Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022051.1 Corchorus olitorius cultivar O-4 contig22084, 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: 5225
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Found at i:4401 original size:35 final size:35
Alignment explanation
Indices: 4304--4408 Score: 122
Period size: 35 Copynumber: 3.0 Consensus size: 35
4294 TCCAGTGCGG
* * * * *
4304 TCATTCCAAGAAGTTTTTAATGATTAGAGTTAATC
1 TCATTTCAAGAAGTTTTTGAGGATCAGAGTTGATC
*
4339 TCGTTTCAAGAAGTTTTTGATGG-TCAGAGTTGATC
1 TCATTTCAAGAAGTTTTTGA-GGATCAGAGTTGATC
* *
4374 TCATTTCAAGAAGTTTTCGAGGATCAGAATTGATC
1 TCATTTCAAGAAGTTTTTGAGGATCAGAGTTGATC
4409 CCAAATGATC
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
34 2 0.03
35 56 0.95
36 1 0.02
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (35 bp):
TCATTTCAAGAAGTTTTTGAGGATCAGAGTTGATC
Found at i:4475 original size:35 final size:35
Alignment explanation
Indices: 4422--4635 Score: 313
Period size: 35 Copynumber: 6.1 Consensus size: 35
4412 AATGATCTAG
* *
4422 TGATCTCATTTCAGGAAGTTTTCGATTATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
* *
4457 TAATCTCCTTTCAAGAAGTTTTCGATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
* *
4492 TGATCTCATTCCAAGAAGTTTT-TATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
* *
4526 TGATCTCCTTTTAAGAAGTTTTCGATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
* * *
4561 TGATCTCGTTTCAAGAAGTTTTCAATGGTCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
*
4596 TGATCTCATTTCAAGAAGTTTTCGAGGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
4631 TGATC
1 TGATC
4636 CCAGATGATC
Statistics
Matches: 158, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
34 30 0.19
35 128 0.81
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (35 bp):
TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
Found at i:4487 original size:88 final size:88
Alignment explanation
Indices: 4336--4496 Score: 241
Period size: 88 Copynumber: 1.8 Consensus size: 88
4326 ATTAGAGTTA
* * * *
4336 ATCTCGTTTCAAGAAGTTTTTGATGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCGAGGATCAG
1 ATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTAATCTCATTTCAAGAAGTTTTCGAGGATCAG
4401 AATTGATCCCAAATGATCTAGTG
66 AATTGATCCCAAATGATCTAGTG
* * * *
4424 ATCTCATTTCAGGAAGTTTTCGATTATCAGAGTTAATCTCCTTTCAAGAAGTTTTCGATGATCAG
1 ATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTAATCTCATTTCAAGAAGTTTTCGAGGATCAG
*
4489 AGTTGATC
66 AATTGATC
4497 TCATTCCAAG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 64 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (88 bp):
ATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTAATCTCATTTCAAGAAGTTTTCGAGGATCAG
AATTGATCCCAAATGATCTAGTG
Found at i:4602 original size:104 final size:105
Alignment explanation
Indices: 4422--4635 Score: 322
Period size: 104 Copynumber: 2.0 Consensus size: 105
4412 AATGATCTAG
* * *
4422 TGATCTCATTTCAGGAAGTTTTCGATTATCAGAGTTAATCTCCTTTCAAGAAGTTTTCGATGATC
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTAATCTCCTTTCAAGAAGTTTTCAATGATC
* *
4487 AGAGTTGATCTCATTCCAAGAAGTTTT-TATGATCAGAGT
66 AGAGTTGATCTCATTCCAAGAAGTTTTCGAGGATCAGAGT
* * * * *
4526 TGATCTCCTTTTAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCAATGGTC
