Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003659.1 Hibiscus syriacus cultivar Beakdansim tig00007788_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: 93818
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Found at i:692 original size:12 final size:13
Alignment explanation
Indices: 664--690 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
654 ATTTCAACTA
664 TTAAAATTAATTT
1 TTAAAATTAATTT
677 TTAAAATTAATTT
1 TTAAAATTAATTT
690 T
1 T
691 AATATTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAAATTAATTT
Found at i:41849 original size:37 final size:37
Alignment explanation
Indices: 41800--41904 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
41790 CCTTTTCGTC
*
41800 CTACTAGAATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
41837 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
41874 CTACTATGATTTAAACTCTTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
41905 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:42477 original size:19 final size:19
Alignment explanation
Indices: 42430--42478 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
42420 TTCATTTGGT
* *
42430 TATTTTTTAATACTATATT
1 TATTTTTTTATACTATATA
42449 TATTATTTTTATA-TATATA
1 TATT-TTTTTATACTATATA
42468 TACTTTTTTTA
1 TA-TTTTTTTA
42479 AAATATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTTTTATACTATATA
Found at i:42694 original size:18 final size:19
Alignment explanation
Indices: 42668--42703 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
42658 TGTTTTGGTT
*
42668 TTTTTATATTA-TATTATA
1 TTTTCATATTACTATTATA
42686 TTTTCATATTACTATTAT
1 TTTTCATATTACTATTAT
42704 TATTGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTCATATTACTATTATA
Found at i:42794 original size:24 final size:23
Alignment explanation
Indices: 42759--42825 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 23
42749 ATATTAATAT
*
42759 TTCATTTATTTATTTATTT-TTCC
1 TTCATTTTTTTATTTATTTATT-C
*
42782 TTTTATTTTTTTACTTATATTTATTC
1 -TTCATTTTTTTA-TT-TATTTATTC
*
42808 TTCATTTTTTCATTTATT
1 TTCATTTTTTTATTTATT
42826 CATTTTTTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
23 4 0.11
24 12 0.33
25 12 0.33
26 6 0.17
27 2 0.06
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (23 bp):
TTCATTTTTTTATTTATTTATTC
Found at i:43155 original size:13 final size:13
Alignment explanation
Indices: 43134--43169 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
43124 TTTTTCAAGT
43134 CGAAGCCCAATCC
1 CGAAGCCCAATCC
*
43147 CGGAGCCCAATCC
1 CGAAGCCCAATCC
43160 CGAAGCCCAA
1 CGAAGCCCAA
43170 CCGAAAGACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.44, G:0.19, T:0.06
Consensus pattern (13 bp):
CGAAGCCCAATCC
Found at i:47297 original size:9 final size:9
Alignment explanation
Indices: 47263--47347 Score: 57
Period size: 9 Copynumber: 9.0 Consensus size: 9
47253 AGATCCAATC
47263 AAGAACAAAA
1 AAGAA-AAAA
*
47273 AAG-AAAAG
1 AAGAAAAAA
47281 AAGCAAAAGAA
1 AAG-AAAA-AA
*
47292 AA-AAAACA
1 AAGAAAAAA
47300 AAGAAAAAA
1 AAGAAAAAA
* *
47309 GAGAAACAA
1 AAGAAAAAA
47318 AAGAAAAAGAGA
1 AAG-AAAA-A-A
*
47330 AAGAACAAA
1 AAGAAAAAA
47339 AAGAAAAAA
1 AAGAAAAAA
47348 GAAAAAGGGA
Statistics
Matches: 58, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
8 9 0.16
9 28 0.48
10 10 0.17
11 7 0.12
12 4 0.07
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:47315 original size:17 final size:17
Alignment explanation
Indices: 47266--47331 Score: 63
Period size: 17 Copynumber: 4.1 Consensus size: 17
47256 TCCAATCAAG
47266 AACAAAA-AAGAAA-AGA
1 AACAAAAGAA-AAAGAGA
*
47282 AGCAAAAG-AAAA-A-A
1 AACAAAAGAAAAAGAGA
47296 AAC-AAAGAAAAAAGAGA
1 AACAAAAG-AAAAAGAGA
47313 AACAAAAGAAAAAGAGA
1 AACAAAAGAAAAAGAGA
47330 AA
1 AA
47332 GAACAAAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
13 4 0.10
14 3 0.07
15 8 0.19
16 8 0.19
17 15 0.36
18 4 0.10
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (17 bp):
AACAAAAGAAAAAGAGA
