Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009986.1 Corchorus olitorius cultivar O-4 contig10018, 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: 14657
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:5776 original size:2 final size:2
Alignment explanation
Indices: 5769--5796 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5759 TACAAACTTA
5769 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
5797 TATTCAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6233 original size:2 final size:2
Alignment explanation
Indices: 6226--6253 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6216 ATTTAATGAA
6226 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
6254 TCTATAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6511 original size:2 final size:2
Alignment explanation
Indices: 6504--6544 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
6494 GGAGCCAAGA
* * *
6504 AT AT AT AT AT AT AT AT AT AT TT AT AT AG AT AT AG AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6545 ATGACCTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:7910 original size:13 final size:13
Alignment explanation
Indices: 7878--7903 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7868 ATGCGAGACT
7878 CTGAGTTTGTCTC
1 CTGAGTTTGTCTC
7891 CTGAGTTTGTCTC
1 CTGAGTTTGTCTC
7904 ACGAGTTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.23, G:0.23, T:0.46
Consensus pattern (13 bp):
CTGAGTTTGTCTC
Found at i:8777 original size:26 final size:27
Alignment explanation
Indices: 8748--8798 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
8738 TTTGCTTTCC
* *
8748 AAAATCTTC-TTTTGGAGTTGCTTAAG
1 AAAAGCTTCTTTTTGAAGTTGCTTAAG
*
8774 AAAAGGTTCTTTTTGAAGTTGCTTA
1 AAAAGCTTCTTTTTGAAGTTGCTTA
8799 CTTTGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (27 bp):
AAAAGCTTCTTTTTGAAGTTGCTTAAG
Found at i:11465 original size:11 final size:11
Alignment explanation
Indices: 11449--11473 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11439 ACCAAATTGT
11449 AAAAAAAAAGA
1 AAAAAAAAAGA
11460 AAAAAAAAAGA
1 AAAAAAAAAGA
11471 AAA
1 AAA
11474 CACATGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:12228 original size:23 final size:23
Alignment explanation
Indices: 12201--12298 Score: 178
Period size: 23 Copynumber: 4.3 Consensus size: 23
12191 CAGCACGCGG
*
12201 GCCAGCGCAGCCCAGCGTGCCAT
1 GCCAGCGCGGCCCAGCGTGCCAT
12224 GCCAGCGCGGCCCAGCGTGCCAT
1 GCCAGCGCGGCCCAGCGTGCCAT
12247 GCCAGCGCGGCCCAGCGTGCCAT
1 GCCAGCGCGGCCCAGCGTGCCAT
*
12270 GCCAGCGCGGCCCAGCGTGCCAA
1 GCCAGCGCGGCCCAGCGTGCCAT
12293 GCCAGC
1 GCCAGC
12299 TCGCGGGCCA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 73 1.00
ACGTcount: A:0.15, C:0.44, G:0.34, T:0.07
Consensus pattern (23 bp):
GCCAGCGCGGCCCAGCGTGCCAT
Found at i:12381 original size:4 final size:4
Alignment explanation
Indices: 12374--12403 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
12364 AAAAAATATA
12374 AAAT AAAT AAAT AAAT AAAT AAAT -AAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
12404 ATAGAAAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:12451 original size:12 final size:12
Alignment explanation
Indices: 12401--12454 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
12391 AATAAATAAT
12401 AAAATAGAAAG-G
1 AAAA-AGAAAGAG
12413 AAAAA-AAAGAAG
1 AAAAAGAAAG-AG
12425 AAAAATG-AAGAG
1 AAAAA-GAAAGAG
*
12437 AAAAAGAAAGGG
1 AAAAAGAAAGAG
12449 AAAAAG
1 AAAAAG
12455 GATATAAGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
10 4 0.11
11 2 0.06
12 27 0.75
13 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.04
Consensus pattern (12 bp):
AAAAAGAAAGAG
Done.