Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005304.1 Hibiscus syriacus cultivar Beakdansim tig00012006_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: 88084
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:304 original size:21 final size:22
Alignment explanation
Indices: 271--319 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 22
261 CCTAATATTG
271 CAATGTCCAAAATTAGGTGCAA
1 CAATGTCCAAAATTAGGTGCAA
293 CAATGT-CAAAATTAGGTGCAA
1 CAATGTCCAAAATTAGGTGCAA
*
314 TAATGT
1 CAATGT
320 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (22 bp):
CAATGTCCAAAATTAGGTGCAA
Found at i:2143 original size:6 final size:6
Alignment explanation
Indices: 2132--2165 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
2122 ATTCTTTTAC
2132 CTACTG CTACTG CTACTG CTACTG CTACTG CTAC
1 CTACTG CTACTG CTACTG CTACTG CTACTG CTAC
2166 AAGTGATCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.35, G:0.15, T:0.32
Consensus pattern (6 bp):
CTACTG
Found at i:5844 original size:17 final size:17
Alignment explanation
Indices: 5822--5858 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
5812 GGGCTACTCT
5822 GATCCCTAACTTGGGTC
1 GATCCCTAACTTGGGTC
5839 GATCCCTAACTTGGGTC
1 GATCCCTAACTTGGGTC
5856 GAT
1 GAT
5859 GCCTGAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.30
Consensus pattern (17 bp):
GATCCCTAACTTGGGTC
Found at i:12681 original size:83 final size:83
Alignment explanation
Indices: 12587--12749 Score: 245
Period size: 83 Copynumber: 2.0 Consensus size: 83
12577 GGAATTTCGA
* * * *
12587 GAGAGTTTTACTCCATCTAAATATCTTTTAATAACTAAATTTAAAAAGATAATAATATATTTTAA
1 GAGAGATTTACTCCAACCAAATATCTTTTAATAACTAAATTTAAAAAGATAACAATATATTTTAA
12652 ATTTAAAATATTAAATCT
66 ATTTAAAATATTAAATCT
* * * * *
12670 GAGAGATTTACTCCAACCAGATATGTTTTAATATCTAAATTTAAACAGATAACAATATCTTTTAA
1 GAGAGATTTACTCCAACCAAATATCTTTTAATAACTAAATTTAAAAAGATAACAATATATTTTAA
12735 ATTTAAAATATTAAA
66 ATTTAAAATATTAAA
12750 CAAATATACA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 71 1.00
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (83 bp):
GAGAGATTTACTCCAACCAAATATCTTTTAATAACTAAATTTAAAAAGATAACAATATATTTTAA
ATTTAAAATATTAAATCT
Found at i:12750 original size:35 final size:35
Alignment explanation
Indices: 12706--12789 Score: 86
Period size: 35 Copynumber: 2.5 Consensus size: 35
12696 TTTAATATCT
*
12706 AAATTTAAACAGATA-ACAATATCTTTTA-AATTTA
1 AAATTTAAACAAATATACAAT-TCTTTTATAATTTA
* *
12740 AAATATTAAACAAATATACACTTCTTTTATTATTT-
1 AAAT-TTAAACAAATATACAATTCTTTTATAATTTA
*
12775 AAA-TTAAATAAATAT
1 AAATTTAAACAAATAT
12790 TATTTAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
33 11 0.26
34 4 0.09
35 20 0.47
36 8 0.19
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.40
Consensus pattern (35 bp):
AAATTTAAACAAATATACAATTCTTTTATAATTTA
Found at i:17034 original size:22 final size:23
Alignment explanation
Indices: 16985--17028 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
16975 GGTTTTGTCA
*
16985 AATATATTTATTTTTATTAAAAT
1 AATATATTTATTTTCATTAAAAT
17008 AATATATTT-TTTTCATTAAAA
1 AATATATTTATTTTCATTAAAA
17029 GTATATTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
AATATATTTATTTTCATTAAAAT
Found at i:23281 original size:18 final size:18
Alignment explanation
Indices: 23255--23295 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
23245 CTAATTATTA
