 Score: 145
Period size: 47 Copynumber: 2.2 Consensus size: 48
5690 CAGGCACTTT
** *
5700 TTTCGGGTAATTTGGGTTTCGAGTCATCTGGAT-TCGGGTTATTCGGG
1 TTTCGGGTAATACGGGTTTCGAGTCATCTGGATCTCGGGTAATTCGGG
* * *
5747 TTTCGGGTTATACGGGTTTCGGGTCATTTGGATCTCGGGTAATTCGGG
1 TTTCGGGTAATACGGGTTTCGAGTCATCTGGATCTCGGGTAATTCGGG
5795 TTTCGGGT
1 TTTCGGGT
5803 CTACCGGGTC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
47 28 0.57
48 21 0.43
ACGTcount: A:0.12, C:0.14, G:0.35, T:0.40
Consensus pattern (48 bp):
TTTCGGGTAATACGGGTTTCGAGTCATCTGGATCTCGGGTAATTCGGG
Found at i:5815 original size:32 final size:32
Alignment explanation
Indices: 5732--5818 Score: 86
Period size: 32 Copynumber: 2.7 Consensus size: 32
5722 GTCATCTGGA
* * * *
5732 TTCGGGTTATTCGGGTTTCGGGTTATACGGGT
1 TTCGGGTCATCCGGGTCTCGGGTAATACGGGT
** * *
5764 TTCGGGTCATTTGGATCTCGGGTAATTCGGGT
1 TTCGGGTCATCCGGGTCTCGGGTAATACGGGT
5796 TTCGGGTC-TACCGGGTCTCGGGT
1 TTCGGGTCAT-CCGGGTCTCGGGT
5819 TGGACGGGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 1 0.02
32 44 0.98
ACGTcount: A:0.09, C:0.17, G:0.37, T:0.37
Consensus pattern (32 bp):
TTCGGGTCATCCGGGTCTCGGGTAATACGGGT
Found at i:6073 original size:42 final size:42
Alignment explanation
Indices: 6026--6107 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
6016 TAGATATTAA
*
6026 TTTTGAATATTAAATACATAATTGATTATCAGGTGAGGTAGG
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
*
6068 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTA
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTA
6108 TGTGTCAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
Found at i:6647 original size:16 final size:15
Alignment explanation
Indices: 6626--6697 Score: 74
Period size: 16 Copynumber: 4.5 Consensus size: 15
6616 TCATTCGAGT
6626 TTCGGGTCATCTGGG
1 TTCGGGTCATCTGGG
*
6641 TTACGGGTCATTTGGG
1 TT-CGGGTCATCTGGG
*
6657 TCTCGGGTTATCTGGG
1 T-TCGGGTCATCTGGG
6673 TTGCGGGTCATGC-GGG
1 TT-CGGGTCAT-CTGGG
6689 TCTCGGGTC
1 T-TCGGGTC
6698 GGACAGGTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
15 3 0.06
16 42 0.88
17 3 0.06
ACGTcount: A:0.07, C:0.19, G:0.40, T:0.33
Consensus pattern (15 bp):
TTCGGGTCATCTGGG
Found at i:6650 original size:32 final size:32
Alignment explanation
Indices: 6612--6697 Score: 118
Period size: 32 Copynumber: 2.7 Consensus size: 32
6602 GTTAACTTCT
* *
6612 CGGGTCATTCGAGTTTCGGGTCATCTGGGTTA
1 CGGGTCATTCGGGTCTCGGGTCATCTGGGTTA
* * *
6644 CGGGTCATTTGGGTCTCGGGTTATCTGGGTTG
1 CGGGTCATTCGGGTCTCGGGTCATCTGGGTTA
*
6676 CGGGTCATGCGGGTCTCGGGTC
1 CGGGTCATTCGGGTCTCGGGTC
6698 GGACAGGTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.08, C:0.20, G:0.40, T:0.33
Consensus pattern (32 bp):
CGGGTCATTCGGGTCTCGGGTCATCTGGGTTA
Done.