Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004680.1 Hibiscus syriacus cultivar Beakdansim tig00010494_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: 45275
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33
Found at i:7239 original size:21 final size:21
Alignment explanation
Indices: 7215--7374 Score: 146
Period size: 21 Copynumber: 7.3 Consensus size: 21
7205 ATAGTATACG
*
7215 AAGTACTACTACAAGTACACA
1 AAGTACTACTCCAAGTACACA
**
7236 AAGTACT-CTTGTTATAGTACACA
1 AAGTACTAC-T-CCA-AGTACACA
*
7259 TAGTACTACTCCAAGTACACA
1 AAGTACTACTCCAAGTACACA
*
7280 AAGTACT-CTTGTCATAGTACACA
1 AAGTACTAC-T-CCA-AGTACACA
* *
7303 TAGTATTACTCCAAGTACACA
1 AAGTACTACTCCAAGTACACA
*
7324 AAATACT-CTTACCATAGTACACA
1 AAGTACTAC-T-CCA-AGTACACA
7347 AAGTACTACTCCAAGTACACA
1 AAGTACTACTCCAAGTACACA
7368 AAGTACT
1 AAGTACT
7375 CTTACGAAAA
Statistics
Matches: 113, Mismatches: 14, Indels: 24
0.75 0.09 0.16
Matches are distributed among these distances:
20 3 0.03
21 51 0.45
22 12 0.11
23 44 0.39
24 3 0.03
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (21 bp):
AAGTACTACTCCAAGTACACA
Found at i:7253 original size:44 final size:44
Alignment explanation
Indices: 7216--7377 Score: 261
Period size: 44 Copynumber: 3.7 Consensus size: 44
7206 TAGTATACGA
* *
7216 AGTACTACTACAAGTACACAAAGTACTCTTGTTATAGTACACAT
1 AGTACTACTCCAAGTACACAAAGTACTCTTGTCATAGTACACAT
7260 AGTACTACTCCAAGTACACAAAGTACTCTTGTCATAGTACACAT
1 AGTACTACTCCAAGTACACAAAGTACTCTTGTCATAGTACACAT
* * ** *
7304 AGTATTACTCCAAGTACACAAAATACTCTTACCATAGTACACAA
1 AGTACTACTCCAAGTACACAAAGTACTCTTGTCATAGTACACAT
7348 AGTACTACTCCAAGTACACAAAGTACTCTT
1 AGTACTACTCCAAGTACACAAAGTACTCTT
7378 ACGAAAATGC
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 109 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (44 bp):
AGTACTACTCCAAGTACACAAAGTACTCTTGTCATAGTACACAT
Found at i:13393 original size:60 final size:59
Alignment explanation
Indices: 13224--13404 Score: 181
Period size: 60 Copynumber: 3.1 Consensus size: 59
13214 TGTATCATAT
* * **
13224 ATCCCTAAACTATG-GCTCAATTT-TAAATTGGTCCCTAAACTTTTGAGTATTCCAATTTC
1 ATCCCTAAACTATGACCTC--TTTCTAAATTGGTCCCTAAACTTTTGAATATTTTAATTTC
* * * * * * * *
13283 ATCCC-AAATTATGA-CTCATTCTAAATTAGTCCTTAATCTTTTAAACATTTTAATTTT
1 ATCCCTAAACTATGACCTCTTTCTAAATTGGTCCCTAAACTTTTGAATATTTTAATTTC
* *
13340 ATCCCTAAACTATGACCCTCTTTCTAAATTGGTCCCCAAACATTTGAATATTTTAATTTC
1 ATCCCTAAACTATGA-CCTCTTTCTAAATTGGTCCCTAAACTTTTGAATATTTTAATTTC
13400 ATCCC
1 ATCCC
13405 CAAATCCATC
Statistics
Matches: 96, Mismatches: 21, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
56 2 0.02
57 32 0.33
58 18 0.19
59 5 0.05
60 39 0.41
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (59 bp):
ATCCCTAAACTATGACCTCTTTCTAAATTGGTCCCTAAACTTTTGAATATTTTAATTTC
Found at i:16915 original size:44 final size:46
Alignment explanation
Indices: 16861--16949 Score: 137
Period size: 44 Copynumber: 2.0 Consensus size: 46
16851 TTGTTTGACT
*
16861 AAAAATTATGACAAATATTCAAATGATAACATATT-TTT-TAAAAA
1 AAAAATTATGACAAATATTAAAATGATAACATATTATTTCTAAAAA
* *
16905 AAAAATTATGACAAGTATTAAAATGATAATATATTATTTCTAAAA
1 AAAAATTATGACAAATATTAAAATGATAACATATTATTTCTAAAA
16950 GAATATAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 32 0.80
45 3 0.08
46 5 0.12
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.35
Consensus pattern (46 bp):
