Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005335.1 Hibiscus syriacus cultivar Beakdansim tig00012081_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: 57569
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:13360 original size:22 final size:20
Alignment explanation
Indices: 13311--13361 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
13301 AATCAAAATA
13311 AAAGAGACAAAAAGAAAAAG
1 AAAGAGACAAAAAGAAAAAG
*
13331 AGAGAGAGACAACAAAGGAAAAG
1 A-A-AGAGACAA-AAAGAAAAAG
13354 CAAAGAGA
1 -AAAGAGA
13362 AAATAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 1 0.04
21 1 0.04
22 13 0.50
23 10 0.38
24 1 0.04
ACGTcount: A:0.67, C:0.08, G:0.25, T:0.00
Consensus pattern (20 bp):
AAAGAGACAAAAAGAAAAAG
Found at i:13360 original size:24 final size:22
Alignment explanation
Indices: 13305--13375 Score: 63
Period size: 24 Copynumber: 3.1 Consensus size: 22
13295 AGATCCAATC
*
13305 AAAATAAA-AGAGACAAAAAGA
1 AAAAGAAAGAGAGACAAAAAGA
* *
13326 AAAAGAGAGAGAGACAACAAAGG
1 AAAAGAAAGAGAGACAA-AAAGA
* *
13349 AAAAGCAAAGAGAAAATAAAAAGA
1 AAAAG-AAAGAG-AGACAAAAAGA
13373 AAA
1 AAA
13376 CAAAAACAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
21 6 0.15
22 8 0.21
23 9 0.23
24 12 0.31
25 4 0.10
ACGTcount: A:0.72, C:0.06, G:0.20, T:0.03
Consensus pattern (22 bp):
AAAAGAAAGAGAGACAAAAAGA
Found at i:15433 original size:65 final size:64
Alignment explanation
Indices: 15329--15500 Score: 187
Period size: 65 Copynumber: 2.8 Consensus size: 64
15319 GCAACACAAT
* * * *
15329 TTACTCGAGATTGAATTTCAACTTCACAACGAATGATATCTAACTCAAAGCCAATTTGGTGAAAC
1 TTACTCAAGATTGAATTTCAACTTCACAACAAAGGATATCCAACTCAAA-CCAATTTGGTGAAAC
* *
15394 TTACTCAAGATTGGATTTCAACTTTACGAA-AAAGGATATCCAACTCAAACCAATTTGGTGAAAC
1 TTACTCAAGATTGAATTTCAACTTCAC-AACAAAGGATATCCAACTCAAACCAATTTGGTGAAAC
* * * *
15458 -AAC-C--G-TTGGATTT-AACTTCACAACGAAGGATATCCAATTCAAA
1 TTACTCAAGATTGAATTTCAACTTCACAACAAAGGATATCCAACTCAAA
15501 GCTCAAATTT
Statistics
Matches: 95, Mismatches: 10, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
57 2 0.02
58 24 0.25
59 8 0.08
60 1 0.01
62 1 0.01
63 2 0.02
64 15 0.16
65 40 0.42
66 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (64 bp):
TTACTCAAGATTGAATTTCAACTTCACAACAAAGGATATCCAACTCAAACCAATTTGGTGAAAC
Found at i:15607 original size:124 final size:124
Alignment explanation
Indices: 15463--15722 Score: 344
Period size: 124 Copynumber: 2.1 Consensus size: 124
15453 GAAACAACCG
* * * *
15463 TTGGATTT-AACTTCACAACGAAGGATATCCAATTCAAAGCTCAAATTTACAATGAATGAGTCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAAATTGACAACGAAGGAGCCAT
* * *
15527 CCATGATTTCAACTTCACGACGA-AGGATATTATGCCCACAAGAAGCATCCATCTCTAGA
66 CCACGATTTCAACTTCACGA-GAGAGGATATCATGCCCACAAGAAGCATCCATCTCTAAA
* * *
15586 TTGGATTTCAACTTCACAACGAAGGATATCCAATTTAAAGCTCAACTTGACCACGAAGGAGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAAATTGACAACGAAGGAGCCAT
* * * * * *
15651 CCACGATTTCAACTTCACGATAGAGGATATCCTGTCCACAAGCATCATCCATTTCTAAA
66 CCACGATTTCAACTTCACGAGAGAGGATATCATGCCCACAAGAAGCATCCATCTCTAAA
*
15710 ATGGATTTCAACT
1 TTGGATTTCAACT
15723 CAAAGTCAAT
Statistics
Matches: 118, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
