Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023231.1 Corchorus olitorius cultivar O-4 contig23264, 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: 12437
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Found at i:3707 original size:6 final size:6
Alignment explanation
Indices: 3696--3756 Score: 79
Period size: 6 Copynumber: 10.2 Consensus size: 6
3686 CTTGCAATGT
* * *
3696 CACCTC CACCTC CA-CTCC CACCCC CAGCTC CAACTC CACCTC CACCTC
1 CACCTC CACCTC CACCT-C CACCTC CACCTC CACCTC CACCTC CACCTC
3744 CACCTC CACCTC C
1 CACCTC CACCTC C
3757 TCCTTACACG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
5 2 0.04
6 45 0.94
7 1 0.02
ACGTcount: A:0.18, C:0.66, G:0.02, T:0.15
Consensus pattern (6 bp):
CACCTC
Found at i:4233 original size:42 final size:42
Alignment explanation
Indices: 4179--4376 Score: 209
Period size: 42 Copynumber: 4.7 Consensus size: 42
4169 CTTACTAGGC
* * *
4179 ATGGAGCTTCGCCACCTCCAGCCCCACCTCCGCCTTCTCAAT
1 ATGGAGTTTCGCCACCTCCACCCCCACCTCCGCCTCCTCAAT
* * * * **
4221 ATAGAGTTTCGCCACCTCCACCACCACCGCCGCCGCCTACTAGGC
1 ATGGAGTTTCGCCACCTCCACCCCCACCTCCGCCTCCT-C-A-AT
* *
4266 ATGGAGCTTCGCCACCTCCACCCCCACCTCCGCCTTCTCAAT
1 ATGGAGTTTCGCCACCTCCACCCCCACCTCCGCCTCCTCAAT
* *
4308 ATGGAGTTTCGCCACCTCC-CCCCCACCACCGCCTCCTCAAC
1 ATGGAGTTTCGCCACCTCCACCCCCACCTCCGCCTCCTCAAT
* * * *
4349 ATGGAGCTTCTCCTCCTCCACCACCACC
1 ATGGAGTTTCGCCACCTCCACCCCCACC
4377 ACCACCACCC
Statistics
Matches: 127, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
41 35 0.28
42 56 0.44
43 2 0.02
44 2 0.02
45 32 0.25
ACGTcount: A:0.18, C:0.49, G:0.14, T:0.19
Consensus pattern (42 bp):
ATGGAGTTTCGCCACCTCCACCCCCACCTCCGCCTCCTCAAT
Found at i:4269 original size:87 final size:86
Alignment explanation
Indices: 4160--4376 Score: 305
Period size: 87 Copynumber: 2.5 Consensus size: 86
4150 ACCAACTTCG
* * *
4160 CCACTGCCGCTTACTAGGCATGGAGCTTCGCCACCTCCAGCCCCACCTCCGCCTTCTCAATATAG
1 CCACCGCCGCCTACTAGGCATGGAGCTTCGCCACCTCCACCCCCACCTCCGCCTTCTCAATATAG
4225 AGTTTCGCCACCTCCACCACCA
66 AGTTTCGCCACCTCC-CCACCA
* *
4247 CCGCCGCCGCCTACTAGGCATGGAGCTTCGCCACCTCCACCCCCACCTCCGCCTTCTCAATATGG
1 CCACCGCCGCCTACTAGGCATGGAGCTTCGCCACCTCCACCCCCACCTCCGCCTTCTCAATATAG
*
4312 AGTTTCGCCACCTCCCCCCCA
66 AGTTTCGCCACCTCCCCACCA
* * * * *
4333 CCACCGCCTCCT-C-A-ACATGGAGCTTCTCCTCCTCCACCACCACC
1 CCACCGCCGCCTACTAGGCATGGAGCTTCGCCACCTCCACCCCCACC
4377 ACCACCACCC
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
83 26 0.22
84 1 0.01
85 1 0.01
86 15 0.13
87 75 0.64
ACGTcount: A:0.18, C:0.49, G:0.14, T:0.19
Consensus pattern (86 bp):
