Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012404.1 Corchorus olitorius cultivar O-4 contig12437, 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: 8058
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Found at i:3066 original size:32 final size:29
Alignment explanation
Indices: 3014--3086 Score: 85
Period size: 28 Copynumber: 2.4 Consensus size: 29
3004 AGGCCCAGCC
3014 TGCCAGCCAGCACGCGAGCGCGACACA-G
1 TGCCAGCCAGCACGCGAGCGCGACACAGG
*
3042 TGCCAGCCAGCACGCGGGCCAGCGCGACCCAGTG
1 TGCCAGCCAGCACGC--G--AGCGCGACACAG-G
3076 TGCCAGCCAGC
1 TGCCAGCCAGC
3087 GCAGCACGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
28 15 0.39
30 1 0.03
32 10 0.26
34 12 0.32
ACGTcount: A:0.21, C:0.41, G:0.33, T:0.05
Consensus pattern (29 bp):
TGCCAGCCAGCACGCGAGCGCGACACAGG
Found at i:3179 original size:12 final size:12
Alignment explanation
Indices: 3148--3180 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3138 GTTCAAAAAA
3148 AATAAAATAAAT
1 AATAAAATAAAT
3160 AA-ATAAATAAAT
1 AATA-AAATAAAT
3172 AATAAAATA
1 AATAAAATA
3181 GAAAGGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.05
12 17 0.89
13 1 0.05
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAAAATAAAT
Found at i:3207 original size:17 final size:18
Alignment explanation
Indices: 3182--3223 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
3172 AATAAAATAG
*
3182 AAAGGAAAAAAAAGA-AA
1 AAAGAAAAAAAAAGAGAA
**
3199 AAAGAAAAAGGAAGAGAA
1 AAAGAAAAAAAAAGAGAA
3217 AAAGAAA
1 AAAGAAA
3224 GGGAAAAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAAAAAGAGAA
Found at i:3216 original size:12 final size:12
Alignment explanation
Indices: 3201--3234 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3191 AAAAGAAAAA
3201 AGAAAAAGGAAG
1 AGAAAAAGGAAG
*
3213 AGAAAAAGAAAG
1 AGAAAAAGGAAG
*
3225 GGAAAAAGGA
1 AGAAAAAGGA
3235 TATAAGGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (12 bp):
AGAAAAAGGAAG
Found at i:7910 original size:12 final size:12
Alignment explanation
Indices: 7895--7949 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
7885 CAGCCTGCCA
7895 GCCAGCACGCGG
1 GCCAGCACGCGG
7907 GCCAGCA--CGG
1 GCCAGCACGCGG
* ** **
7917 CCCAGCGTGCCA
1 GCCAGCACGCGG
7929 GCCAGCACGCGG
1 GCCAGCACGCGG
7941 GCCAGCACG
1 GCCAGCACG
7950 GCCCAGCGTG
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
10 8 0.25
12 24 0.75
ACGTcount: A:0.18, C:0.44, G:0.36, T:0.02
Consensus pattern (12 bp):
GCCAGCACGCGG
Found at i:7957 original size:34 final size:34
Alignment explanation
Indices: 7881--7960 Score: 151
Period size: 34 Copynumber: 2.4 Consensus size: 34
7871 GCCAGGCGCA
*
7881 GGCCCAGCCTGCCAGCCAGCACGCGGGCCAGCAC
1 GGCCCAGCGTGCCAGCCAGCACGCGGGCCAGCAC
7915 GGCCCAGCGTGCCAGCCAGCACGCGGGCCAGCAC
1 GGCCCAGCGTGCCAGCCAGCACGCGGGCCAGCAC
7949 GGCCCAGCGTGC
1 GGCCCAGCGTGC
7961 TAGGCTTGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.16, C:0.45, G:0.35, T:0.04
Consensus pattern (34 bp):
GGCCCAGCGTGCCAGCCAGCACGCGGGCCAGCAC
Done.