Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005339.1 Hibiscus syriacus cultivar Beakdansim tig00012091_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: 85691
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:8860 original size:2 final size:2
Alignment explanation
Indices: 8853--8896 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
8843 TTAAAAGTAT
* * *
8853 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA AA TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8895 TA
1 TA
8897 AAATAGTATA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:8907 original size:18 final size:20
Alignment explanation
Indices: 8853--8901 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
8843 TTAAAAGTAT
* * *
8853 TATATATATATATATATATA
1 TATATAAATAAATATATAAA
8873 TATATAAATAAATATATAAA
1 TATATAAATAAATATATAAA
8893 TATA-AAATA
1 TATATAAATA
8902 GTATATGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TATATAAATAAATATATAAA
Found at i:14425 original size:11 final size:11
Alignment explanation
Indices: 14409--14433 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
14399 GATCCCGTGT
14409 CAGATCCGACC
1 CAGATCCGACC
14420 CAGATCCGACC
1 CAGATCCGACC
14431 CAG
1 CAG
14434 CGTGTCCGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.44, G:0.20, T:0.08
Consensus pattern (11 bp):
CAGATCCGACC
Found at i:15348 original size:27 final size:27
Alignment explanation
Indices: 15318--15370 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
15308 ATTTTATTTA
* *
15318 ATATATCCGATCTTATTATAAAATAAT
1 ATATATACGATCTTATTAGAAAATAAT
*
15345 ATATATATGATCTTATTAGAAAATAA
1 ATATATACGATCTTATTAGAAAATAA
15371 AAGTTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (27 bp):
ATATATACGATCTTATTAGAAAATAAT
Found at i:27059 original size:30 final size:29
Alignment explanation
Indices: 27023--27113 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 29
27013 TGGATCAATT
* * *
27023 TGATATTTTATCTAAAGTTTACGGTCAAAA
1 TGATATTTTATCTAAAATTCAAGGTC-AAA
*
27053 TGATATTTCATCTAAAATTCAAGGTCAAA
1 TGATATTTTATCTAAAATTCAAGGTCAAA
* *
27082 TTAGTATTTTATCTAAAACTCAGAGGTCAAA
1 TGA-TATTTTATCTAAAATTCA-AGGTCAAA
27113 T
1 T
27114 AAAAATTAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 5 0.10
30 38 0.73
31 9 0.17
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.37
Consensus pattern (29 bp):
TGATATTTTATCTAAAATTCAAGGTCAAA
Found at i:29872 original size:31 final size:32
Alignment explanation
Indices: 29830--29892 Score: 110
Period size: 33 Copynumber: 2.0 Consensus size: 32
29820 ATTTTGTTCG
29830 GGTC-GGTTTTTTAAGTGTGATATTCGGGTCA
1 GGTCGGGTTTTTTAAGTGTGATATTCGGGTCA
29861 GGTCGGGTTTTTTTAAGTGTGATATTCGGGTC
1 GGTCGGG-TTTTTTAAGTGTGATATTCGGGTC
29893 GAGTTCGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 4 0.13
32 2 0.07
33 24 0.80
ACGTcount: A:0.14, C:0.10, G:0.33, T:0.43
Consensus pattern (32 bp):
GGTCGGGTTTTTTAAGTGTGATATTCGGGTCA
Found at i:35303 original size:19 final size:19
Alignment explanation
Indices: 35264--35303 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
35254 GAGGAAAGCT
* *
35264 GAATTTATATTTGTATCTG
1 GAATTTATATTTATATATG
35283 GAATTTATATTTATATATG
1 GAATTTATATTTATATATG
35302 GA
1 GA
35304 TTTTGTGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.50
Consensus pattern (19 bp):
GAATTTATATTTATATATG
Found at i:38041 original size:26 final size:26
Alignment explanation
Indices: 38000--38066 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
37990 CTTTATATTT
38000 TTTTATAATATATTATCATTATT-TAAAA
1 TTTTATAA-AT-TTAT-ATTATTCTAAAA
* *
38028 TTTTATAAATTTATTTTCTTCTAAAA
1 TTTTATAAATTTATATTATTCTAAAA
*
38054 TTTTATATATTTA
1 TTTTATAAATTTA
38067 AAATTTCTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.11
26 21 0.60
27 2 0.06
28 8 0.23
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTTATAAATTTATATTATTCTAAAA
Found at i:45320 original size:35 final size:35
Alignment explanation
Indices: 45269--45350 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 35
45259 TAGTATTTTT