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTAATCTCCTTTCAAGAAGTTTTCAATGATC
*
4591 AGAGTTGATCTCATTTCAAGAAGTTTTCGAGGATCAGAGT
66 AGAGTTGATCTCATTCCAAGAAGTTTTCGAGGATCAGAGT
4631 TGATC
1 TGATC
4636 CCAGATGATC
Statistics
Matches: 98, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
104 83 0.85
105 15 0.15
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (105 bp):
TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTAATCTCCTTTCAAGAAGTTTTCAATGATC
AGAGTTGATCTCATTCCAAGAAGTTTTCGAGGATCAGAGT
Found at i:4713 original size:87 final size:88
Alignment explanation
Indices: 4561--4722 Score: 263
Period size: 87 Copynumber: 1.9 Consensus size: 88
4551 TGATCAGAGT
* *
4561 TGATCTCGTTTCAAGAAGTTTTCAATGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCGAGGATC
1 TGATCTCATTTCAAGAAGTTTTCAATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGAGGATC
4626 AGAGTTGATCCCAGATGATCCAG
66 AGAGTTGATCCCAGATGATCCAG
* ** *
4649 TGATCTCATTTCAAGAAG-TTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATC
1 TGATCTCATTTCAAGAAGTTTTCAATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGAGGATC
4713 AGAGTTGATC
66 AGAGTTGATC
4723 TCATTTCAAG
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
87 51 0.75
88 17 0.25
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (88 bp):
TGATCTCATTTCAAGAAGTTTTCAATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGAGGATC
AGAGTTGATCCCAGATGATCCAG
Found at i:4718 original size:35 final size:35
Alignment explanation
Indices: 4649--4918 Score: 420
Period size: 35 Copynumber: 7.8 Consensus size: 35
4639 GATGATCCAG
*
4649 TGATCTCATTTCAAGAAG-TTTCGATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTTGATGATCAGAGT
*
4683 TGATCTCATTTCAAGAAGTTTTTTATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTTGATGATCAGAGT
4718 TGATCTCATTTCAAGAAGTTTTT-ATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTTGATGATCAGAGT
* *
4752 TGATCTCCTTTCAAGAAGCTTTTGATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTTGATGATCAGAGT
* * *
4787 TGATCTCGTTTCAAGAAGTTTTCGGTGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTTGATGATCAGAGT
*
4822 TGATCTCCTTTCAAGAAGTTTTTGATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTTGATGATCAGAGT
* *
4857 TGATCACATTTTAAGAAGTTTTTGATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTTGATGATCAGAGT
*
4892 TGATCGCATTTCAAGAAGTTTTT-ATGA
1 TGATCTCATTTCAAGAAGTTTTTGATGA
4919 GTTGATCTTC
Statistics
Matches: 218, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
34 54 0.25
35 164 0.75
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (35 bp):
TGATCTCATTTCAAGAAGTTTTTGATGATCAGAGT
Found at i:4782 original size:261 final size:261
Alignment explanation
Indices: 4422--4896 Score: 745
Period size: 261 Copynumber: 1.8 Consensus size: 261
4412 AATGATCTAG
* * *
4422 TGATCTCATTTCAGGAAGTTTTCGATTATCAGAGTTAATCTCCTTTCAAGAAGTTTTCGATGATC
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTAATCTCATTTCAAGAAGTTTTCGATGATC
* *
4487 AGAGTTGATCTCATTCCAAGAAGTTTTTATGATCAGAGTTGATCTCCTTTTAAGAAGTTTTCGAT
66 AGAGTTGATCTCATTCCAAGAAGTTTTGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGAT
* * *
4552 GATCAGAGTTGATCTCGTTTCAAGAAGTTTTCAATGGTCAGAGTTGATCTCATTTCAAGAAGTTT
131 GATCAGAGTTGATCTCCTTTCAAGAAGTTTTCAATGATCAGAGTTGATCACATTTCAAGAAGTTT
4617 TCGAGGATCAGAGTTGATCCCAGATGATCCAGTGATCTCATTTCAAGAAGTTTCGATGATCAGAG