123 9 0.08
124 109 0.92
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (124 bp):
TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAAATTGACAACGAAGGAGCCAT
CCACGATTTCAACTTCACGAGAGAGGATATCATGCCCACAAGAAGCATCCATCTCTAAA
Found at i:15858 original size:34 final size:34
Alignment explanation
Indices: 15820--15906 Score: 147
Period size: 34 Copynumber: 2.6 Consensus size: 34
15810 TCCTTGGATT
* *
15820 TCAACTTCACGATGAAGGATATTCAACTCCAAGC
1 TCAACTTCACGACGAAGGATATCCAACTCCAAGC
15854 TCAACTTCACGACGAAGGATATCCAACTCCAAGC
1 TCAACTTCACGACGAAGGATATCCAACTCCAAGC
*
15888 TCAACTTCACAACGAAGGA
1 TCAACTTCACGACGAAGGA
15907 GCCATCCACG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.37, C:0.29, G:0.15, T:0.20
Consensus pattern (34 bp):
TCAACTTCACGACGAAGGATATCCAACTCCAAGC
Found at i:16166 original size:83 final size:83
Alignment explanation
Indices: 16018--16347 Score: 380
Period size: 83 Copynumber: 3.9 Consensus size: 83
16008 CAACCAAGTG
* * **
16018 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAATG-AAACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTC-A-GCAAATCTTTAAGTTCGATTACATTCAGC
16082 TCAAGGACATATCAAATTTA
64 TCAAGGACATATCAAATTTA
* * * *
16102 CAACATAGCTCAAGGCAAGAAGGGCTATTTGTTAGCAAATCTTTAAGTTCGATTACATTCAGCTC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAGCAAATCTTTAAGTTCGATTACATTCAGCTC
*
16167 ATGGACATATCAAATTTA
66 AAGGACATATCAAATTTA
* * * * ** *
16185 -ATGCATAGCTTAAGGCGAGAAGAGCTATCTGTCAGTAAACCTTCGAGCTCGATTACATTCAGCT
1 CA-GCATAGCTCAAGGCGAGAAGGGCTATCTGTCAGCAAATCTTTAAGTTCGATTACATTCAGCT
*
16249 CATGGACATATCAAATTTA
65 CAAGGACATATCAAATTTA
* * *
16268 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAGAAT-TTTCAAGTTCGATTTCATTCAG
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAGC-A-AATCTTT-AAGTTCGATTACATTCAG
*
16332 TTCGAAGG-CATATCAA
63 CTC-AAGGACATATCAA
16348 CCGCATGGTA
Statistics
Matches: 207, Mismatches: 32, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
82 2 0.01
83 143 0.69
84 32 0.15
85 27 0.13
86 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (83 bp):
CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAGCAAATCTTTAAGTTCGATTACATTCAGCTC
AAGGACATATCAAATTTA
Found at i:17567 original size:26 final size:27
Alignment explanation
Indices: 17533--17591 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
17523 CTCTGTTTTA
*
17533 TTTAT-TTA-TGATTTTGACACTTAAG
1 TTTATGTTATTGATTTAGACACTTAAG
* *
17558 TTTATGTTATTTATTTAGTCACTTAAG
1 TTTATGTTATTGATTTAGACACTTAAG
17585 TTT-TGTT
1 TTTATGTT
17592 TTTGCTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 5 0.17
26 7 0.24
27 17 0.59
ACGTcount: A:0.24, C:0.07, G:0.12, T:0.58
Consensus pattern (27 bp):
TTTATGTTATTGATTTAGACACTTAAG
Found at i:28327 original size:21 final size:20
Alignment explanation
Indices: 28266--28327 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 20
28256 ACGAAATTTG
*
28266 ACAATTTGCAAGCCAAACCTA
1 ACAATTTG-AAGCCAAATCTA
* *
28287 ACAA-TT---GCCAAATTTG
1 ACAATTTGAAGCCAAATCTA
28303 ACAATTTGGAAGCCAAATCTA
1 ACAATTT-GAAGCCAAATCTA
28324 ACAA
1 ACAA
28328 CTACGTGGTC
Statistics