*
45269 TAAATAGTTATATTTTTTATATT--AAT-ATATTTATG
1 TAAATA-TTAT-TTTTTT-TATTAAAATAATATTTATA
45304 TAAATATTATTTTTTTTATTAAAATAATATTTATA
1 TAAATATTATTTTTTTTATTAAAATAATATTTATA
*
45339 TAATTATTATTT
1 TAAATATTATTT
45351 ATTTAGAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
32 4 0.10
33 6 0.14
34 7 0.17
35 25 0.60
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (35 bp):
TAAATATTATTTTTTTTATTAAAATAATATTTATA
Found at i:47101 original size:21 final size:21
Alignment explanation
Indices: 47071--47118 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
47061 GCAGGGGTAC
* *
47071 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
47092 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
47113 ATGCCA
1 ATGCCA
47119 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:47148 original size:21 final size:21
Alignment explanation
Indices: 47122--47215 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
47112 TATGCCATCT
* *
47122 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
47143 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
47164 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
47185 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
47206 CCGCAGGGTT
1 CCGCAGGGTT
47216 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:47786 original size:33 final size:33
Alignment explanation
Indices: 47737--47832 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 33
47727 AAATGTTTTT
*
47737 AAAATACAAATTATATTATTCGAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAATTTAAAATA
* * * *
47770 AAAATAAAAATAATATTATTCAAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAATTTAAAATA
* *
47803 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCG-AATTTAA
47833 CATTAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 46 0.87
34 7 0.13
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (33 bp):
AAAATAAAAATTATATTATTCGAATTTAAAATA
Found at i:48444 original size:126 final size:126
Alignment explanation
Indices: 48219--48697 Score: 940
Period size: 126 Copynumber: 3.8 Consensus size: 126
48209 TTTAAGTTAT
*
48219 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
48284 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
48345 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
48410 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
48471 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
48536 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCAAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
48597 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
48662 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
48698 CCGATTATAG
Statistics
Matches: 351, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 351 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.21
Consensus pattern (126 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:48777 original size:8 final size:8
Alignment explanation
Indices: 48764--48804 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
48754 TCACAATCTT
48764 TCAAATTC
1 TCAAATTC
48772 TCAAATTC
1 TCAAATTC
* *
48780 CCAAACTC
1 TCAAATTC
48788 T-AAATTC
1 TCAAATTC
48795 TCAAATTC
1 TCAAATTC
48803 TC
1 TC
48805 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:69671 original size:18 final size:18
Alignment explanation
Indices: 69645--69684 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
69635 AAAGGCGATG
* *
69645 GCGGTATCATATATGGTT
1 GCGGCATCATAAATGGTT
69663 GCGGCATCATAAATGGTT
1 GCGGCATCATAAATGGTT
69681 GCGG
1 GCGG
69685 TGGCTGTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.30
Consensus pattern (18 bp):
GCGGCATCATAAATGGTT
Found at i:71206 original size:17 final size:18
Alignment explanation
Indices: 71163--71203 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
71153 GAATTATATT
71163 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
71180 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
71198 ATTAAA
1 AGTAAA
