Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012002.1 Corchorus olitorius cultivar O-4 contig12035, 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: 11533
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Found at i:5893 original size:16 final size:16
Alignment explanation
Indices: 5848--5894 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
5838 CTCGGGTTAG
*
5848 GGAAGAAGATAAAATGA
1 GGAAGAAGAGAAAA-GA
5865 -GAAGAAGAGAAAAGAA
1 GGAAGAAGAGAAAAG-A
5881 GGAAGAAGA-AAAAG
1 GGAAGAAGAGAAAAG
5895 GAAGATGCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 1 0.04
16 18 0.67
17 8 0.30
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (16 bp):
GGAAGAAGAGAAAAGA
Found at i:7952 original size:28 final size:28
Alignment explanation
Indices: 7896--8021 Score: 180
Period size: 28 Copynumber: 4.4 Consensus size: 28
7886 AGTACACTTG
*
7896 AAATGACCAAAATGCTCCCTGAACATGAA
1 AAATGACCAAAATGC-CCCTGGACATGAA
*
7925 AAATGACCAAAATGCCCCTGGACCTGAA
1 AAATGACCAAAATGCCCCTGGACATGAA
*
7953 AAATGACCAAAATGCCCATGGACATGAA
1 AAATGACCAAAATGCCCCTGGACATGAA
* * *
7981 AAGTGACCAAAATGCCCTCTGGACCTAAA
1 AAATGACCAAAATGCCC-CTGGACATGAA
8010 AAATGACCAAAA
1 AAATGACCAAAA
8022 CGGGAAGTAA
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
28 53 0.61
29 34 0.39
ACGTcount: A:0.44, C:0.25, G:0.16, T:0.15
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGACATGAA
Found at i:7960 original size:57 final size:57
Alignment explanation
Indices: 7896--8021 Score: 200
Period size: 57 Copynumber: 2.2 Consensus size: 57
7886 AGTACACTTG
* *
7896 AAATGACCAAAATGCTCCCTGAACATGAAAAATGACCAAAATGCCC-CTGGACCTGAA
1 AAATGACCAAAATGC-CCATGAACATGAAAAATGACCAAAATGCCCTCTGGACCTAAA
* *
7953 AAATGACCAAAATGCCCATGGACATGAAAAGTGACCAAAATGCCCTCTGGACCTAAA
1 AAATGACCAAAATGCCCATGAACATGAAAAATGACCAAAATGCCCTCTGGACCTAAA
8010 AAATGACCAAAA
1 AAATGACCAAAA
8022 CGGGAAGTAA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
56 27 0.42
57 37 0.58
ACGTcount: A:0.44, C:0.25, G:0.16, T:0.15
Consensus pattern (57 bp):
AAATGACCAAAATGCCCATGAACATGAAAAATGACCAAAATGCCCTCTGGACCTAAA
Found at i:8307 original size:50 final size:50
Alignment explanation
Indices: 8235--8753 Score: 829
Period size: 50 Copynumber: 10.5 Consensus size: 50
8225 CGATCCACTT
* * *
8235 CTTCGAATTGTCTTCTAATTCAATCTTAAAAGGGCCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* * *
8285 CTTTGAACTGTCTTCCACTTCAATCTTAAAAGGACCATCTTCCGCTTA--
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
8333 --TC---CT-TCTTCCAATTTAATCTTAAAAGGATCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
8377 CTTCGAACTGGCTTCCAATTCAATCTTAAAAGGACTGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
8427 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
8477 CTTGGAACTGTCTTCCAATTCAATCTTAAAAAGACCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
8527 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* * *
8577 CGTCGAACTGTCTTCCAATTCAATCTTAAACGGACTGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
8627 CTTCGAACTATCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCCTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
8677 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
8727 CTTCGAACTGTCTTCCAATTCAATCTT
1 CTTCGAACTGTCTTCCAATTCAATCTT
8754 GATATCTGGT
Statistics
Matches: 430, Mismatches: 31, Indels: 16
0.90 0.06 0.03
Matches are distributed among these distances:
42 34 0.08
43 2 0.00
46 3 0.01
49 2 0.00
50 389 0.90
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (50 bp):
CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
Found at i:9374 original size:2 final size:2
Alignment explanation
Indices: 9369--9411 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
9359 TAACACACAC
*
9369 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9411 A
1 A
9412 GGGGTGCCAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Done.