196 TCGAGGATCAGAGTTGATCCCAGATGATCCAGTGATCTCATTTCAAGAAGTTTCGATGATCAGAG
4682 T
261 T
** * *
4683 TGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTT-TATGATC
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTAATCTCATTTCAAGAAGTTTTCGATGATC
* * * *
4747 AGAGTTGATCTCCTTTCAAGAAGCTTTTGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGG
66 AGAGTTGATCTCATTCCAAGAAG-TTTTGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGA
** *
4812 TGATCAGAGTTGATCTCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATCACATTTTAAGAAGTT
130 TGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCAATGATCAGAGTTGATCACATTTCAAGAAGTT
* *
4877 TTTGATGATCAGAGTTGATC
195 TTCGAGGATCAGAGTTGATC
4897 GCATTTCAAG
Statistics
Matches: 192, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
260 27 0.14
261 165 0.86
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (261 bp):
TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTAATCTCATTTCAAGAAGTTTTCGATGATC
AGAGTTGATCTCATTCCAAGAAGTTTTGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGAT
GATCAGAGTTGATCTCCTTTCAAGAAGTTTTCAATGATCAGAGTTGATCACATTTCAAGAAGTTT
TCGAGGATCAGAGTTGATCCCAGATGATCCAGTGATCTCATTTCAAGAAGTTTCGATGATCAGAG
T
Found at i:4784 original size:226 final size:226
Alignment explanation
Indices: 4310--4861 Score: 881
Period size: 226 Copynumber: 2.4 Consensus size: 226
4300 GCGGTCATTC
* * * *
4310 CAAGAAGTTTTTAATGATTAGAGTTAATCTCGTTTCAAGAAGTTTTTGATGGTCAGAGTTGATCT
1 CAAGAAG-TTTTGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGATGGTCAGAGTTGATCT
* * *
4375 CATTTCAAGAAGTTTTCGAGGATCAGAATTGATCCCAAATGATCTAGTGATCTCATTTCAGGAAG
65 CATTTCAAGAAGTTTTCGAGGATCAGAGTTGATCCCAAATGATCCAGTGATCTCATTTCAAGAAG
* *
4440 TTTTCGATTATCAGAGTTAATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTCCA
130 TTTTCGATGATCAGAGTTAATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTCCA
4505 AGAAGTTTTTATGATCAGAGTTGATCTCCTTT
195 AGAAGTTTTTATGATCAGAGTTGATCTCCTTT
* *
4537 TAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCAATGGTCAGAGTTGATCT
1 CAAGAAGTTTT-GATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGATGGTCAGAGTTGATCT
*
4602 CATTTCAAGAAGTTTTCGAGGATCAGAGTTGATCCCAGATGATCCAGTGATCTCATTTCAAGAAG
65 CATTTCAAGAAGTTTTCGAGGATCAGAGTTGATCCCAAATGATCCAGTGATCTCATTTCAAGAAG
* ** *
4667 -TTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCA
130 TTTTCGATGATCAGAGTTAATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTCCA
4731 AGAAGTTTTTATGATCAGAGTTGATCTCCTTT
195 AGAAGTTTTTATGATCAGAGTTGATCTCCTTT
* *
4763 CAAGAAGCTTTTGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGGTGATCAGAGTTGATCT
1 CAAGAAG-TTTTGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGATGGTCAGAGTTGATCT
* * *
4828 CCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
65 CATTTCAAGAAGTTTTCGAGGATCAGAGTTGATC
4862 ACATTTTAAG
Statistics
Matches: 300, Mismatches: 23, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
226 181 0.60
227 119 0.40
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.37
Consensus pattern (226 bp):
CAAGAAGTTTTGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGATGGTCAGAGTTGATCTC
ATTTCAAGAAGTTTTCGAGGATCAGAGTTGATCCCAAATGATCCAGTGATCTCATTTCAAGAAGT
TTTCGATGATCAGAGTTAATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTCCAA
GAAGTTTTTATGATCAGAGTTGATCTCCTTT
Done.