*
23255 AAAATTATAAAATAATAT
1 AAAACTATAAAATAATAT
23273 AAAACTATAAAATAATAT
1 AAAACTATAAAATAATAT
23291 AAAAC
1 AAAAC
23296 AATATGCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAACTATAAAATAATAT
Found at i:23299 original size:10 final size:10
Alignment explanation
Indices: 23260--23300 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
23250 TATTAAAAAT
*
23260 TATAAAATAA
1 TATAAAACAA
23270 TATAAAAC--
1 TATAAAACAA
*
23278 TATAAAATAA
1 TATAAAACAA
23288 TATAAAACAA
1 TATAAAACAA
23298 TAT
1 TAT
23301 GCACTCTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
8 7 0.27
10 19 0.73
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (10 bp):
TATAAAACAA
Found at i:30924 original size:30 final size:30
Alignment explanation
Indices: 30888--30947 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
30878 CTGAGTGCAA
30888 GAAAGGTCGTGAAAACTCCTATTCTAGGTC
1 GAAAGGTCGTGAAAACTCCTATTCTAGGTC
30918 GAAAGGTCGTGAAAACTCCTATTCTAGGTC
1 GAAAGGTCGTGAAAACTCCTATTCTAGGTC
30948 AGTCAAAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (30 bp):
GAAAGGTCGTGAAAACTCCTATTCTAGGTC
Found at i:36185 original size:22 final size:23
Alignment explanation
Indices: 36151--36237 Score: 69
Period size: 22 Copynumber: 3.9 Consensus size: 23
36141 AAAAATAAAA
*
36151 AAAATATT-TAAATTTAAAATAT
1 AAAATATTAAAAATTTAAAATAT
*
36173 AAAATA-TAAAAATACTCAAAATA-
1 AAAATATTAAAAAT--TTAAAATAT
36196 AATTAATATTAAAAA--TAAAA-AT
1 AA--AATATTAAAAATTTAAAATAT
*
36218 AAATTATTAAAAATTTAAAA
1 AAAATATTAAAAATTTAAAA
36238 ATTATATACT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
20 10 0.19
21 2 0.04
22 21 0.40
23 2 0.04
24 7 0.13
25 4 0.08
26 6 0.12
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
AAAATATTAAAAATTTAAAATAT
Found at i:36720 original size:15 final size:15
Alignment explanation
Indices: 36702--36737 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
36692 TTTAAATGAT
*
36702 ATATTTAATTTTTGA
1 ATATTTAATTTTTAA
*
36717 ATATTTATTTTTTAA
1 ATATTTAATTTTTAA
36732 ATATTT
1 ATATTT
36738 TAAATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
ATATTTAATTTTTAA
Found at i:48428 original size:31 final size:32
Alignment explanation
Indices: 48371--48433 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 32
48361 ATGAATTCTC
* * *
48371 ATTGTAATGTTCATCTTTTC-TTTTTTGAACA
1 ATTGTAATGTCCATCTTTTCGATTTTGGAACA
48402 ATTGTAATGTCCATCTTATT-GATTTTGGAACA
1 ATTGTAATGTCCATCTT-TTCGATTTTGGAACA
48434 CGACGTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (32 bp):
ATTGTAATGTCCATCTTTTCGATTTTGGAACA
Found at i:51072 original size:18 final size:18
Alignment explanation
Indices: 51012--51074 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
51002 ATTATAATAA
*
51012 ATATTAATTATGATAATT
1 ATATTAATTATGATTATT
* *
51030 AAATTAATAAATAGACTTATT
1 ATATTAAT-TAT-GA-TTATT
*
51051 ATATTAATTATGATTCTT
1 ATATTAATTATGATTATT
51069 ATATTA
1 ATATTA
51075 TGATTCTTAG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
18 17 0.47
19 4 0.11
20 4 0.11
21 11 0.31
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (18 bp):
ATATTAATTATGATTATT
Found at i:51076 original size:14 final size:14
Alignment explanation
Indices: 51057--51083 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
51047 TATTATATTA
51057 ATTATGATTCTTAT
1 ATTATGATTCTTAT
51071 ATTATGATTCTTA
1 ATTATGATTCTTA