Matches: 31, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
16 11 0.35
17 2 0.06
20 2 0.06
21 16 0.52
ACGTcount: A:0.44, C:0.23, G:0.11, T:0.23
Consensus pattern (20 bp):
ACAATTTGAAGCCAAATCTA
Found at i:30067 original size:39 final size:35
Alignment explanation
Indices: 30024--30101 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 35
30014 ATTATTTTTA
*
30024 AATTTAATTATAAATATTTGTAATATTATAA-TATTATAT
1 AATTTAATT-TAAATAGTT-T-AT-TTATAATTA-TATAT
30063 AATTTTAATTTAAATAGTTTATTTATAATTATATAT
1 AA-TTTAATTTAAATAGTTTATTTATAATTATATAT
30099 AAT
1 AAT
30102 ACATATATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
35 1 0.03
36 13 0.36
37 4 0.11
38 1 0.03
39 10 0.28
40 7 0.19
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (35 bp):
AATTTAATTTAAATAGTTTATTTATAATTATATAT
Found at i:31249 original size:39 final size:39
Alignment explanation
Indices: 31204--31321 Score: 227
Period size: 39 Copynumber: 3.0 Consensus size: 39
31194 ATGTCACTTT
31204 CTGATTAATTTGTTAATGGAACTATGAAAATGTGAAATG
1 CTGATTAATTTGTTAATGGAACTATGAAAATGTGAAATG
*
31243 CTGATTAATTTGTTAATAGAACTATGAAAATGTGAAATG
1 CTGATTAATTTGTTAATGGAACTATGAAAATGTGAAATG
31282 CTGATTAATTTGTTAATGGAACTATGAAAATGTGAAATG
1 CTGATTAATTTGTTAATGGAACTATGAAAATGTGAAATG
31321 C
1 C
31322 ATAGGAAATG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (39 bp):
CTGATTAATTTGTTAATGGAACTATGAAAATGTGAAATG
Found at i:33175 original size:21 final size:22
Alignment explanation
Indices: 33149--33198 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
33139 CACCGAAGTG
33149 CCACATA-TTTGTCCCAAAGGA
1 CCACATAGTTTGTCCCAAAGGA
33170 CCACATAGTTTTGTCCCAAAGGA
1 CCACATAG-TTTGTCCCAAAGGA
*
33193 CTACAT
1 CCACAT
33199 TGAACCATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 7 0.27
23 19 0.73
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (22 bp):
CCACATAGTTTGTCCCAAAGGA
Found at i:33899 original size:18 final size:20
Alignment explanation
Indices: 33858--33903 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
33848 TTCCTCTTGG
*
33858 TATCGATACCTCCACATCAG
1 TATCGATACCTCCACATCAA
*
33878 TATCGATA-CTTCA-ATCAA
1 TATCGATACCTCCACATCAA
33896 TATCGATA
1 TATCGATA
33904 TTGTTCATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 12 0.50
19 4 0.17
20 8 0.33
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (20 bp):
TATCGATACCTCCACATCAA
Found at i:40008 original size:14 final size:14
Alignment explanation
Indices: 39989--40018 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
39979 TATATCAAAA
39989 CATCAAAATGTTTT
1 CATCAAAATGTTTT
40003 CATCAAAATGTTTT
1 CATCAAAATGTTTT
40017 CA
1 CA
40019 ACAATCTCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.40
Consensus pattern (14 bp):
CATCAAAATGTTTT
Found at i:40090 original size:13 final size:13
Alignment explanation
Indices: 40072--40104 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
40062 TAAGATTTTC
*
40072 TTTGAAAATCATT
1 TTTGAAAATCAGT
40085 TTTG-AAATCAGT
1 TTTGAAAATCAGT
40097 TTTGAAAA
1 TTTGAAAA
40105 ATTACTCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.42
Consensus pattern (13 bp):
TTTGAAAATCAGT
Found at i:40382 original size:16 final size:16
