Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022947.1 Corchorus olitorius cultivar O-4 contig22980, 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: 21506
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2111 original size:21 final size:21
Alignment explanation
Indices: 2087--2131 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2077 GGCGCCCACA
* *
2087 TGGTTGCCTTGAGCACCCATG
1 TGGTTGCCTTGAGAACCCAGG
**
2108 TGGTTTTCTTGAGAACCCAGG
1 TGGTTGCCTTGAGAACCCAGG
2129 TGG
1 TGG
2132 GCAGTGTCAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (21 bp):
TGGTTGCCTTGAGAACCCAGG
Found at i:3759 original size:15 final size:15
Alignment explanation
Indices: 3709--3759 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
3699 AGAAGATGGT
3709 GGCACCAAAATCGAC
1 GGCACCAAAATCGAC
* * * *
3724 GACATCGAAGAT-GAT
1 GGCA-CCAAAATCGAC
3739 GGCACCAAAATCGAC
1 GGCACCAAAATCGAC
3754 GGCACC
1 GGCACC
3760 GAAAGTGTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 5 0.19
15 16 0.62
16 5 0.19
ACGTcount: A:0.37, C:0.29, G:0.24, T:0.10
Consensus pattern (15 bp):
GGCACCAAAATCGAC
Found at i:6415 original size:49 final size:48
Alignment explanation
Indices: 6345--6478 Score: 159
Period size: 49 Copynumber: 2.8 Consensus size: 48
6335 ATGTTTTACA
*
6345 TTTCC-TGCACTTTTTCTCAATTTTTACA-ACAAAATTGAACCTTTAAT
1 TTTCCTTGCACTTTTTCTCAATTTTTA-AGACAAAATTGAACATTTAAT
* *
6392 TTTCCTTGCACCTTTTTCTCAATTTTTAAGACAAAATTGAATATTTACT
1 TTTCCTTGCA-CTTTTTCTCAATTTTTAAGACAAAATTGAACATTTAAT
* * *
6441 TTTCATTGCTCTTTTTATCAATTTTT--GTACAAAATTGA
1 TTTCCTTGCACTTTTTCTCAATTTTTAAG-ACAAAATTGA
6479 TTGGCACACT
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
46 1 0.01
47 15 0.19
48 20 0.26
49 41 0.53
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.48
Consensus pattern (48 bp):
TTTCCTTGCACTTTTTCTCAATTTTTAAGACAAAATTGAACATTTAAT
Found at i:6731 original size:87 final size:87
Alignment explanation
Indices: 6585--6759 Score: 314
Period size: 87 Copynumber: 2.0 Consensus size: 87
6575 AGCCAACTTT
*
6585 GCAACTTCCACACGGGGTTAGGTATGATATATCTGTAAACCACTGCCTCCCAAGCATCACTCAAT
1 GCAACTTCCACACGGGGTTAGGCATGATATATCTGTAAACCACTGCCTCCCAAGCATCACTCAAT
6650 GCATGTGGAATCGGTTTTCTGG
66 GCATGTGGAATCGGTTTTCTGG
*
6672 GCAACTTCCACACGGGGTTAGGCATGATATATCTGTAAACCGCTGCCTCCCAAGCATCACTCAAT
1 GCAACTTCCACACGGGGTTAGGCATGATATATCTGTAAACCACTGCCTCCCAAGCATCACTCAAT
* *
6737 GCATGTGGAGTCGGTTTTTTGG
66 GCATGTGGAATCGGTTTTCTGG
6759 G
1 G
6760 AATTCAAGAC
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.27
Consensus pattern (87 bp):
GCAACTTCCACACGGGGTTAGGCATGATATATCTGTAAACCACTGCCTCCCAAGCATCACTCAAT
GCATGTGGAATCGGTTTTCTGG
Found at i:10524 original size:92 final size:95
Alignment explanation
Indices: 10343--10537 Score: 256
Period size: 92 Copynumber: 2.1 Consensus size: 95
10333 GTTGCAAAGC
*
10343 ATTTGAGATCATATTTATAGAATATTAATCAGCAAAAATAAAAAAATATATTAAGAAAGATAAAA
1 ATTTGAGATCATATTTATAGAATATTAATCAGCAAAAATAAAAAAATATATCAAGAAAGATAAAA
* * *
10408 GAAAAAAAGGTGAATGACTAATAGAAAACT
66 GAAAAAAAGATAAATGACAAATAGAAAACT
* * *
10438 GTTTGAGATCATATTTATAG-ATCATTAATGAG-AAAACTAAAAAAA-A-ATCAA-AATAGATAA
1 ATTTGAGATCATATTTATAGAAT-ATTAATCAGCAAAAATAAAAAAATATATCAAGAA-AGATAA
* *
10498 AATAAAAAAAGATAAATGACAAATAGAAAAGT
64 AAGAAAAAAAGATAAATGACAAATAGAAAACT
10530 ATTTGAGA
1 ATTTGAGA
10538 ACATTTTTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
91 2 0.02
92 44 0.50
93 1 0.01
94 14 0.16
95 27 0.31
ACGTcount: A:0.57, C:0.05, G:0.13, T:0.25
Consensus pattern (95 bp):
ATTTGAGATCATATTTATAGAATATTAATCAGCAAAAATAAAAAAATATATCAAGAAAGATAAAA
GAAAAAAAGATAAATGACAAATAGAAAACT
Found at i:14852 original size:37 final size:37
Alignment explanation
Indices: 14811--14881 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
14801 ACATAATTAT
* *
14811 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
14848 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
14882 GTTGATCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Done.