Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008378.1 Corchorus capsularis cultivar CVL-1 contig08399, 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: 14577
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:4687 original size:29 final size:29
Alignment explanation
Indices: 4642--4706 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
4632 CTTAAATGAT
* *
4642 TCCAAATTGTAAATTT-AGGGTGCAAAACG
1 TCCAAAATGTAAATTTAAGGG-ACAAAACG
4671 TCCAAAAT-TAAAGTTTAAGGGACAAAACG
1 TCCAAAATGTAAA-TTTAAGGGACAAAACG
4700 T-CAAAAT
1 TCCAAAAT
4707 CATACAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 10 0.31
29 18 0.56
30 4 0.12
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.25
Consensus pattern (29 bp):
TCCAAAATGTAAATTTAAGGGACAAAACG
Found at i:6949 original size:29 final size:31
Alignment explanation
Indices: 6899--6962 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
6889 CATTTGGATG
*
6899 TTTTGTCCCCTTGGATATCAATTTTG-GACA
1 TTTTGTCCCCTTGAATATCAATTTTGAGACA
*
6929 TTTTGTCCCCTT-AACT-TCAATTTTGAGACG
1 TTTTGTCCCCTTGAA-TATCAATTTTGAGACA
6959 TTTT
1 TTTT
6963 ACGCCCTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.19, C:0.20, G:0.14, T:0.47
Consensus pattern (31 bp):
TTTTGTCCCCTTGAATATCAATTTTGAGACA
Found at i:7243 original size:24 final size:24
Alignment explanation
Indices: 7216--7263 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
7206 GTAGTTTAGT
7216 CATAAATGTAGTATTAAACGTCAA
1 CATAAATGTAGTATTAAACGTCAA
7240 CATAAATGTAGTATTAAACGTCAA
1 CATAAATGTAGTATTAAACGTCAA
7264 TTATTAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29
Consensus pattern (24 bp):
CATAAATGTAGTATTAAACGTCAA
Found at i:8738 original size:14 final size:14
Alignment explanation
Indices: 8719--8745 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8709 AATGATTGAA
8719 GGTATAGCGATTGT
1 GGTATAGCGATTGT
8733 GGTATAGCGATTG
1 GGTATAGCGATTG
8746 CAGTTACAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.37, T:0.33
Consensus pattern (14 bp):
GGTATAGCGATTGT
Found at i:9375 original size:63 final size:64
Alignment explanation
Indices: 9305--9444 Score: 210
Period size: 63 Copynumber: 2.2 Consensus size: 64
9295 CGGGCTTGTA
* *
9305 TCGGGTTCGGGTTGGATTTGGGTCAGGTTAATTCGGGTTCAGGTT-AATTTGGGTTAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAATTCGGGTTCAGGTTGAATTTGGGTCAGGTTAAT
* * *
9368 TCGGGTTCGAGTTGAATTTGGGTCAGGTTAATTCGGGTTCGGGTTGAATTTGGGTCAGGTTCAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAATTCGGGTTCAGGTTGAATTTGGGTCAGGTTAAT
* *
9432 TCAGCTTCGGGTT
1 TCGGGTTCGGGTT
9445 CTGTTTGGGT
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
63 42 0.62
64 26 0.38
ACGTcount: A:0.15, C:0.11, G:0.36, T:0.39
Consensus pattern (64 bp):
TCGGGTTCGGGTTGAATTTGGGTCAGGTTAATTCGGGTTCAGGTTGAATTTGGGTCAGGTTAAT
Found at i:9441 original size:32 final size:32
Alignment explanation
Indices: 9305--9444 Score: 210
Period size: 32 Copynumber: 4.4 Consensus size: 32
9295 CGGGCTTGTA
*
9305 TCGGGTTCGGGTTGGATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
* *
9337 TCGGGTTCAGGTT-AATTTGGGTTAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