Alignment explanation
Indices: 40341--40376 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
40331 TAAAATAATG
*
40341 CAAAAAATAAT-AAAC
1 CAAAAAAAAATCAAAC
40356 CAAAAAAAAATCAAAC
1 CAAAAAAAAATCAAAC
40372 CAAAA
1 CAAAA
40377 CCAAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.75, C:0.17, G:0.00, T:0.08
Consensus pattern (16 bp):
CAAAAAAAAATCAAAC
Found at i:41862 original size:12 final size:13
Alignment explanation
Indices: 41845--41882 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
41835 ATAGGCAAAA
*
41845 TTTGAAAACTAT-
1 TTTGAAAACAATG
41857 TTTGAAAACAATG
1 TTTGAAAACAATG
41870 TTTGAAAATCAAT
1 TTTGAAAA-CAAT
41883 ATGTAGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.48
13 8 0.35
14 4 0.17
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.37
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:46657 original size:56 final size:57
Alignment explanation
Indices: 46550--46657 Score: 157
Period size: 56 Copynumber: 1.9 Consensus size: 57
46540 ATGCATATAC
*
46550 CATGCATCGATACACTCAGGGTTTTATGAAAACATCGAATGCATTTGATGCACCAGT
1 CATGCATCGATACACTCAGGCTTTTATGAAAACATCGAATGCATTTGATGCACCAGT
* * *
46607 CATGCATCGATGCACTTAGGCTATTT-TG-AAACATCGAATGCATTTTATGCA
1 CATGCATCGATACACTCAGGCT-TTTATGAAAACATCGAATGCATTTGATGCA
46658 TCAATGCACT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
56 22 0.48
57 21 0.46
58 3 0.07
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (57 bp):
CATGCATCGATACACTCAGGCTTTTATGAAAACATCGAATGCATTTGATGCACCAGT
Found at i:50511 original size:19 final size:21
Alignment explanation
Indices: 50468--50519 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
50458 GAATCCCCTT
50468 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
50489 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
50508 TGAAGATACATG
1 TGAAAATACATG
50520 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:51441 original size:30 final size:31
Alignment explanation
Indices: 51400--51459 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
51390 ACATGCTGCC
**
51400 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
51431 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
51460 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:54671 original size:19 final size:21
Alignment explanation
Indices: 54637--54681 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
54627 CCCTTTGAAA
54637 ACATGATTTTTAAATGAAAAT
1 ACATGATTTTTAAATGAAAAT
*
54658 ACATGA-TTTT-AATGAAGAT
1 ACATGATTTTTAAATGAAAAT
54677 ACATG
1 ACATG
54682 CTCTTGGCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.57
20 4 0.17
21 6 0.26
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (21 bp):
ACATGATTTTTAAATGAAAAT
Found at i:55517 original size:29 final size:31
Alignment explanation
Indices: 55477--55535 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
55467 ACATGCTGCC
**
55477 ATGATATCTAAATGATATG-AAACATAATAA
1 ATGATATCTAAAACATATGTAAACATAATAA
55507 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGTAAACATAATA
55536 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.29
Consensus pattern (31 bp):
ATGATATCTAAAACATATGTAAACATAATAA
Done.