71204 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:71270 original size:12 final size:10
Alignment explanation
Indices: 71253--71281 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
71243 GAGAGAGTAT
71253 TTGAGAGAAA
1 TTGAGAGAAA
71263 TTGAGAGAAA
1 TTGAGAGAAA
71273 TTGAGAGAA
1 TTGAGAGAA
71282 TTTGGTGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:76252 original size:67 final size:67
Alignment explanation
Indices: 76166--76297 Score: 203
Period size: 67 Copynumber: 2.0 Consensus size: 67
76156 TTTTCGCTCA
** * *
76166 ATTTATTATATTCTTAACTTTCAAACTCTTCTATTTAGTT-GAGAGATTTAGAGTAATACAAATG
1 ATTTATTATATTCACAACTTTCAAACTCTTCTATTTA-TTCAAGAGATCTAGAGTAATACAAATG
76230 TCG
65 TCG
*
76233 ATTTGTTATATTCACAACTTTCAAACTCTTCTATTTATTCAAGAGATCTAGAGTAATACAAATGT
1 ATTTATTATATTCACAACTTTCAAACTCTTCTATTTATTCAAGAGATCTAGAGTAATACAAATGT
76298 TATTATAGAG
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 2 0.03
67 57 0.97
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (67 bp):
ATTTATTATATTCACAACTTTCAAACTCTTCTATTTATTCAAGAGATCTAGAGTAATACAAATGT
CG
Found at i:81286 original size:2 final size:2
Alignment explanation
Indices: 81279--81314 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
81269 AGGATTAAAT
81279 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
81315 AATTTAAGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:82764 original size:156 final size:156
Alignment explanation
Indices: 82525--82834 Score: 477
Period size: 156 Copynumber: 2.0 Consensus size: 156
82515 TATTTATTTT
*
82525 TATAGTTATTAATTTTTACCTAAATTTGACATAACATAGAAATTATAAAATTATTTTTAAATAAA
1 TATAGTTATTAATTTTTACCTAAATTTGACATAACATAGAAATGATAAAATTATTTTTAAATAAA
* *
82590 AGTATTGATTAAAGTTTAACTTTTAATAATATTGATGTGACATT-TGTATAAT-ATACACGTTCG
66 AGTA-TGATTAAAGTTTAACTTTTAATAATACTGACGTGACATTCTGTATAATAATACACGTTCG
82653 ATGCTCACAT-A-ATTATCTATCAACA
130 ATGCTCACATAATATTATCTATCAACA
*
82678 TATAGTTCTTAATTTTTACCTAAATTTTGACCATCAACATAGAAATGATAAAATTATTTTTTAAA
1 TATAGTTATTAATTTTTACCTAAA-TTTGA-CAT-AACATAGAAATGATAAAATTA-TTTTTAAA
* *
82743 TGAAAGTA-GATTAAAATTTTAACTTTTAATAATACTGACGTGACATTCTGTATAATAATACACG
62 TAAAAGTATGATT-AAAGTTTAACTTTTAATAATACTGACGTGACATTCTGTATAATAATACACG
82807 TTCGATGCTCACATAATATTATCTATCA
126 TTCGATGCTCACATAATATTATCTATCA
82835 TCAGGACGAA
Statistics
Matches: 142, Mismatches: 6, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
153 23 0.16
154 5 0.04
155 7 0.05
156 51 0.36
157 23 0.16
158 21 0.15
159 1 0.01
160 11 0.08
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (156 bp):
TATAGTTATTAATTTTTACCTAAATTTGACATAACATAGAAATGATAAAATTATTTTTAAATAAA
AGTATGATTAAAGTTTAACTTTTAATAATACTGACGTGACATTCTGTATAATAATACACGTTCGA
TGCTCACATAATATTATCTATCAACA
Found at i:83789 original size:20 final size:20
Alignment explanation
Indices: 83764--83821 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
83754 TTTGGTTCAC
83764 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
83784 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
**
83804 GGAATAAAAGATTACCAG
1 GGAATGTAAGATTACCAG
83822 GGAATATGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.40, C:0.10, G:0.28, T:0.22
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:83826 original size:18 final size:19
Alignment explanation
Indices: 83771--83827 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
83761 CACGGAATGT
**
83771 AAGATTACCAGTGGGAATGT
1 AAGATTACCAG-GGGAATAA
83791 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
83811 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
83828 TGATTACTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.20
20 28 0.80
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:83961 original size:18 final size:17
Alignment explanation
Indices: 83940--83988 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
83930 AAATTGTCCT
*
83940 TATTATATATTTGTATAA
1 TATTATATATTT-TAAAA
* *
83958 TATTACAAATTTTAAAA
1 TATTATATATTTTAAAA
83975 TATTTATATATTTT
1 TA-TTATATATTTT
83989 TTAAAAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TATTATATATTTTAAAA
Done.