Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008210.1 Hibiscus syriacus cultivar Beakdansim tig00110832_pilon, 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: 43486
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:12514 original size:15 final size:15
Alignment explanation
Indices: 12496--12525 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12486 CCACGGTGCT
12496 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
12511 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
12526 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:15448 original size:11 final size:11
Alignment explanation
Indices: 15432--15460 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
15422 GGGTATAAAA
15432 CATCGATTTGT
1 CATCGATTTGT
15443 CATCGATTTGT
1 CATCGATTTGT
15454 CATCGAT
1 CATCGAT
15461 CGGTCACGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (11 bp):
CATCGATTTGT
Found at i:15466 original size:22 final size:21
Alignment explanation
Indices: 15432--15472 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
15422 GGGTATAAAA
**
15432 CATCGATTTGTCATCGATTTGT
1 CATCGATCGGTCA-CGATTTGT
15454 CATCGATCGGTCACGATTT
1 CATCGATCGGTCACGATTT
15473 CATGGGGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (21 bp):
CATCGATCGGTCACGATTTGT
Found at i:16259 original size:24 final size:22
Alignment explanation
Indices: 16226--16272 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
16216 GTAAAATATT
*
16226 TTTATTTTGAAAAATAATTAAATA
1 TTTATATTGAAAAAT-A-TAAATA
*
16250 TTTATATTGATAAATATAAATA
1 TTTATATTGAAAAATATAAATA
16272 T
1 T
16273 GGCTTAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 1 0.05
24 13 0.62
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TTTATATTGAAAAATATAAATA
Found at i:30296 original size:26 final size:26
Alignment explanation
Indices: 30266--30333 Score: 113
Period size: 26 Copynumber: 2.7 Consensus size: 26
30256 ATCTATTTAC
30266 AAAATCATATCTCTATAGGAATGGTA
1 AAAATCATATCTCTATAGGAATGGTA
30292 AAAATCATATCTCTATAGGAATGGTA
1 AAAATCATATCTCTATAGGAATGGTA
30318 ACAAATC--ATCTCTATA
1 A-AAATCATATCTCTATA
30334 ATTCCTATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
25 9 0.22
26 27 0.66
27 5 0.12
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.31
Consensus pattern (26 bp):
AAAATCATATCTCTATAGGAATGGTA
Found at i:39737 original size:5 final size:5
Alignment explanation
Indices: 39730--39783 Score: 99
Period size: 5 Copynumber: 10.8 Consensus size: 5
39720 GTCCGTCCGT
*
39730 CTCGT CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
39780 CTCG
1 CTCG
39784 TGGTCGTGGT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.00, C:0.41, G:0.37, T:0.22
Consensus pattern (5 bp):
CTCGG
Found at i:39792 original size:6 final size:6
Alignment explanation
Indices: 39781--39823 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
39771 TCGGCTCGGC
39781 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
39824 AATACGTGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:40556 original size:31 final size:32
Alignment explanation
Indices: 40496--40559 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
40486 TGAATGGGGA
40496 TCTAGATGAGGAGATTTACATGGAGCAGCCAC
1 TCTAGATGAGGAGATTTACATGGAGCAGCCAC
40528 TCTAGATGAGGAGATTTACAT-GAGCAGCCAC
1 TCTAGATGAGGAGATTTACATGGAGCAGCCAC
40559 T
1 T
40560 AGGTTTTGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 11 0.34
32 21 0.66
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (32 bp):
TCTAGATGAGGAGATTTACATGGAGCAGCCAC
Found at i:42718 original size:5 final size:5
Alignment explanation
Indices: 42704--42752 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
42694 GTCCGTCCGT
* * * *
42704 CTCGT CTCGG CTCGG CACGG CACGG CTCGG CTCGG CTCGG CTTGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
42753 TGGTCGTGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.04, C:0.39, G:0.37, T:0.20
Consensus pattern (5 bp):
CTCGG
Found at i:42761 original size:6 final size:6
Alignment explanation
Indices: 42750--42810 Score: 104
Period size: 6 Copynumber: 10.2 Consensus size: 6
42740 TCGGCTTGGC
* *
42750 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
42798 TCGTGG TCGTGG T
1 TCGTGG TCGTGG T
42811 AATACGTGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Done.