Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003538.1 Hibiscus syriacus cultivar Beakdansim tig00007465_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: 49516
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Found at i:4823 original size:14 final size:14
Alignment explanation
Indices: 4806--4833 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4796 ATCATAACAA
4806 AATTATATAACTAT
1 AATTATATAACTAT
4820 AATTATATAACTAT
1 AATTATATAACTAT
4834 TTTTTCACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:5598 original size:19 final size:18
Alignment explanation
Indices: 5574--5616 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
5564 TTATAATGTT
*
5574 ATTTAATATATCAAATAC
1 ATTTAATATATAAAATAC
*
5592 AATTTAAATTTATAAAATAC
1 -ATTT-AATATATAAAATAC
5612 ATTTA
1 ATTTA
5617 GAATATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 8 0.38
20 12 0.57
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTAATATATAAAATAC
Found at i:17454 original size:37 final size:37
Alignment explanation
Indices: 17401--17493 Score: 141
Period size: 37 Copynumber: 2.5 Consensus size: 37
17391 ATATTTTTTA
* ***
17401 AATTATAAGTCAAATATTAATTTTATACTTATAAAAT
1 AATTATAAGTCAAATATAAAAAATATACTTATAAAAT
*
17438 AATTATAAGTCGAATATAAAAAATATACTTATAAAAT
1 AATTATAAGTCAAATATAAAAAATATACTTATAAAAT
17475 AATTATAAGTCAAATATAA
1 AATTATAAGTCAAATATAA
17494 GTATATTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (37 bp):
AATTATAAGTCAAATATAAAAAATATACTTATAAAAT
Found at i:17455 original size:22 final size:21
Alignment explanation
Indices: 17430--17493 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
17420 ATTTTATACT
17430 TATAAAATAATTATAAGTCGAA
1 TATAAAATAATTATAAGTC-AA
*
17452 TATAAAA-AA-TAT-A--C-T
1 TATAAAATAATTATAAGTCAA
17467 TATAAAATAATTATAAGTCAAA
1 TATAAAATAATTATAAGTC-AA
17489 TATAA
1 TATAA
17494 GTATATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
15 7 0.21
16 2 0.06
17 4 0.12
18 1 0.03
19 1 0.03
20 4 0.12
21 2 0.06
22 12 0.36
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (21 bp):
TATAAAATAATTATAAGTCAA
Found at i:18505 original size:16 final size:16
Alignment explanation
Indices: 18481--18519 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
18471 CATCAATTTT
*
18481 CTCATTCTTAAATCTC
1 CTCAATCTTAAATCTC
*
18497 CTCAATCTTATATCTC
1 CTCAATCTTAAATCTC
18513 CTCAATC
1 CTCAATC
18520 CCTAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.41
Consensus pattern (16 bp):
CTCAATCTTAAATCTC
Found at i:21276 original size:20 final size:20
Alignment explanation
Indices: 21251--21302 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
21241 AGGTAAGAGA
21251 AGTATCGATACTCTCTAGGT
1 AGTATCGATACTCTCTAGGT
21271 AGTATCGATACTCTCTAGGT
1 AGTATCGATACTCTCTAGGT
21291 AGTATCGATACT
1 AGTATCGATACT
21303 ACTAGATGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (20 bp):
AGTATCGATACTCTCTAGGT
Found at i:35941 original size:27 final size:28
Alignment explanation
Indices: 35905--35969 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 28
35895 AAAATGAAAC
*
35905 AAAAAA-TAAATGTTACGTATGATTT-T
1 AAAAAATTAAATGTTACGTATGATTTAA
35931 AAAAAATTAAATGTTACGTATGATTTAA
1 AAAAAATTAAATGTTACGTATGATTTAA
35959 AAAAAATTAAA
1 AAAAAATTAAA
35970 AGTTTAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 6 0.17
27 19 0.53
28 11 0.31
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (28 bp):
AAAAAATTAAATGTTACGTATGATTTAA
Found at i:36875 original size:29 final size:29
Alignment explanation
Indices: 36841--36899 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
36831 CCTAAATTAA
36841 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
36870 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
36899 T
1 T
36900 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:41550 original size:29 final size:28
Alignment explanation
Indices: 41514--41572 Score: 109
Period size: 29 Copynumber: 2.1 Consensus size: 28
41504 CTTAAATTAA
41514 TTTTATGTCATTGCTTACATCAATTTAG
1 TTTTATGTCATTGCTTACATCAATTTAG
41542 TTTTGATGTCATTGCTTACATCAATTTAG
1 TTTT-ATGTCATTGCTTACATCAATTTAG
41571 TT
1 TT
41573 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.13
29 26 0.87
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.51
Consensus pattern (28 bp):
TTTTATGTCATTGCTTACATCAATTTAG
Found at i:47925 original size:21 final size:21
Alignment explanation
Indices: 47901--47959 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 21
47891 TCAGTGTAGA
*
47901 GGGAATCGATACCCCTTGAAG
1 GGGAACCGATACCCCTTGAAG
*
47922 GGGAACCGATCCCCCCTTTGAAG
1 GGGAACCGAT-ACCCC-TTGAAG
*
47945 GGGAACCGATTCCCC
1 GGGAACCGATACCCC
47960 CTGTAGAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.27
22 8 0.24
23 16 0.48
ACGTcount: A:0.24, C:0.32, G:0.27, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCCTTGAAG
Found at i:47946 original size:23 final size:23
Alignment explanation
Indices: 47912--47961 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
47902 GGAATCGATA
47912 CCCC-TTGAAGGGGAACCGATCC
1 CCCCTTTGAAGGGGAACCGATCC
*
47934 CCCCTTTGAAGGGGAACCGATTC
1 CCCCTTTGAAGGGGAACCGATCC
47957 CCCCT
1 CCCCT
47962 GTAGAGAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.20, C:0.38, G:0.24, T:0.18
Consensus pattern (23 bp):
CCCCTTTGAAGGGGAACCGATCC
Found at i:49492 original size:17 final size:16
Alignment explanation
Indices: 49467--49511 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
49457 GACGACTCTG
*
49467 ACGATGAACAAGAACA
1 ACGAGGAACAAGAACA
*
49483 CACGAGGAACAAGCACA
1 -ACGAGGAACAAGAACA
*
49500 ACAAGGAACAAG
1 ACGAGGAACAAG
49512 TATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.53, C:0.22, G:0.22, T:0.02
Consensus pattern (16 bp):
ACGAGGAACAAGAACA
Found at i:49508 original size:16 final size:17
Alignment explanation
Indices: 49472--49511 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
49462 CTCTGACGAT
*
49472 GAACAAGAACACACGAG
1 GAACAAGAACACACAAG
*
49489 GAACAAGCACA-ACAAG
1 GAACAAGAACACACAAG
49505 GAACAAG
1 GAACAAG
49512 TATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.55, C:0.23, G:0.23, T:0.00
Consensus pattern (17 bp):
GAACAAGAACACACAAG
Done.