Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001346.1 Hibiscus syriacus cultivar Beakdansim tig00002624_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: 77735
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4407 original size:30 final size:31
Alignment explanation
Indices: 4371--4428 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
4361 ATTTAATGTC
**
4371 GTGACATTGTGGGTAGGGA-TGAACATTAAT
1 GTGACATTGAAGGTAGGGATTGAACATTAAT
4401 GTGACATTGAAGGTAGGGATTGAACATT
1 GTGACATTGAAGGTAGGGATTGAACATT
4429 TGATCCAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.31, C:0.07, G:0.33, T:0.29
Consensus pattern (31 bp):
GTGACATTGAAGGTAGGGATTGAACATTAAT
Found at i:12134 original size:21 final size:21
Alignment explanation
Indices: 12102--12146 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
12092 TTTTTAAAAC
12102 TTATTTTTT-AAATTATATTT
1 TTATTTTTTAAAATTATATTT
12122 TTATTTCTTTAAAAATTATATTT
1 TTATTT-TTT-AAAATTATATTT
12145 TT
1 TT
12147 TGAAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.27
21 3 0.14
23 13 0.59
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
TTATTTTTTAAAATTATATTT
Found at i:12152 original size:17 final size:16
Alignment explanation
Indices: 12085--12173 Score: 72
Period size: 18 Copynumber: 5.2 Consensus size: 16
12075 ACATGTACGT
*
12085 TTATATTTTTTTAAAA
1 TTATATTTTTTAAAAA
*
12101 CT-TATTTTTTAAATTATA
1 TTATATTTTTTAAA--A-A
*
12119 TTTTTATTTCTTTAAAAA
1 -TTATATTT-TTTAAAAA
12137 TTATATTTTTTGAAAAAA
1 TTATATTTTTT--AAAAA
*
12155 TTATATTTTCTAAAAA
1 TTATATTTTTTAAAAA
12171 TTA
1 TTA
12174 AAATTATTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
15 10 0.17
16 12 0.20
17 8 0.13
18 17 0.28
19 2 0.03
20 5 0.08
21 6 0.10
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (16 bp):
TTATATTTTTTAAAAA
Found at i:12163 original size:16 final size:17
Alignment explanation
Indices: 12132--12173 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
12122 TTATTTCTTT
*
12132 AAAAATTATATTTTTTGA
1 AAAAATTATA-TTTTTCA
*
12150 AAAAATTATA-TTTTCT
1 AAAAATTATATTTTTCA
12166 AAAAATTA
1 AAAAATTA
12174 AAATTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 12 0.55
18 10 0.45
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
AAAAATTATATTTTTCA
Found at i:15861 original size:18 final size:18
Alignment explanation
Indices: 15828--15952 Score: 196
Period size: 18 Copynumber: 6.9 Consensus size: 18
15818 GCGTAGAATT
*
15828 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
** * *
15846 TGTCATGAAGGTCCACTG
1 TGTCCCGAAGGACCACTA
15864 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
15882 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
15900 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
15918 TATCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
15936 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
15953 GATAATCTCT
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 96 1.00
ACGTcount: A:0.26, C:0.32, G:0.22, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:23140 original size:17 final size:16
Alignment explanation
Indices: 23118--23151 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
23108 TAAACACAGT
23118 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
23135 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
23151 A
1 A
23152 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:33272 original size:17 final size:16
Alignment explanation
Indices: 33250--33283 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
33240 TAAAGACAGT
33250 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
33267 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
33283 A
1 A
33284 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:37020 original size:17 final size:17
Alignment explanation
Indices: 36998--37030 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
36988 ATTAAATTTA
*
36998 AAATTAAATTTTTTATC
1 AAATTAAAGTTTTTATC
37015 AAATTAAAGTTTTTAT
1 AAATTAAAGTTTTTAT
37031 TCATATCTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (17 bp):
AAATTAAAGTTTTTATC
Found at i:41538 original size:112 final size:112
Alignment explanation
Indices: 41341--41565 Score: 432
Period size: 112 Copynumber: 2.0 Consensus size: 112
41331 ATTCTAGAGG
*
41341 TCATCTAACCAAACCAATCAACTCAATACTTATGAGGAAAGGAACAAGAACATATTACCTTCCTT