Found at i:47326 original size:37 final size:38
Alignment explanation
Indices: 47263--47353 Score: 100
Period size: 37 Copynumber: 2.4 Consensus size: 38
47253 AGATCCAATC
* * *
47263 AAGAACAAAAAAGAAAAGAAGCAAAAGA-AAA-AA-AACA
1 AAGAA-AAAAGAGAAAAAAAGAAAAAGAGAAAGAACAA-A
47300 AAGAAAAAAGAGAAACAAAAGAAAAAGAGAAAGAACAAA
1 AAGAAAAAAGAGAAA-AAAAGAAAAAGAGAAAGAACAAA
47339 AAGAAAAAAGA-AAAA
1 AAGAAAAAAGAGAAAA
47354 GGGACAAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
36 9 0.19
37 16 0.34
38 6 0.13
39 14 0.30
40 2 0.04
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.00
Consensus pattern (38 bp):
AAGAAAAAAGAGAAAAAAAGAAAAAGAGAAAGAACAAA
Found at i:47362 original size:22 final size:20
Alignment explanation
Indices: 47270--47354 Score: 70
Period size: 18 Copynumber: 4.3 Consensus size: 20
47260 ATCAAGAACA
*
47270 AAAAAGAA-AAGAAGCAAAAG
1 AAAAAGAACAA-AAGAAAAAG
*
47290 AAAAAAAAC-AAAGAAAAA-
1 AAAAAGAACAAAAGAAAAAG
* *
47308 AGAGA-AACAAAAGAAAAAG
1 AAAAAGAACAAAAGAAAAAG
*
47327 AGAAAGAACAAAAAGAAAAAAG
1 AAAAAGAAC-AAAAG-AAAAAG
47349 AAAAAG
1 AAAAAG
47355 GGACAAAAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
17 3 0.06
18 12 0.23
19 11 0.21
20 11 0.21
21 5 0.09
22 11 0.21
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAAGAACAAAAGAAAAAG
Found at i:49051 original size:106 final size:106
Alignment explanation
Indices: 48922--49979 Score: 1425
Period size: 106 Copynumber: 10.0 Consensus size: 106
48912 ATATCGTGCC
* * * *
48922 ACTCGAGACAACACAAGTTCAACTTCACGATGAAGGGA-CGACTGGTTGTCAACAAACAACTTCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAACAATTTCC
*
48986 TAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
49028 ACCCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
49093 AATTTCAGAGCCAATTTCAACTTCACAACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
49134 ACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
49199 AATTTCAAAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * *
49240 ACTCCAGACAACGTAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
**
49305 AATTTCAGAGATAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
49346 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
49411 AATTTCAGAACCAATTTCAACTTCACATCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
49452 ACTCAAGACAACACAAGTTCAACTTCACAACGAAAGGGACGGCTGGTTGTCAA-CAATAATTTCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACG-AAGGGACCGCTGGTTGTCAATAAACAATTTCC
* *
49516 CAATTTCAGAGCCAGTTTCAACTTCGCAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
49558 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCA
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
49623 AATTTCAGAGCCAATTTTAACTTCACAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
49664 ACTCCAGACAACGCATGTTCAACTTCACGAAGAAGGGACCGTTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * *
49729 AATTTCAGAGCCAATTTCAACTTCTCAGCCAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * * * *
49770 AC-CCAAGACAACACAAGACCAACTTCACGATGAAGGGGCGGCTGATTGTCAAT-AA-AATTT--
1 ACTCC-AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCC
* *
49830 C-A-TTCAGAGTCAATTTCAACTTCACAGCGAATGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * *
49870 ACTCGAGACAACACAAGTTCAACTTCACAAAGAAGGGACGGTTGATTGTCAACAAATAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
** * * *
49935 GGTTCCAGAGCCAATTTCAACTTCAAAACGGAA-GATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGC-GAAGGATATTGG
49976 ACTC
1 ACTC
49980 GGAACAATAC
Statistics
Matches: 848, Mismatches: 92, Indels: 24
0.88 0.10 0.02
Matches are distributed among these distances:
100 76 0.09
101 4 0.00
102 6 0.01
104 5 0.01
105 23 0.03
106 710 0.84
107 24 0.03
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:50736 original size:37 final size:37
Alignment explanation
Indices: 50678--50783 Score: 140
Period size: 37 Copynumber: 2.9 Consensus size: 37
50668 CCTTTTCGTC
*