51084 GGTTATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (14 bp):
ATTATGATTCTTAT
Found at i:51703 original size:27 final size:24
Alignment explanation
Indices: 51646--51708 Score: 126
Period size: 24 Copynumber: 2.6 Consensus size: 24
51636 ATAAATTATA
51646 AGGCAACAACAACCAGTAAGTAGC
1 AGGCAACAACAACCAGTAAGTAGC
51670 AGGCAACAACAACCAGTAAGTAGC
1 AGGCAACAACAACCAGTAAGTAGC
51694 AGGCAACAACAACCA
1 AGGCAACAACAACCA
51709 ATATTTCTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.48, C:0.27, G:0.19, T:0.06
Consensus pattern (24 bp):
AGGCAACAACAACCAGTAAGTAGC
Found at i:52527 original size:104 final size:104
Alignment explanation
Indices: 52329--52537 Score: 233
Period size: 104 Copynumber: 2.0 Consensus size: 104
52319 GGGGAAGAAT
* * * *
52329 ACGGATGAACAAGGGTTGAATTTTTGGGTGTTTGACCCAAAAAAATAGGAATGAGTTTGGGTTTT
1 ACGGATGAAAAAGGGTTAAATTTTTGGGTGTTTGACCCAAAAAAATAGAAATGAGTTTGAGTTTT
** * *
52394 GGTGTTTGTAAAGATTAAATGAGGGTTTTTGGGATAAAC
66 GGTGTTTGTAAAGACCAAAGGAGGATTTTTGGGATAAAC
* * * * *
52433 ACGGATGAATAAAGGTTTAAATTTTTTGTTGTTTGATCGAAAAAACATA-AAATG-GTTTGAGTT
1 ACGGATGAA-AAAGGGTTAAATTTTTGGGTGTTTGACCCAAAAAA-ATAGAAATGAGTTTGAGTT
* * * *
52496 TTGGTGTTTGTGAAGACCGAAGGATGATTTTTGGGATGAAC
64 TTGGTGTTTGTAAAGACCAAAGGAGGATTTTTGGGATAAAC
52537 A
1 A
52538 ATGATGAACA
Statistics
Matches: 86, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
104 51 0.59
105 32 0.37
106 3 0.03
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.35
Consensus pattern (104 bp):
ACGGATGAAAAAGGGTTAAATTTTTGGGTGTTTGACCCAAAAAAATAGAAATGAGTTTGAGTTTT
GGTGTTTGTAAAGACCAAAGGAGGATTTTTGGGATAAAC
Found at i:52996 original size:2 final size:2
Alignment explanation
Indices: 52989--53145 Score: 55
Period size: 2 Copynumber: 79.0 Consensus size: 2
52979 TAATATAAAC
* * *
52989 TA TA TA TA TA TA GTT TA TA T- TA -A TA AA TCA TA TA GTT TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA T-A TA TA -TA TA TA
* *
53030 TA TA GTA TA TA -A TA TA -A TT TA TA TA TA GT- TCA TA TA TA CA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA TA
* * * * *
53070 CTA CA TA T- TT TA TA TA CA -A TA TA TA -A AA T- TA TA AA TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
53109 AA CTA TA TA GTT TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53146 ATTGTTTTAA
Statistics
Matches: 115, Mismatches: 21, Indels: 38
0.66 0.12 0.22
Matches are distributed among these distances:
1 10 0.09
2 94 0.82
3 11 0.10
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:53007 original size:11 final size:11
Alignment explanation
Indices: 52993--53067 Score: 71
Period size: 11 Copynumber: 6.7 Consensus size: 11
52983 ATAAACTATA
52993 TATATATAGTT
1 TATATATAGTT
* *
53004 TATAT-TAATA
1 TATATATAGTT
*
53014 AATCATATAGTT
1 TAT-ATATAGTT
*
53026 TATATATAGTA
1 TATATATAGTT
*
53037 TATAATATAATT
1 TAT-ATATAGTT
53049 TATATATAGTT
1 TATATATAGTT
*
53060 CATATATA
1 TATATATA
53068 CACTACATAT
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
10 5 0.10
11 31 0.62
12 14 0.28
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (11 bp):
TATATATAGTT
Found at i:53015 original size:28 final size:29
Alignment explanation
Indices: 52952--53006 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
52942 TATATAAAGT
*
52952 ATATAAACTATAAAATATGTAGTTTATTA
1 ATATAAACTATAAAATATATAGTTTATTA
*