1 TCATCTAACCAAACCAATCAACTCAATACTTACGAGGAAAGGAACAAGAACATATTACCTTCCTT
*
41406 CATCCACTTCATAATGCAAAACTATTTTTCGCTCATCGAGTCAGATT
66 CATCCACTTCATAATGCAAAACTATTTTTCGCTCATCAAGTCAGATT
41453 TCATCTAACCAAACCAATCAACTCAATACTTACGAGGAAAGGAACAAGAACATATTACCTTCCTT
1 TCATCTAACCAAACCAATCAACTCAATACTTACGAGGAAAGGAACAAGAACATATTACCTTCCTT
41518 CATCCACTTCATAATGCAAAACTATTTTTCGCTCATCAAGTCAGATT
66 CATCCACTTCATAATGCAAAACTATTTTTCGCTCATCAAGTCAGATT
41565 T
1 T
41566 TCTCTAGGAT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 111 1.00
ACGTcount: A:0.37, C:0.25, G:0.09, T:0.28
Consensus pattern (112 bp):
TCATCTAACCAAACCAATCAACTCAATACTTACGAGGAAAGGAACAAGAACATATTACCTTCCTT
CATCCACTTCATAATGCAAAACTATTTTTCGCTCATCAAGTCAGATT
Found at i:41801 original size:22 final size:22
Alignment explanation
Indices: 41776--41850 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
41766 ATCAAACATT
41776 ATACTTCATGCAAACAACAATC
1 ATACTTCATGCAAACAACAATC
* * *
41798 ATACTT--TGTAAATTAATCAAACAC
1 ATACTTCATGCAAA-CAA-C-AA-TC
41822 TATACTTCATGCAAACAACAATC
1 -ATACTTCATGCAAACAACAATC
41845 ATACTT
1 ATACTT
41851 TGTAAATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
20 5 0.12
21 2 0.05
22 13 0.32
23 3 0.08
24 3 0.08
25 7 0.17
26 2 0.05
27 5 0.12
ACGTcount: A:0.44, C:0.23, G:0.04, T:0.29
Consensus pattern (22 bp):
ATACTTCATGCAAACAACAATC
Found at i:41833 original size:47 final size:47
Alignment explanation
Indices: 41764--41867 Score: 190
Period size: 47 Copynumber: 2.2 Consensus size: 47
41754 AGTGGAAAAA
*
41764 TAATCAAACATTATACTTCATGCAAACAACAATCATACTTTGTAAAT
1 TAATCAAACACTATACTTCATGCAAACAACAATCATACTTTGTAAAT
41811 TAATCAAACACTATACTTCATGCAAACAACAATCATACTTTGTAAAT
1 TAATCAAACACTATACTTCATGCAAACAACAATCATACTTTGTAAAT
*
41858 TAATCGAACA
1 TAATCAAACA
41868 AGTTATAAGG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (47 bp):
TAATCAAACACTATACTTCATGCAAACAACAATCATACTTTGTAAAT
Found at i:47783 original size:32 final size:34
Alignment explanation
Indices: 47747--47827 Score: 87
Period size: 32 Copynumber: 2.5 Consensus size: 34
47737 AGTTCTCAAT
*
47747 ACAAAATATTAATAAA-TAACATTTTAAGTTAC-
1 ACAAAATATTAATAAATTAAAATTTTAAGTTACG
* * *
47779 AC-AAATATTAAAAAATTAAAATTTTAGGTTGCG
1 ACAAAATATTAATAAATTAAAATTTTAAGTTACG
* *
47812 ACAAAAAATTATTAAA
1 ACAAAATATTAATAAA
47828 CTTTTTTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
31 12 0.31
32 15 0.38
33 2 0.05
34 10 0.26
ACGTcount: A:0.54, C:0.07, G:0.06, T:0.32
Consensus pattern (34 bp):
ACAAAATATTAATAAATTAAAATTTTAAGTTACG
Found at i:47785 original size:31 final size:31
Alignment explanation
Indices: 47746--47804 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
47736 CAGTTCTCAA
* *
47746 TACAAAATATTAATAAA-TAACATTTTAAGT
1 TACAAAATATTAAAAAATTAAAATTTTAAGT
47776 TACACAAATATTAAAAAATTAAAATTTTA
1 TACA-AAATATTAAAAAATTAAAATTTTA
47805 GGTTGCGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 12 0.48
32 9 0.36
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (31 bp):
TACAAAATATTAAAAAATTAAAATTTTAAGT
Found at i:48287 original size:25 final size:27
Alignment explanation
Indices: 48231--48289 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
48221 ACATGTAACT
48231 TATAAAA-TGATTTATCAGTATGCATA
1 TATAAAACTGATTTATCAGTATGCATA
*
48257 AATAAAACTGATTT-TCAG-ACT-CATA
1 TATAAAACTGATTTATCAGTA-TGCATA
48282 TATAAAAC
1 TATAAAAC
48290 AAAATACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 12 0.41
26 11 0.38
27 6 0.21
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (27 bp):
TATAAAACTGATTTATCAGTATGCATA
Found at i:48914 original size:24 final size:24
Alignment explanation
Indices: 48880--48950 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
48870 AAACGGATAT
* * *
48880 ATCAGGAATCAAAACAAAATTCAA
1 ATCAGAAATCATAACAGAATTCAA
* * * *
48904 ATCAGATATCATAATAGAATCCAG
1 ATCAGAAATCATAACAGAATTCAA
48928 ATCAGAAATCATAACAGAATTCA
1 ATCAGAAATCATAACAGAATTCA
48951 GGTCATGTAT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCATAACAGAATTCAA
Found at i:49690 original size:20 final size:20
Alignment explanation
Indices: 49665--49725 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
49655 GCCCTTAACT
49665 TTAAACCCTAAATCATAAAC
1 TTAAACCCTAAATCATAAAC
*
49685 TTAAACTCTAAAT-ATTAAACC
1 TTAAACCCTAAATCA-TAAA-C
* * *
49706 CTAAATCTTAAATCATAAAC
1 TTAAACCCTAAATCATAAAC
49726 CCTAAACCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
