Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021053.1 Corchorus olitorius cultivar O-4 contig21086, 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: 18853
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:8255 original size:31 final size:30
Alignment explanation
Indices: 8217--8317 Score: 105
Period size: 31 Copynumber: 3.3 Consensus size: 30
8207 AAGTACCTGA
*
8217 TTAGTCCCTGTACTATAGAAAAAAGATCAAT
1 TTAGTCCCTCTACTAT-GAAAAAAGATCAAT
* * * ***
8248 TTAGTCCCTCCATTATCAAATCTG-TCAAT
1 TTAGTCCCTCTACTATGAAAAAAGATCAAT
*
8277 TTAGTCCCTCTACTATTGAAAAGAGATCAAT
1 TTAGTCCCTCTACTA-TGAAAAAAGATCAAT
8308 TTAGTCCCTC
1 TTAGTCCCTC
8318 CGTGAAATTG
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
29 18 0.33
30 9 0.16
31 28 0.51
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.34
Consensus pattern (30 bp):
TTAGTCCCTCTACTATGAAAAAAGATCAAT
Found at i:9568 original size:14 final size:15
Alignment explanation
Indices: 9544--9573 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
9534 TTATATTTTA
9544 AAAAGCTAAACAATT
1 AAAAGCTAAACAATT
9559 AAAA-CTAAACAATT
1 AAAAGCTAAACAATT
9573 A
1 A
9574 TTATCATCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.63, C:0.13, G:0.03, T:0.20
Consensus pattern (15 bp):
AAAAGCTAAACAATT
Found at i:12134 original size:40 final size:40
Alignment explanation
Indices: 12079--12158 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
12069 CTGGTAGGTG
12079 TACCGTGCCTGGAAGGTGAGGTCCTGAGTTCAAGTCTCAC
1 TACCGTGCCTGGAAGGTGAGGTCCTGAGTTCAAGTCTCAC
*
12119 TACCGTGCCTGGAAGGTGAGGTCCTGGGTTCAAGTCTCAC
1 TACCGTGCCTGGAAGGTGAGGTCCTGAGTTCAAGTCTCAC
12159 GGAATGTGAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (40 bp):
TACCGTGCCTGGAAGGTGAGGTCCTGAGTTCAAGTCTCAC
Found at i:12448 original size:47 final size:47
Alignment explanation
Indices: 12394--12486 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
12384 AAATCTGGAA
12394 TTAATTTGTTATCTTAATTATTAGGCGGGATAACTGGTGGTAAAATT
1 TTAATTTGTTATCTTAATTATTAGGCGGGATAACTGGTGGTAAAATT
12441 TTAATTTGTTATCTTAATTATTAGGCGGGATAACTGGTGGTAAAAT
1 TTAATTTGTTATCTTAATTATTAGGCGGGATAACTGGTGGTAAAAT
12487 CAGGCGGGTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.30, C:0.06, G:0.22, T:0.42
Consensus pattern (47 bp):
TTAATTTGTTATCTTAATTATTAGGCGGGATAACTGGTGGTAAAATT
Found at i:12526 original size:28 final size:28
Alignment explanation
Indices: 12494--12548 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
12484 AATCAGGCGG
12494 GTCAAAAAATATTTTCCATCACCAACGA
1 GTCAAAAAATATTTTCCATCACCAACGA
*
12522 GTCAAAAAATATTTTCCGTCACCAACG
1 GTCAAAAAATATTTTCCATCACCAACG
12549 GAATAATAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.25
Consensus pattern (28 bp):
GTCAAAAAATATTTTCCATCACCAACGA
Found at i:14718 original size:27 final size:27
Alignment explanation
Indices: 14655--14722 Score: 102
Period size: 27 Copynumber: 2.5 Consensus size: 27
14645 AAGGGATAAA
*
14655 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCGGAGGCTGCTCGGATGTATAGG
*
14682 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCGGAGGCTGCTCGGATGTATAGG
14709 GAGAG-GGAGGCTGC
1 GAG-GCGGAGGCTGC
14723 CGCTGGTGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 38 0.97
28 1 0.03
ACGTcount: A:0.19, C:0.15, G:0.47, T:0.19
Consensus pattern (27 bp):
GAGGCGGAGGCTGCTCGGATGTATAGG
Found at i:14721 original size:33 final size:27
Alignment explanation
Indices: 14655--14711 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
14645 AAGGGATAAA
14655 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCTGAGGCTGCTCGGATGTATAGG
14682 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCTGAGGCTGCTCGGATGTATAGG
14709 GAG
1 GAG
14712 AGGGAGGCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.14, G:0.46, T:0.21
Consensus pattern (27 bp):
GAGGCTGAGGCTGCTCGGATGTATAGG
Found at i:16779 original size:20 final size:20
Alignment explanation
Indices: 16750--16788 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16740 TATTTTGGGA
16750 TTTTTATGGATGTTTATGTC
1 TTTTTATGGATGTTTATGTC
* *
16770 TTTTTTTGGATTTTTATGT
1 TTTTTATGGATGTTTATGT
16789 ATATTGGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.18, T:0.67
Consensus pattern (20 bp):
TTTTTATGGATGTTTATGTC
Found at i:17647 original size:3 final size:3
Alignment explanation
Indices: 17588--17627 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
17578 ATGAATACAT
17588 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17628 CTAAACTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Done.