Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008264.1 Hibiscus syriacus cultivar Beakdansim tig00110918_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: 82187
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3609 original size:29 final size:29
Alignment explanation
Indices: 3575--3633 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3565 CCTAAATTAA
3575 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
3604 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
3633 T
1 T
3634 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:8121 original size:20 final size:21
Alignment explanation
Indices: 8083--8122 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
8073 TCCTAGAGGG
8083 TGGGAAGAACAAAAAGAAGAA
1 TGGGAAGAACAAAAAGAAGAA
* *
8104 TGGGAA-AACAGAATGAAGA
1 TGGGAAGAACAAAAAGAAGA
8123 TGCTGGAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.57, C:0.05, G:0.30, T:0.07
Consensus pattern (21 bp):
TGGGAAGAACAAAAAGAAGAA
Found at i:13362 original size:25 final size:25
Alignment explanation
Indices: 13333--13381 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
13323 ATAAAACCTG
13333 GAGAAAAAAAGAAGGGACGGAAAGT
1 GAGAAAAAAAGAAGGGACGGAAAGT
13358 GAGAAAAAAAGAAGGGACGGAAAG
1 GAGAAAAAAAGAAGGGACGGAAAG
13382 AAAGGGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.57, C:0.04, G:0.37, T:0.02
Consensus pattern (25 bp):
GAGAAAAAAAGAAGGGACGGAAAGT
Found at i:15667 original size:45 final size:45
Alignment explanation
Indices: 15611--15717 Score: 112
Period size: 47 Copynumber: 2.3 Consensus size: 45
15601 TGCATCAATC
*
15611 CATGGATCGATGCA-TCATTGA-ATAAATTG-AACATCGAATGCATTA
1 CATGCATCGATGCACTC--TGATATAAA-TGAAACATCGAATGCATTA
* *
15656 CATGCATCGATGCACTCTGATTTTAAATGAAAACATCGAATGCATTT
1 CATGCATCGATGCACTCTGA-TATAAATG-AAACATCGAATGCATTA
*
15703 GATGCATCGATGCAC
1 CATGCATCGATGCAC
15718 ACACTATGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
44 3 0.06
45 15 0.28
46 6 0.11
47 29 0.55
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (45 bp):
CATGCATCGATGCACTCTGATATAAATGAAACATCGAATGCATTA
Found at i:30490 original size:18 final size:18
Alignment explanation
Indices: 30469--30509 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
30459 TCATCCTCTT
*
30469 CTTCATCTTCACCCTCAG
1 CTTCATCATCACCCTCAG
* *
30487 CTTCTTCATCACCCTCAT
1 CTTCATCATCACCCTCAG
30505 CTTCA
1 CTTCA
30510 GCATTATTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.44, G:0.02, T:0.37
Consensus pattern (18 bp):
CTTCATCATCACCCTCAG
Found at i:34227 original size:17 final size:17
Alignment explanation
Indices: 34205--34246 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
34195 TCGTTCGTGT
34205 TTTTAAATAA-ATGTTTA
1 TTTTAAATAATAT-TTTA
*
34222 TTTTAATTAATATTTTA
1 TTTTAAATAATATTTTA
34239 TTTTAAAT
1 TTTTAAAT
34247 TTTAATCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 20 0.91
18 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTTAAATAATATTTTA
Found at i:34836 original size:219 final size:219
Alignment explanation
Indices: 34591--35005 Score: 735
Period size: 219 Copynumber: 1.9 Consensus size: 219
34581 TTGTTCAAAT
34591 ATTAATTAAAGATATACGACAGTGAAAAATAACTCAATC-TCTGATATATCAAATATTAATTATT
1 ATTAATTAAAGATATACGACAGTGAAAAATAACTCAATCGT-TGATATATCAAATATTAATTATT
*
34655 AATTTGAAATAAATGAAATAAAATAAAAATTAATTAGAGTTCAATTATACAACATATTAAAGATA
65 AATATGAAATAAATGAAATAAAATAAAAATTAATTAGAGTTCAATTATACAACATATTAAAGATA
* *
34720 ATTTAAAAACTAATTAAAC-TTTTATTATTTTGTAATTTAAAATACTAAATCATTTCCTTTTTTA
130 ATTTAAAAACTAATTAAACTTTTTATTATTTTGCAATTTAAAATAATAAATCA-TTCCTTTTTTA
34784 TAATCATCAGTATTTGATCCCGACTA
194 TAATCATCAGTATTTGATCCCGACTA
*
34810 ATTAATTAAAGATATACGACAGTGAAAAATAACTCCATCGTTGATATATCAAATATTAATTATTA
1 ATTAATTAAAGATATACGACAGTGAAAAATAACTCAATCGTTGATATATCAAATATTAATTATTA
* *
34875 ATATGAAATAAATGAAATAAAATAAAAATTAATTAGAGTTTAATTATACAATATATTAAAGATAA
66 ATATGAAATAAATGAAATAAAATAAAAATTAATTAGAGTTCAATTATACAACATATTAAAGATAA
*
34940 TTTAAAAACTAATTAAACTTTTTATTATTTTGCAATTTAAAATAATAAATCATTCTTTTTTTATA
131 TTTAAAAACTAATTAAACTTTTTATTATTTTGCAATTTAAAATAATAAATCATTCCTTTTTTATA
35005 A
196 A
35006 ACATTTGTAT
Statistics
Matches: 187, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