50678 CTACTAGAATTCAAACTCCTAAAAATAGGATCGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATCGAATT
* * * *
50715 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATCGAATT
* * *
50752 CTACTATGATTTAAACTCCTAAAGATAGGATC
1 CTACTAGGATTCAAACTCCTAAAAATAGGATC
50784 CACAAGCATT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATCGAATT
Found at i:51383 original size:2 final size:2
Alignment explanation
Indices: 51376--51402 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
51366 GCATTATTAC
51376 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
51403 TGTAATTATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51613 original size:2 final size:2
Alignment explanation
Indices: 51606--51630 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
51596 TTTTCTATTT
51606 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
51631 TTTAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51683 original size:15 final size:16
Alignment explanation
Indices: 51649--51687 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
51639 TTCATTTATT
* *
51649 TATTTATTTTTCCTTT
1 TATTTATTTTTACTTA
51665 TATTT-TTTTTACTTA
1 TATTTATTTTTACTTA
51680 TATTTATT
1 TATTTATT
51688 CTTCATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTATTTTTACTTA
Found at i:59419 original size:59 final size:59
Alignment explanation
Indices: 59320--59456 Score: 168
Period size: 59 Copynumber: 2.3 Consensus size: 59
59310 CAACATGCTG
** * **
59320 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGTACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
* ** *
59379 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
*
59438 CATACTCGGG-ATAGCACTA
1 CATATTCGGGAATA-CACTA
59457 CGGTGCTTAT
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
58 1 0.02
59 62 0.98
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
Found at i:59578 original size:44 final size:45
Alignment explanation
Indices: 59538--59624 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
59528 GTTATGGAAT
* *
59538 AATGGCAAGTGTATTGGTAAAATAAGTTTACGAGCTTATGGTACA
1 AATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGTACA
* *
59583 AATGGTAAGTATTTTGGTAAAATAAGCTTACGAGCTTATGGT
1 AATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGT
59625 TAATAAATGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.33
Consensus pattern (45 bp):
AATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGTACA
Found at i:65867 original size:59 final size:59
Alignment explanation
Indices: 65768--65904 Score: 168
Period size: 59 Copynumber: 2.3 Consensus size: 59
65758 CAACATGCTG
** * **
65768 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGTACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
* ** *
65827 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
*
65886 CATACTCGGG-ATAGCACTA
1 CATATTCGGGAATA-CACTA
65905 CGGTGCTTAT
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
58 1 0.02
59 62 0.98
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
Found at i:66026 original size:44 final size:45
Alignment explanation
Indices: 65986--66072 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
65976 GTTATGGAAT
* *
65986 AATGGCAAGTGTATTGGTAAAATAAGTTTACGAGCTTATGGTACA
1 AATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGTACA
* *
66031 AATGGTAAGTATTTTGGTAAAATAAGCTTACGAGCTTATGGT
1 AATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGT
66073 TAATAAATGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.33
Consensus pattern (45 bp):
AATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGTACA
Found at i:80560 original size:14 final size:15
Alignment explanation
Indices: 80541--80582 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
80531 GATTTCAACT
80541 ATTAAAATTAATTA-
1 ATTAAAATTAATTAC
80555 ATTAAAATTAATTAC
1 ATTAAAATTAATTAC
* *
80570 TTTAGAATTAATT
1 ATTAAAATTAATT
80583 TTAATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (15 bp):
ATTAAAATTAATTAC
Done.