52981 ATATAAACTAT-ATATATATAGTTTAT
1 ATATAAACTATAAAATATATAGTTTAT
53007 ATTAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (29 bp):
ATATAAACTATAAAATATATAGTTTATTA
Found at i:53050 original size:23 final size:23
Alignment explanation
Indices: 52989--53058 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
52979 TAATATAAAC
*
52989 TATATATATATAGTTTATAT-TAA
1 TATATA-ATATAGTTTATATATAG
* *
53012 TAAATCATATAGTTTATATATAG
1 TATATAATATAGTTTATATATAG
*
53035 TATATAATATAATTTATATATAG
1 TATATAATATAGTTTATATATAG
53058 T
1 T
53059 TCATATATAC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
22 13 0.32
23 27 0.68
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (23 bp):
TATATAATATAGTTTATATATAG
Found at i:58740 original size:21 final size:22
Alignment explanation
Indices: 58716--58760 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
58706 TGATAAAAAA
58716 TTATATAAAATATTAAT-TTTT
1 TTATATAAAATATTAATGTTTT
* *
58737 TTATCTAAACTATTAATGTTTT
1 TTATATAAAATATTAATGTTTT
58759 TT
1 TT
58761 TACTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (22 bp):
TTATATAAAATATTAATGTTTT
Found at i:59845 original size:15 final size:15
Alignment explanation
Indices: 59811--59845 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
59801 ATTAAATTAT
*
59811 ATTTACTTTTTTAAA
1 ATTTAATTTTTTAAA
59826 A-TTAATTTTTTAAA
1 ATTTAATTTTTTAAA
59840 ATTTAA
1 ATTTAA
59846 ATAAAATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTAATTTTTTAAA
Found at i:59850 original size:25 final size:24
Alignment explanation
Indices: 59822--59868 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
59812 TTTACTTTTT
* *
59822 TAAAATTAATTTTTTAAAATTTAAA
1 TAAAATCAATATTTT-AAATTTAAA
59847 TAAAATCAATATTTTAAATTTA
1 TAAAATCAATATTTTAAATTTA
59869 TCCAATGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAAATCAATATTTTAAATTTAAA
Found at i:61620 original size:13 final size:13
Alignment explanation
Indices: 61602--61627 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61592 TTATCTTATC
61602 AATTCATATATTT
1 AATTCATATATTT
61615 AATTCATATATTT
1 AATTCATATATTT
61628 GTTAATCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTCATATATTT
Found at i:61759 original size:4 final size:4
Alignment explanation
Indices: 61750--61776 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
61740 TTCAACTTTG
61750 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
61777 ACATGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:65801 original size:28 final size:24
Alignment explanation
Indices: 65744--65796 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
65734 CAGTTATATC
65744 TTTGAACTATATATATCAAGTTAG
1 TTTGAACTATATATATCAAGTTAG
65768 TTTGAACTATATATATCAAGTTAG
1 TTTGAACTATATATATCAAGTTAG
65792 TTTGA
1 TTTGA
65797 GTGAAGAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (24 bp):
TTTGAACTATATATATCAAGTTAG
Found at i:78126 original size:30 final size:30
Alignment explanation
Indices: 78090--78161 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
78080 ACATGATCAC
***
78090 GAGCTGGTTCGGTCCCATGCGTATTGTAAT
1 GAGCTGGTTCGGTCCCATGCGTAACATAAT
*
78120 GAGCTGGTTCGGTCCCATGCGTAACATTAT
1 GAGCTGGTTCGGTCCCATGCGTAACATAAT
78150 GAGCTGGTTCGG
1 GAGCTGGTTCGG
78162 CGACCCCATG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.31
Consensus pattern (30 bp):
GAGCTGGTTCGGTCCCATGCGTAACATAAT
Done.