219 155 0.83
220 32 0.17
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.38
Consensus pattern (219 bp):
ATTAATTAAAGATATACGACAGTGAAAAATAACTCAATCGTTGATATATCAAATATTAATTATTA
ATATGAAATAAATGAAATAAAATAAAAATTAATTAGAGTTCAATTATACAACATATTAAAGATAA
TTTAAAAACTAATTAAACTTTTTATTATTTTGCAATTTAAAATAATAAATCATTCCTTTTTTATA
ATCATCAGTATTTGATCCCGACTA
Found at i:35795 original size:18 final size:18
Alignment explanation
Indices: 35772--35842 Score: 133
Period size: 18 Copynumber: 3.9 Consensus size: 18
35762 CTGAATATTT
*
35772 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
35790 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
35808 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
35826 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
35843 GTTAATCCCT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.27, C:0.34, G:0.21, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:40636 original size:18 final size:18
Alignment explanation
Indices: 40613--40647 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
40603 ATTGAATATT
40613 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
40631 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
40648 GTTAATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:47588 original size:3 final size:3
Alignment explanation
Indices: 47580--47635 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
47570 ATTTGTAAAT
* **
47580 TAA TAA TAA TAA TAG TAA TAA TAA TAA T-A TAA CGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
47627 TAA TAA TAA
1 TAA TAA TAA
47636 CGATAAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:51878 original size:18 final size:18
Alignment explanation
Indices: 51855--51889 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
51845 ATTATTCTAG
51855 TTGAATTATCGAGTCAAC
1 TTGAATTATCGAGTCAAC
51873 TTGAATTATCGAGTCAA
1 TTGAATTATCGAGTCAA
51890 TTTTCGAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (18 bp):
TTGAATTATCGAGTCAAC
Found at i:59185 original size:2 final size:2
Alignment explanation
Indices: 59178--59204 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59168 GGCACTAAGC
59178 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
59205 AGGCAAGGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:63198 original size:21 final size:21
Alignment explanation
Indices: 63156--63198 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
63146 CTTCTTCTTC
* *
63156 CCGCTCGCGTTCCCGGTTCCT
1 CCGCTCGCGTTCCCGATCCCT
63177 CCGCTCG-GATTCCCGATCCCT
1 CCGCTCGCG-TTCCCGATCCCT
63198 C
1 C
63199 TCCCGCTGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.05, C:0.49, G:0.21, T:0.26
Consensus pattern (21 bp):
CCGCTCGCGTTCCCGATCCCT
Found at i:64303 original size:27 final size:26
Alignment explanation
Indices: 64264--64375 Score: 70
Period size: 27 Copynumber: 4.1 Consensus size: 26
64254 CATTAGGTAA
64264 AAATTA-CAAAAATATCTTTATGAGTAG
1 AAATTATC-AAAATA-CTTTATGAGTAG
* *
64291 AAATTATCAAAATACTCTTAT-ACATAA
1 AAATTATCAAAATACT-TTATGA-GTAG
*
64318 AAATTATTAAAATACCTTTATG-GATAG
1 AAATTATCAAAATA-CTTTATGAG-TAG
* *
64345 AAAATGACCAAAATACTCTTAT-ATGTAG
1 -AAATTATCAAAATACT-TTATGA-GTAG
64373 AAA
1 AAA
64376 GTACCAATAT
Statistics
Matches: 67, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
26 3 0.04
27 42 0.63
28 21 0.31
29 1 0.01
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (26 bp):
AAATTATCAAAATACTTTATGAGTAG
Found at i:64321 original size:54 final size:55
Alignment explanation
Indices: 64261--64367 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 55
64251 TACCATTAGG
* * *
64261 TAAAAATTACAAAAATATCTTTAT-GAGTAG-AAATTATCAAAATACTCTTATACA
1 TAAAAATTACAAAAATACCTTTATGGA-TAGAAAATGACCAAAATACTCTTATACA
**
64315 TAAAAATTATTAAAATACCTTTATGGATAGAAAATGACCAAAATACTCTTATA
1 TAAAAATTACAAAAATACCTTTATGGATAGAAAATGACCAAAATACTCTTATA
64368 TGTAGAAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
54 24 0.52
55 22 0.48
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.33
Consensus pattern (55 bp):
TAAAAATTACAAAAATACCTTTATGGATAGAAAATGACCAAAATACTCTTATACA
Found at i:64373 original size:28 final size:28
Alignment explanation
Indices: 64298--64375 Score: 72