*
9368 TCGGGTTCGAGTTGAATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
*
9400 TCGGGTTCGGGTTGAATTTGGGTCAGGTTCAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
* *
9432 TCAGCTTCGGGTT
1 TCGGGTTCGGGTT
9445 CTGTTTGGGT
Statistics
Matches: 97, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
31 27 0.28
32 70 0.72
ACGTcount: A:0.15, C:0.11, G:0.36, T:0.39
Consensus pattern (32 bp):
TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
Found at i:9613 original size:16 final size:16
Alignment explanation
Indices: 9592--9692 Score: 103
Period size: 16 Copynumber: 6.3 Consensus size: 16
9582 TTTTCATAAA
*
9592 TTTTCGGATTCGAGTT
1 TTTTCGGATTCGAGCT
*
9608 TTTTCGGATTTGAGCT
1 TTTTCGGATTCGAGCT
* * *
9624 TTTTCGGGTTCGGGGT
1 TTTTCGGATTCGAGCT
* *
9640 TTTTCGGGTTTGAGCT
1 TTTTCGGATTCGAGCT
* * *
9656 TTTTCGGGTTCGTGTT
1 TTTTCGGATTCGAGCT
*
9672 TTTTCGGATTTGAGCT
1 TTTTCGGATTCGAGCT
9688 TTTTC
1 TTTTC
9693 AGGTTCGGAT
Statistics
Matches: 69, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 69 1.00
ACGTcount: A:0.07, C:0.13, G:0.29, T:0.51
Consensus pattern (16 bp):
TTTTCGGATTCGAGCT
Found at i:9643 original size:32 final size:32
Alignment explanation
Indices: 9592--9707 Score: 169
Period size: 32 Copynumber: 3.6 Consensus size: 32
9582 TTTTCATAAA
* *
9592 TTTTCGGATTCGAGTTTTTTCGGATTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGATTTGAGCT
* *
9624 TTTTCGGGTTCGGGGTTTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGATTTGAGCT
*
9656 TTTTCGGGTTCGTGTTTTTTCGGATTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGATTTGAGCT
* *
9688 TTTTCAGGTTCGGATTTTTT
1 TTTTCGGGTTCGGGTTTTTT
9708 TGTGTTCAGG
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 74 1.00
ACGTcount: A:0.08, C:0.12, G:0.28, T:0.52
Consensus pattern (32 bp):
TTTTCGGGTTCGGGTTTTTTCGGATTTGAGCT
Found at i:9728 original size:64 final size:64
Alignment explanation
Indices: 9600--9731 Score: 149
Period size: 64 Copynumber: 2.1 Consensus size: 64
9590 AATTTTCGGA
* * * ***
9600 TTCGAGTTTTTTCGGATTTGAGCTTTTTCGGGTTCGGGGTTTTTCGGGTTTGAGCTTTTTCGGG
1 TTCGAGTTTTTTCGGATTTGAGCTTTTTCAGGTTCGGAGTTTTTCGGGTTTCAGCTTAGACGGG
* * * * *
9664 TTCGTGTTTTTTCGGATTTGAGCTTTTTCAGGTTCGGATTTTTTTGTG-TTCAGGTTCAGACGGG
1 TTCGAGTTTTTTCGGATTTGAGCTTTTTCAGGTTCGGAGTTTTTCGGGTTTCAGCTT-AGACGGG
9728 TTCG
1 TTCG
9732 GATAGTTGAC
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
63 6 0.11
64 50 0.89
ACGTcount: A:0.08, C:0.13, G:0.30, T:0.48
Consensus pattern (64 bp):
TTCGAGTTTTTTCGGATTTGAGCTTTTTCAGGTTCGGAGTTTTTCGGGTTTCAGCTTAGACGGG
Found at i:12440 original size:33 final size:33
Alignment explanation
Indices: 12390--12480 Score: 128
Period size: 33 Copynumber: 2.8 Consensus size: 33
12380 TGTGTTCGTT
12390 GAGGCACAATATTAGTGGGAGCAATCTCATTCC
1 GAGGCACAATATTAGTGGGAGCAATCTCATTCC
* * * *
12423 GAGGCACAACATCAGTGGCAGCAATCTCATTCT
1 GAGGCACAATATTAGTGGGAGCAATCTCATTCC
* *
12456 GAGGCATAATATTAGTGGGAACAAT
1 GAGGCACAATATTAGTGGGAGCAAT
12481 AGAATCCAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (33 bp):
GAGGCACAATATTAGTGGGAGCAATCTCATTCC
Done.