Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012123.1 Corchorus capsularis cultivar CVL-1 contig12144, 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: 24993
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:880 original size:11 final size:11
Alignment explanation
Indices: 864--888 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
854 TCTCTGGTAA
864 TATTATATTAT
1 TATTATATTAT
875 TATTATATTAT
1 TATTATATTAT
886 TAT
1 TAT
889 AATAATAATT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTATATTAT
Found at i:5033 original size:9 final size:9
Alignment explanation
Indices: 5016--5101 Score: 68
Period size: 9 Copynumber: 9.6 Consensus size: 9
5006 GAGACACGAA
5016 AAGCATGAG
1 AAGCATGAG
*
5025 AAGCGTGAG
1 AAGCATGAG
* *
5034 AGGCACGAG
1 AAGCATGAG
*
5043 AAGCGTGAG
1 AAGCATGAG
* *
5052 AGGCACGAG
1 AAGCATGAG
*
5061 AAGCGTGAG
1 AAGCATGAG
5070 -AGACATGAG
1 AAG-CATGAG
*
5079 AAGCGTGAG
1 AAGCATGAG
5088 -AGACATGAG
1 AAG-CATGAG
5097 AAGCA
1 AAGCA
5102 CTATTCTAAT
Statistics
Matches: 57, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
8 4 0.07
9 49 0.86
10 4 0.07
ACGTcount: A:0.38, C:0.14, G:0.40, T:0.08
Consensus pattern (9 bp):
AAGCATGAG
Found at i:5045 original size:18 final size:18
Alignment explanation
Indices: 5022--5100 Score: 122
Period size: 18 Copynumber: 4.4 Consensus size: 18
5012 CGAAAAGCAT
*
5022 GAGAAGCGTGAGAGGCAC
1 GAGAAGCGTGAGAGACAC
*
5040 GAGAAGCGTGAGAGGCAC
1 GAGAAGCGTGAGAGACAC
*
5058 GAGAAGCGTGAGAGACAT
1 GAGAAGCGTGAGAGACAC
*
5076 GAGAAGCGTGAGAGACAT
1 GAGAAGCGTGAGAGACAC
5094 GAGAAGC
1 GAGAAGC
5101 ACTATTCTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 59 1.00
ACGTcount: A:0.37, C:0.14, G:0.42, T:0.08
Consensus pattern (18 bp):
GAGAAGCGTGAGAGACAC
Found at i:7324 original size:20 final size:20
Alignment explanation
Indices: 7301--7341 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
7291 TTTCAGAGGA
7301 AGGGATGATTTCCAAAGCTG
1 AGGGATGATTTCCAAAGCTG
7321 AGGGATGATTTCCAAAGCTG
1 AGGGATGATTTCCAAAGCTG
7341 A
1 A
7342 AGATGTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (20 bp):
AGGGATGATTTCCAAAGCTG
Found at i:8940 original size:11 final size:11
Alignment explanation
Indices: 8924--8948 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
8914 TTTCAATAGC
8924 AAACAGAACAT
1 AAACAGAACAT
8935 AAACAGAACAT
1 AAACAGAACAT
8946 AAA
1 AAA
8949 GAGTCCAGAG
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:0.68, C:0.16, G:0.08, T:0.08
Consensus pattern (11 bp):
AAACAGAACAT
Found at i:12725 original size:18 final size:18
Alignment explanation
Indices: 12699--12758 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
12689 AGTACAGGCA
* *
12699 GATGCTCCACTGCCGCAG
1 GATGTTCCACTGCCACAG
*
12717 GATGTTCCACTGCTACAG
1 GATGTTCCACTGCCACAG
* *
12735 AATGTTCCATTGCCACAG
1 GATGTTCCACTGCCACAG
12753 GATGTT
1 GATGTT
12759 TCGCTGCTGC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (18 bp):
GATGTTCCACTGCCACAG
Found at i:16653 original size:31 final size:30
Alignment explanation
Indices: 16585--16662 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 30
16575 TTTTTACCCA
* **
16585 CCAATTTGAATCTAAACCTTTTAAAAGTTG
1 CCAATTTGAACCTAAACCTTTTAAAAGGGG
*
16615 CCTAATTTGAACCTAAACCTTTCTAAAGGGGG
1 CC-AATTTGAACCTAAACCTTT-TAAAAGGGG
*
16647 CCAATTTGAGCCTAAA
1 CCAATTTGAACCTAAA
16663 AACAAAAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 2 0.05
31 31 0.76
32 8 0.20
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31
Consensus pattern (30 bp):
CCAATTTGAACCTAAACCTTTTAAAAGGGG
Done.