Period size: 28 Copynumber: 2.8 Consensus size: 28
64288 TAGAAATTAT
** * *
64298 CAAAATACTCTTATACATA-AAAATTAT
1 CAAAATACTCTTATATGTAGAAAATGAC
*
64325 TAAAATAC-CTT-TATGGATAGAAAATGAC
1 CAAAATACTCTTATAT-G-TAGAAAATGAC
64353 CAAAATACTCTTATATGTAGAAA
1 CAAAATACTCTTATATGTAGAAA
64376 GTACCAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
25 2 0.05
26 3 0.08
27 9 0.22
28 19 0.47
29 4 0.10
30 3 0.08
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.31
Consensus pattern (28 bp):
CAAAATACTCTTATATGTAGAAAATGAC
Found at i:67098 original size:19 final size:20
Alignment explanation
Indices: 67061--67098 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
67051 ATCTTTTAAG
67061 ATAAAATATTTACTCAAACA
1 ATAAAATATTTACTCAAACA
*
67081 ATAAATTATTTACT-AAAC
1 ATAAAATATTTACTCAAAC
67099 TAATCTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (20 bp):
ATAAAATATTTACTCAAACA
Found at i:70956 original size:17 final size:17
Alignment explanation
Indices: 70934--70972 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
70924 CTGTGTCCCG
*
70934 ACCCGGATGTTACGGGT
1 ACCCGGATGTTACAGGT
* *
70951 ACCCGGATTTTGCAGGT
1 ACCCGGATGTTACAGGT
70968 ACCCG
1 ACCCG
70973 TTTTTTCTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.28, G:0.31, T:0.23
Consensus pattern (17 bp):
ACCCGGATGTTACAGGT
Found at i:72116 original size:185 final size:185
Alignment explanation
Indices: 71804--72194 Score: 635
Period size: 185 Copynumber: 2.1 Consensus size: 185
71794 TTTTCTAATT
* * * *
71804 TATATAA-AAATTAAATGTTTTTTAATTAAAAAAAGTTTATAATTAATTTAAATAATATATAATT
1 TATATAATATATTTAATATTTTTTAATTAAAAAAAGTTTACAATTAATTTAAATAATATATAATT
71868 ATAAAATAAAAAAATTTCAGATAGATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATAAAAT-AAAAAATTTCAGATAGATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
* * * *
71933 TTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTTAGCCCATATGTTA
130 TTAGATCTTAAATTATTAATTGGGTTTCAAATAGTTTGGGCTAAGCCCATATGTTA
71989 TATATAATATATTTAATATTTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATT-AAAAAA-AGTTTACAATTAATTTAAATAATATATAA
* *
72054 TTATAAAAT-AAAAATTTTATATA-ATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
64 TTATAAAATAAAAAATTTCAGATAGATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
*
72117 ATTAGATCTTAAATTATTAATTGGGTTTCAAATAGTTTGGGCTAAGCCTATATGTTA
129 ATTAGATCTTAAATTATTAATTGGGTTTCAAATAGTTTGGGCTAAGCCCATATGTTA
72174 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
72195 AAAATTTAAT
Statistics
Matches: 192, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
185 120 0.62
186 29 0.15
187 6 0.03
188 37 0.19
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (185 bp):
TATATAATATATTTAATATTTTTTAATTAAAAAAAGTTTACAATTAATTTAAATAATATATAATT
ATAAAATAAAAAATTTCAGATAGATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
TAGATCTTAAATTATTAATTGGGTTTCAAATAGTTTGGGCTAAGCCCATATGTTA
Found at i:73547 original size:21 final size:21
Alignment explanation
Indices: 73517--73558 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
73507 AATATAAATT
*
73517 GTGTATCGATGCACTACTACA
1 GTGTACCGATGCACTACTACA
*
73538 GTGTACCGATGCACTGCTACA
1 GTGTACCGATGCACTACTACA
73559 ATACTGCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
GTGTACCGATGCACTACTACA
Found at i:74138 original size:22 final size:22
Alignment explanation
Indices: 74104--74154 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
74094 CTGAGTGGCA
*
74104 TATGAAATTTGTCCCAAAGGACC
1 TATG-AATATGTCCCAAAGGACC
* **
74127 TGTGAATATGTCCTGAAGGACC
1 TATGAATATGTCCCAAAGGACC
74149 TATGAA
1 TATGAA
74155 ACCCTCGACT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (22 bp):
TATGAATATGTCCCAAAGGACC
Found at i:74553 original size:43 final size:43
Alignment explanation
Indices: 74492--74578 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
74482 TCACCTTGGC
*
74492 CTTCTTGCGTTGGTTCAATCCTAATTCTTCGATTATTCCGGAA
1 CTTCTTGCGTTGGTTCAATCCTAATTCTTCGATTAGTCCGGAA
74535 CTTCTTGCGTTGGTTCAATCCTAATTCTTCGATTAGTCCGGAA
1 CTTCTTGCGTTGGTTCAATCCTAATTCTTCGATTAGTCCGGAA
74578 C
1 C
74579 GAAATTACGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.40
Consensus pattern (43 bp):
CTTCTTGCGTTGGTTCAATCCTAATTCTTCGATTAGTCCGGAA
Done.