CCACCGCCGCCTACTAGGCATGGAGCTTCGCCACCTCCACCCCCACCTCCGCCTTCTCAATATAG
AGTTTCGCCACCTCCCCACCA
Found at i:4477 original size:30 final size:27
Alignment explanation
Indices: 4418--4498 Score: 83
Period size: 27 Copynumber: 2.9 Consensus size: 27
4408 CCTCCTCCAG
* * *
4418 CATTTGGAGCCCCTCCACCCCCT-CCC
1 CATTTGGAGCACCACCACCACCTCCCC
* *
4444 CATTGCATGGAGTACCACCCCCACCTCCCC
1 CATT---TGGAGCACCACCACCACCTCCCC
4474 CATTTGGAGCACCACCACCACCTCC
1 CATTTGGAGCACCACCACCACCTCC
4499 TCCAGCTTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
26 4 0.09
27 19 0.43
29 14 0.32
30 7 0.16
ACGTcount: A:0.19, C:0.52, G:0.12, T:0.17
Consensus pattern (27 bp):
CATTTGGAGCACCACCACCACCTCCCC
Found at i:4888 original size:63 final size:63
Alignment explanation
Indices: 4527--4885 Score: 628
Period size: 63 Copynumber: 5.7 Consensus size: 63
4517 GCCACCTCCA
*
4527 CCGCCACCTCCTATGCGTGGACCACCACCTCCACCAGCGCCTCCAGGTGGAGCACCGCCACCG
1 CCGCCACCTCCTATGCGTGGACCACCACCTCCACCACCGCCTCCAGGTGGAGCACCGCCACCG
4590 CCGCCACCTCCTATGCGTGGACCACCACCTCCACCACCGCCTCCAGGTGGAGCACCGCCACCG
1 CCGCCACCTCCTATGCGTGGACCACCACCTCCACCACCGCCTCCAGGTGGAGCACCGCCACCG
* *
4653 CCGCCACCTCCTATGCGTGGACCACCACCTCCACCACCCCCTCCAGGTGGAGCACCGCCACCA
1 CCGCCACCTCCTATGCGTGGACCACCACCTCCACCACCGCCTCCAGGTGGAGCACCGCCACCG
* *
4716 CCACCACCTCCTATGCGTGGACCACCACCTCCACCACCGCCTCCAGGTGGAGCACCGCCCCCG
1 CCGCCACCTCCTATGCGTGGACCACCACCTCCACCACCGCCTCCAGGTGGAGCACCGCCACCG
* * *
4779 CCACCGCCTCCTATGCGTGGACCACCACCTCCACCACCGCCTCCTGGTGGAGCACCGCCACCG
1 CCGCCACCTCCTATGCGTGGACCACCACCTCCACCACCGCCTCCAGGTGGAGCACCGCCACCG
* *
4842 CCGCCGCCTCCTATGCGTGGAGCACCACCTCCACCACCGCCTCC
1 CCGCCACCTCCTATGCGTGGACCACCACCTCCACCACCGCCTCC
4886 TGGAGGTCGA
Statistics
Matches: 284, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 284 1.00
ACGTcount: A:0.17, C:0.52, G:0.20, T:0.12
Consensus pattern (63 bp):
CCGCCACCTCCTATGCGTGGACCACCACCTCCACCACCGCCTCCAGGTGGAGCACCGCCACCG
Found at i:6208 original size:2 final size:2
Alignment explanation
Indices: 6201--6250 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
6191 CATAGATGTG
6201 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6243 AT AT AT AT
1 AT AT AT AT
6251 CAGCAGATTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7951 original size:20 final size:20
Alignment explanation
Indices: 7926--7963 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7916 CAAAAAAAAA
*
7926 AGAAGAAAAAAGGAAGAAGC
1 AGAAGAAAAAAGAAAGAAGC
*
7946 AGAAGAAGAAAGAAAGAA
1 AGAAGAAAAAAGAAAGAA
7964 AGAAAGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.29, T:0.00
Consensus pattern (20 bp):
AGAAGAAAAAAGAAAGAAGC
Done.