Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015342.1 Corchorus capsularis cultivar CVL-1 contig15363, 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: 20254
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.33
Found at i:3803 original size:15 final size:16
Alignment explanation
Indices: 3783--3821 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
3773 AGGTGGGTTC
3783 GGGTTCGGATA-CTTT
1 GGGTTCGGATATCTTT
* *
3798 GGGTTCGGCTATTTTT
1 GGGTTCGGATATCTTT
3814 GGGTTCGG
1 GGGTTCGG
3822 GTTATGTCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.08, C:0.13, G:0.38, T:0.41
Consensus pattern (16 bp):
GGGTTCGGATATCTTT
Found at i:4053 original size:30 final size:29
Alignment explanation
Indices: 3998--4054 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 29
3988 TATTATAAGT
*
3998 TTATTGATAATATATAATATAATATAACA
1 TTATTGATAATATATAATAAAATATAACA
*
4027 TTATT-ATCATATATATATAAAGATATAA
1 TTATTGATAATATATA-ATAAA-ATATAA
4055 TATAACCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.38
29 9 0.38
30 6 0.25
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (29 bp):
TTATTGATAATATATAATAAAATATAACA
Found at i:4555 original size:23 final size:23
Alignment explanation
Indices: 4529--4573 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
4519 GGGTTCGGGT
*
4529 TCGGACTCAGGTTGGGATCGAGC
1 TCGGACTCAGGTCGGGATCGAGC
* * *
4552 TCGGTCTCGGGTCGGGTTCGAG
1 TCGGACTCAGGTCGGGATCGAG
4574 TATTTTCGGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.42, T:0.24
Consensus pattern (23 bp):
TCGGACTCAGGTCGGGATCGAGC
Found at i:4935 original size:68 final size:68
Alignment explanation
Indices: 4826--4954 Score: 249
Period size: 68 Copynumber: 1.9 Consensus size: 68
4816 ACCTTTAACG
*
4826 TGCAAGAAAAGTAATGAATTTATTGCTTAATAGATTTTATATGGAAAGACACACTGTTCAAAAAA
1 TGCAAGAAAAGTAATGAATTTATTGCTTAATAGATTTTATATGGAAAGACACACCGTTCAAAAAA
4891 AAA
66 AAA
4894 TGCAAGAAAAGTAATGAATTTATTGCTTAATAGATTTTATATGGAAAGACACACCGTTCAA
1 TGCAAGAAAAGTAATGAATTTATTGCTTAATAGATTTTATATGGAAAGACACACCGTTCAA
4955 TCTATAAATG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 60 1.00
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (68 bp):
TGCAAGAAAAGTAATGAATTTATTGCTTAATAGATTTTATATGGAAAGACACACCGTTCAAAAAA
AAA
Found at i:5667 original size:16 final size:16
Alignment explanation
Indices: 5646--5732 Score: 86
Period size: 16 Copynumber: 5.4 Consensus size: 16
5636 GGTTAACTTC
*
5646 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
5662 TCGGGTCATACGGGTC
1 TCGGGTCATTCGGGTT
* *
5678 TCGGATTATTCGGGTT
1 TCGGGTCATTCGGGTT
*
5694 TCGGATCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
* *
5710 ACGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
5726 TCGGGTC
1 TCGGGTC
5733 GGGTTGTTTA
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
15 2 0.04
16 53 0.93
17 2 0.04
ACGTcount: A:0.10, C:0.20, G:0.36, T:0.34
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:5687 original size:32 final size:32
Alignment explanation
Indices: 5644--5732 Score: 110
Period size: 32 Copynumber: 2.8 Consensus size: 32
5634 CGGGTTAACT
5644 TCTCGGGTTATTCGGGTTTCGGGTCATAC-GGG
1 TCTCGGGTTATTCGGGTTTCGGGTCAT-CTGGG
* *
5676 TCTCGGATTATTCGGGTTTCGGATCATCTGGG
1 TCTCGGGTTATTCGGGTTTCGGGTCATCTGGG
* *
5708 T-TACGGGTCATTCGGGTCTCGGGTC
1 TCT-CGGGTTATTCGGGTTTCGGGTC
5733 GGGTTGTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
31 2 0.04
32 47 0.96
ACGTcount: A:0.10, C:0.20, G:0.35, T:0.35
Consensus pattern (32 bp):
TCTCGGGTTATTCGGGTTTCGGGTCATCTGGG
Found at i:7434 original size:143 final size:143
Alignment explanation
Indices: 7176--7462 Score: 565
Period size: 143 Copynumber: 2.0 Consensus size: 143
7166 TGGTTGCTCT
7176 ATGATGTAGTAAAACGGTCTCATTTAATATTTTTTTCTTTTTAAGAGGGGGAAGAATTTTGAGAT
1 ATGATGTAGTAAAACGGTCTCATTTAATATTTTTTTCTTTTTAAGAGGGGGAAGAATTTTGAGAT
7241 TGATGGGTTGAAGATGAAATTAAATACTTAGGTTCAATTAACTTGTCCAAAAAAAAATCGTCAAA
66 TGATGGGTTGAAGATGAAATTAAATACTTAGGTTCAATTAACTTGTCCAAAAAAAAATCGTCAAA
7306 ATTACATGTCAAA
131 ATTACATGTCAAA
7319 ATGATGTAGTAAAACGGTCTCATTTAATATTTTTTTCTTTTTAAGAGGGGGAAGAATTTTGAGAT
1 ATGATGTAGTAAAACGGTCTCATTTAATATTTTTTTCTTTTTAAGAGGGGGAAGAATTTTGAGAT
7384 TGATGGGTTGAAGATGAAATTAAATACTTAGGTTCAATTAACTTGTCCAAAAAAAAATCGTCAAA
66 TGATGGGTTGAAGATGAAATTAAATACTTAGGTTCAATTAACTTGTCCAAAAAAAAATCGTCAAA
*
7449 ATTATATGTCAAA
131 ATTACATGTCAAA
7462 A
1 A
7463 AGTTAGTAAC
Statistics
Matches: 143, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
143 143 1.00
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (143 bp):
ATGATGTAGTAAAACGGTCTCATTTAATATTTTTTTCTTTTTAAGAGGGGGAAGAATTTTGAGAT
TGATGGGTTGAAGATGAAATTAAATACTTAGGTTCAATTAACTTGTCCAAAAAAAAATCGTCAAA
ATTACATGTCAAA
Done.