Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018843.1 Corchorus olitorius cultivar O-4 contig18876, 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: 33190
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:6874 original size:206 final size:206
Alignment explanation
Indices: 6520--6907 Score: 668
Period size: 206 Copynumber: 1.9 Consensus size: 206
6510 TTTATTTTTT
* * *
6520 AAACATATTTCTTAAATGTCATTGCTTAATTATTATAGTTTTATTCTACTAGAAACTCTATTTTT
1 AAACATATTTCTTAAATGCCATTGCTTAACTATTATAGTTTTATTCTACTAGAAACTCTATTTTA
* * *
6585 ATTCAATTAAATCTAATATCTTTATAATTACTTTATTTTTACCAATTTAGTCTTTTTCAATGAAA
66 ATTCAATTAAATCTAATATCTTTATAATTACTTTATTTTTACCAATTTACTATTTTTCAATAAAA
* * * *
6650 ATTCGGATATATTAAAATTTTTTAATATATAGTTTTATTCTACTAAAAACTCAACTTTTGAATCG
131 ATTAGAATATATTAAAATTTTTTAATATACAATTTTATTCTACTAAAAACTCAACTTTTGAATCG
6715 ACCATTATACC
196 ACCATTATACC
6726 AAACATATTTCTTAAATGCCATTGCTTAACTATTATAGTTTTATTCTACTAGAAACTCTATTTTA
1 AAACATATTTCTTAAATGCCATTGCTTAACTATTATAGTTTTATTCTACTAGAAACTCTATTTTA
* *
6791 ATTCAATTAAATCTAATATCTTTATAATTACTTTATTTTTACCATTTTACTATTTTTTAATAAAA
66 ATTCAATTAAATCTAATATCTTTATAATTACTTTATTTTTACCAATTTACTATTTTTCAATAAAA
6856 ATTAGAATATATTAAAATTTTTTAATATACAATTTTATTCTACTAAAAACTC
131 ATTAGAATATATTAAAATTTTTTAATATACAATTTTATTCTACTAAAAACTC
6908 TATTTTCATT
Statistics
Matches: 170, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
206 170 1.00
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (206 bp):
AAACATATTTCTTAAATGCCATTGCTTAACTATTATAGTTTTATTCTACTAGAAACTCTATTTTA
ATTCAATTAAATCTAATATCTTTATAATTACTTTATTTTTACCAATTTACTATTTTTCAATAAAA
ATTAGAATATATTAAAATTTTTTAATATACAATTTTATTCTACTAAAAACTCAACTTTTGAATCG
ACCATTATACC
Found at i:8138 original size:10 final size:10
Alignment explanation
Indices: 8123--8149 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
8113 CAATTTTGTA
8123 AAAAAAAAAT
1 AAAAAAAAAT
8133 AAAAAAAAAT
1 AAAAAAAAAT
8143 AAAAAAA
1 AAAAAAA
8150 GGCTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAAAAT
Found at i:9857 original size:7 final size:7
Alignment explanation
Indices: 9845--9873 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
9835 AGAAATAAAT
9845 AATTGTG
1 AATTGTG
9852 AATTGTG
1 AATTGTG
9859 AATTGTG
1 AATTGTG
9866 AATTGTG
1 AATTGTG
9873 A
1 A
9874 TGCCACAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (7 bp):
AATTGTG
Found at i:11202 original size:2 final size:2
Alignment explanation
Indices: 11189--11221 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
11179 CTGGTTTATT
*
11189 TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11222 TAACATGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22173 original size:28 final size:29
Alignment explanation
Indices: 22141--22217 Score: 147
Period size: 28 Copynumber: 2.7 Consensus size: 29
22131 TATTTTGGCT
22141 AAAAAACTAATTATGAATTTATTGCC-AA
1 AAAAAACTAATTATGAATTTATTGCCAAA
22169 AAAAAACTAATTATGAATTTATTGCCAAA
1 AAAAAACTAATTATGAATTTATTGCCAAA
22198 AAAAAACTAATTATGAATTT
1 AAAAAACTAATTATGAATTT
22218 TTCGCTTAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 26 0.54
29 22 0.46
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAAAACTAATTATGAATTTATTGCCAAA
Found at i:29662 original size:70 final size:70
Alignment explanation
Indices: 29580--29720 Score: 237
Period size: 70 Copynumber: 2.0 Consensus size: 70
29570 CTAATCTGTT
* *
29580 TTAAATTAAATGAAGGTTAAAAACTTAAGCATACTATTAATTTTGTCTTAAAGAAGTCAATTATT
1 TTAAATTAAATGAAGGTTAAAAACTTAAGCATACTACTAATTTTGTCTTAAAGAAGCCAATTATT
29645 AGAGC
66 AGAGC
* **
29650 TTAAATTAAATGAAGGTTCAAATTTTAAGCATACTACTAATTTTGTCTTAAAGAAGCCAATTATT
1 TTAAATTAAATGAAGGTTAAAAACTTAAGCATACTACTAATTTTGTCTTAAAGAAGCCAATTATT
29715 AGAGC
66 AGAGC
29720 T
1 T
29721 GGCAAAATTT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (70 bp):
TTAAATTAAATGAAGGTTAAAAACTTAAGCATACTACTAATTTTGTCTTAAAGAAGCCAATTATT
AGAGC
Found at i:31029 original size:91 final size:91
Alignment explanation
Indices: 30874--31053 Score: 267
Period size: 91 Copynumber: 2.0 Consensus size: 91
30864 TTTAAAAAAC
**
30874 AAAATTAATTCAGAAAATGGGTATGCGTCAACTCCCCAGCCTGCTTGTGGAGTCCAAAATTTACA
1 AAAATTAATTCAGAAAATGGACATGCGTCAACTCCCCAGCCTGCTTGTGGAGTCCAAAATTTACA
30939 CTGA-CAGTATATCAAATAATTATCCT
66 CT-ATCAGTATATCAAATAATTATCCT
*
30965 AAAATTAATTCAGAAAATGGACATGTGTCAA-TCCCTCA-CCTCGCTTGTGGAGTCCAAAATTTA
1 AAAATTAATTCAGAAAATGGACATGCGTCAACTCCC-CAGCCT-GCTTGTGGAGTCCAAAATTTA
* *
31028 CAGTATCAGTGTATCAAATAATTATC
64 CACTATCAGTATATCAAATAATTATC
31054 TTATATATAT
Statistics
Matches: 81, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
90 8 0.10
91 73 0.90
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (91 bp):
AAAATTAATTCAGAAAATGGACATGCGTCAACTCCCCAGCCTGCTTGTGGAGTCCAAAATTTACA
CTATCAGTATATCAAATAATTATCCT
Found at i:32679 original size:31 final size:30
Alignment explanation
Indices: 32608--32680 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
32598 CCCGAAAATC
* **
32608 CAATTCAGGATATAACGTTTGATGAGGTGA
1 CAATTCAGGATATAACGTTCGAAAAGGTGA
32638 CAATTCAGGATATAACGTTACGAAAAGGTTG-
1 CAATTCAGGATATAACGTT-CGAAAAGG-TGA
*
32669 CAATTAAGGATA
1 CAATTCAGGATA
32681 ATTTCAGACG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 19 0.51
31 16 0.43
32 2 0.05
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.27
Consensus pattern (30 bp):
CAATTCAGGATATAACGTTCGAAAAGGTGA
Done.