19 1 0.03
20 17 0.52
21 14 0.42
22 1 0.03
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (20 bp):
TTAAACCCTAAATCATAAAC
Found at i:49724 original size:14 final size:14
Alignment explanation
Indices: 49673--49724 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
49663 CTTTAAACCC
49673 TAAATCATAAA-CT
1 TAAATCATAAATCT
*
49686 TAAACTC-TAAATAT
1 TAAA-TCATAAATCT
* *
49700 TAAACCCTAAATCT
1 TAAATCATAAATCT
49714 TAAATCATAAA
1 TAAATCATAAA
49725 CCCTAAACCT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 9 0.29
14 22 0.71
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAATCATAAATCT
Found at i:49738 original size:34 final size:34
Alignment explanation
Indices: 49666--49739 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
49656 CCCTTAACTT
* * *
49666 TAAACCCTAAATCATAAACTTAAACTCTAAATAT
1 TAAACCCTAAATCATAAACATAAACCCTAAATAC
* *
49700 TAAACCCTAAATCTTAAATCATAAACCCTAAA-CC
1 TAAACCCTAAATCATAAA-CATAAACCCTAAATAC
49734 TAAACC
1 TAAACC
49740 TTACTCCTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 23 0.68
35 11 0.32
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (34 bp):
TAAACCCTAAATCATAAACATAAACCCTAAATAC
Found at i:50196 original size:6 final size:6
Alignment explanation
Indices: 50185--50226 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
50175 GTCATGAACC
50185 ATAATT ATAATT ATAATT ATAATT ATAATT ATAATT ATAATT
1 ATAATT ATAATT ATAATT ATAATT ATAATT ATAATT ATAATT
50227 TATTTAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:50545 original size:11 final size:11
Alignment explanation
Indices: 50529--50558 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
50519 AACTATTTTC
50529 AAATCGAGCTT
1 AAATCGAGCTT
50540 AAATCGAGCTT
1 AAATCGAGCTT
*
50551 CAATCGAG
1 AAATCGAG
50559 TTCGAGTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (11 bp):
AAATCGAGCTT
Found at i:59035 original size:15 final size:16
Alignment explanation
Indices: 59000--59035 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
58990 TAATTAATAA
59000 AATT-AAAATATAAAT
1 AATTAAAAATATAAAT
59015 AA-TAAAAATA-AAAT
1 AATTAAAAATATAAAT
59029 AATTAAA
1 AATTAAA
59036 TTTATTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AATTAAAAATATAAAT
Found at i:60148 original size:17 final size:18
Alignment explanation
Indices: 60119--60153 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
60109 AACGAAAAAA
60119 TTATTATTAAATAATAAT
1 TTATTATTAAATAATAAT
60137 TTATTATT-AATAATAAT
1 TTATTATTAAATAATAAT
60154 ATTTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATTATTAAATAATAAT
Found at i:61027 original size:79 final size:76
Alignment explanation
Indices: 60845--61030 Score: 203
Period size: 77 Copynumber: 2.4 Consensus size: 76
60835 CGTCCAACTT
* *
60845 AAAAAGTTATACAAATATATAACATTTTCAATTGTAATCGAAAAATATTACATTACAATGATTTT
1 AAAAAATTATACAAATTTATAACATTTTCAATTGTAATCGAAAAATATTACATTACAA-GATTTT
* *
60910 GAATTTACAACC
65 GAACTTACAACA
* * ** * *
60922 GAAAAATTATACAATTTTATAACATTTTCGGTTGTAATTGAAAAATATTACATTAAGGCACA-CT
1 AAAAAATTATACAAATTTATAACATTTTCAATTGTAATCGAAAAATATTACATT-A--CA-AGAT
** *
60986 TTTGGGCTTACAATA
62 TTTGAACTTACAACA
61001 AAAAAATTATACAAATTTATAACATTTTCA
1 AAAAAATTATACAAATTTATAACATTTTCA
61031 GTTTAAAAAA
Statistics
Matches: 89, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
77 47 0.53
78 1 0.01
79 38 0.43
80 2 0.02
81 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (76 bp):
AAAAAATTATACAAATTTATAACATTTTCAATTGTAATCGAAAAATATTACATTACAAGATTTTG
AACTTACAACA
Found at i:72291 original size:21 final size:22
Alignment explanation
Indices: 72266--72316 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
72256 TATATAAAAG
72266 TATAAAAAGAT-AAATATA-TCT
1 TATAAAAAGATCAAATATAGT-T
* *
72287 TATAAAAATATCAATTATAGTT
1 TATAAAAAGATCAAATATAGTT
72309 TATAAAAA
1 TATAAAAA
72317 AAAATTCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 10 0.38
22 15 0.58
23 1 0.04
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (22 bp):
TATAAAAAGATCAAATATAGTT
Found at i:72603 original size:2 final size:2
Alignment explanation
Indices: 72596--72651 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
72586 ATTTACACAT
72596 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
72638 TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA T
72652 TTTAAAAAGT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.