Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009365.1 Hibiscus syriacus cultivar Beakdansim tig00113190_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: 53665
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:9338 original size:12 final size:12
Alignment explanation
Indices: 9321--9345 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9311 CGCATTAATT
9321 GTTCAAGCTCAG
1 GTTCAAGCTCAG
9333 GTTCAAGCTCAG
1 GTTCAAGCTCAG
9345 G
1 G
9346 ATCGTTGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (12 bp):
GTTCAAGCTCAG
Found at i:15571 original size:20 final size:19
Alignment explanation
Indices: 15527--15580 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
15517 CTTGAGCGTG
*
15527 GGGGAATCGGTACCCCTCA
1 GGGGAATCGGTTCCCCTCA
15546 GGGGAATCGGTTCCCCTCA
1 GGGGAATCGGTTCCCCTCA
15565 TGGGGAATCGGTTCCC
1 -GGGGAATCGGTTCCC
15581 TAAGTGTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.17, C:0.30, G:0.33, T:0.20
Consensus pattern (19 bp):
GGGGAATCGGTTCCCCTCA
Found at i:24348 original size:28 final size:26
Alignment explanation
Indices: 24285--24350 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 26
24275 GGAAGTTGTT
24285 CGAAAGAAAAAAGAAAAGAAAAAAGA
1 CGAAAGAAAAAAGAAAAGAAAAAAGA
*
24311 CGTAAA-AAAAATGGAAAATGAAAAAAGAA
1 CG-AAAGAAAAA-AGAAAA-GAAAAAAG-A
24340 C-AAAGAAAAAA
1 CGAAAGAAAAAA
24351 ATACATTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
26 7 0.21
27 11 0.33
28 13 0.39
29 2 0.06
ACGTcount: A:0.74, C:0.05, G:0.17, T:0.05
Consensus pattern (26 bp):
CGAAAGAAAAAAGAAAAGAAAAAAGA
Found at i:26037 original size:18 final size:18
Alignment explanation
Indices: 26016--26052 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
26006 ATCATTATTT
*
26016 ATTTAATCTCTTTTTACC
1 ATTTAATCTCATTTTACC
*
26034 ATTTAATTTCATTTTACC
1 ATTTAATCTCATTTTACC
26052 A
1 A
26053 AAACCCCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTAATCTCATTTTACC
Found at i:28345 original size:35 final size:35
Alignment explanation
Indices: 28306--28372 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
28296 TTTTTTTTCA
*
28306 CTTTTTTTCTTT-TTGGTTATTCCTAAACTAAAGAC
1 CTTTTTTTCTTTACTGGTTATTCC-AAACTAAAGAC
* *
28341 CTTTTTTTGTTTACTGGTTATTCCAAATTAAA
1 CTTTTTTTCTTTACTGGTTATTCCAAACTAAA
28373 TGAAAATGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 18 0.64
36 10 0.36
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (35 bp):
CTTTTTTTCTTTACTGGTTATTCCAAACTAAAGAC
Found at i:28829 original size:24 final size:23
Alignment explanation
Indices: 28758--28817 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 23
28748 TAGGTTAGGG
28758 TAGGCTCCGGGTCGAGTTTAGTT
1 TAGGCTCCGGGTCGAGTTTAGTT
*
28781 T-GTGTTCCGGGTCGAGTTCTAGTT
1 TAG-GCTCCGGGTCGAGTT-TAGTT
28805 TAGGCTCCGGGTC
1 TAGGCTCCGGGTC
28818 TGGGTTTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 1 0.03
23 15 0.47
24 15 0.47
25 1 0.03
ACGTcount: A:0.10, C:0.20, G:0.35, T:0.35
Consensus pattern (23 bp):
TAGGCTCCGGGTCGAGTTTAGTT
Found at i:28894 original size:13 final size:12
Alignment explanation
Indices: 28852--28885 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 12
28842 TTAGGACCTG
28852 TTTGGGTTTAAA
1 TTTGGGTTTAAA
28864 TTTGGGGTTTAAA
1 TTT-GGGTTTAAA
28877 TTTGGGTTT
1 TTTGGGTTT
28886 TATGTTTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (12 bp):
TTTGGGTTTAAA
Found at i:29840 original size:20 final size:20
Alignment explanation
Indices: 29811--29854 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
29801 TCAAATTCAA
* *
29811 GGGTCGGGTTGACTCGGTTT
1 GGGTCAGGTTGACTCAGTTT
29831 GGGTCAGGTTGACTCAGTTT
1 GGGTCAGGTTGACTCAGTTT
29851 GGGT
1 GGGT
29855 TAATAGACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.14, G:0.43, T:0.34
Consensus pattern (20 bp):
GGGTCAGGTTGACTCAGTTT
Found at i:32392 original size:2 final size:2
Alignment explanation
Indices: 32380--32418 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
32370 ACTTATATGT
* *
32380 TA TA T- TA TA TA TA TA TA TA TG TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32419 CATTTTGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32404 original size:14 final size:14
Alignment explanation
Indices: 32387--32418 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
32377 TGTTATATTA
32387 TATATATATATATG
1 TATATATATATATG
32401 TATATATATATATG
1 TATATATATATATG
32415 TATA
1 TATA
32419 CATTTTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (14 bp):
TATATATATATATG
Found at i:32418 original size:12 final size:12
Alignment explanation
Indices: 32373--32411 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
32363 TTATTTTACT
32373 TATATGT-TATA
1 TATATGTATATA
*
32384 T-TATATATATA
1 TATATGTATATA
32395 TATATGTATATA
1 TATATGTATATA
32407 TATAT
1 TATAT
32412 ATGTATACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 4 0.17
11 6 0.25
12 14 0.58
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (12 bp):
TATATGTATATA
Found at i:44840 original size:105 final size:105
Alignment explanation
Indices: 44164--44832 Score: 1214
Period size: 105 Copynumber: 6.4 Consensus size: 105
44154 CAGGTTTTCC
*
44164 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
44229 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
44269 CAGAGCCAATTTCAACTTCAC-ACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
44333 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
44373 CAGAGCCAATTTCAACTTTACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
44438 ACGAAGGGACCGCTGATTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
44478 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
44543 ACGAAGGGACCACTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
44583 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
44648 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* ** *
44688 CAGAGCCAATTGCTGCTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
44753 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
44793 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
44833 GAAACAACAC
Statistics
Matches: 543, Mismatches: 20, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
104 101 0.19
105 442 0.81
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:50281 original size:18 final size:18
Alignment explanation
Indices: 50258--50295 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
50248 GACCGGTCAC
50258 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
50276 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
50294 AC
1 AC
50296 GTTGACCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.50, G:0.21, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:52709 original size:24 final size:24
Alignment explanation
Indices: 52682--52790 Score: 132
Period size: 24 Copynumber: 4.6 Consensus size: 24
52672 ATGATTTGAA
*
52682 TCTGATATGATACTTGACATGGAT
1 TCTGATCTGATACTTGACATGGAT
52706 TCTGATCTGATA-TCTGACATGGAT
1 TCTGATCTGATACT-TGACATGGAT
*
52730 TCTGATCTGATACTTGACTTGGAT
1 TCTGATCTGATACTTGACATGGAT
* * *
52754 TTTGATCTGTTACTTGACCT-GAT
1 TCTGATCTGATACTTGACATGGAT
* *
52777 TTTGATATGATACT
1 TCTGATCTGATACT
52791 GACTTGAATT
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
23 16 0.21
24 59 0.78
25 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (24 bp):
TCTGATCTGATACTTGACATGGAT
Done.