AAAAATTATGACAAATATTAAAATGATAACATATTATTTCTAAAAA
Found at i:17829 original size:12 final size:13
Alignment explanation
Indices: 17812--17845 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
17802 TGAATAGTGA
*
17812 TGAACAGTA-CCG
1 TGAACAATATCCG
17824 TGAACAATATCCG
1 TGAACAATATCCG
17837 TGAACAATA
1 TGAACAATA
17846 AACAGTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (13 bp):
TGAACAATATCCG
Found at i:18392 original size:47 final size:46
Alignment explanation
Indices: 18323--18495 Score: 201
Period size: 47 Copynumber: 3.8 Consensus size: 46
18313 TATAAAATCT
*
18323 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
18368 TTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTCTACCAAAATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* **
18415 CTTACCATTTAGATTCCATAAGCTTGTAAGCTTAATTTT-CCATTATA
1 CTTACCATTTA-ATTCCATAAGCTCGTAAGCTT-ATTTTACCAAAATA
* * * *
18462 CTTGCCA-TT-ATTTCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
18496 GCATGGTTAC
Statistics
Matches: 111, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
43 4 0.04
44 17 0.15
45 9 0.08
46 3 0.03
47 74 0.67
48 4 0.04
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.39
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:18655 original size:40 final size:40
Alignment explanation
Indices: 18600--18721 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
18590 ACTGTAGTGC
18600 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
18640 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
18680 TACACATGAGGTCTTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
18720 TA
1 TA
18722 TAAACCTGCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:21779 original size:22 final size:22
Alignment explanation
Indices: 21753--21819 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
21743 TATGCACTCA
21753 ACATATCTTCTAATATATGAAT
1 ACATATCTTCTAATATATGAAT
21775 ACATATCTTCTAATATATGAAT
1 ACATATCTTCTAATATATGAAT
21797 ACATATCTTCTAATATATGAAT
1 ACATATCTTCTAATATATGAAT
21819 A
1 A
21820 GTACTTTCTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.40
Consensus pattern (22 bp):
ACATATCTTCTAATATATGAAT
Found at i:22484 original size:6 final size:6
Alignment explanation
Indices: 22475--22550 Score: 75
Period size: 6 Copynumber: 12.8 Consensus size: 6
22465 TTTTTTTCTT
* * *
22475 TTTTTC TTTTTC GTTTTC TTTTTC TTTTTC TATTTT- TTTTT- TTTCTG
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC
* * *
22522 TTTTTT TTTTTC TTCTTC TGTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
22551 TTTCTTATAA
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
5 8 0.14
6 46 0.79
7 4 0.07
ACGTcount: A:0.01, C:0.13, G:0.04, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:22493 original size:20 final size:19
Alignment explanation
Indices: 22468--22552 Score: 81
Period size: 18 Copynumber: 4.6 Consensus size: 19
22458 TCTCTCATTT
22468 TTTTCTTTTTTTCTTTTTC
1 TTTTCTTTTTTTCTTTTTC
22487 GTTTTC--TTTTTCTTTTTC
1 -TTTTCTTTTTTTCTTTTTC
* * *
22505 TATT-TTTTTTT-TTTCTG
1 TTTTCTTTTTTTCTTTTTC
*
22522 TTTT-TTTTTTTCTTCTTC
1 TTTTCTTTTTTTCTTTTTC
22540 TGTTTCTTTTTTT
1 T-TTTCTTTTTTT
22553 TCTTATAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
17 17 0.32
18 21 0.40
19 3 0.06
20 12 0.23
ACGTcount: A:0.01, C:0.13, G:0.04, T:0.82
Consensus pattern (19 bp):
TTTTCTTTTTTTCTTTTTC
Found at i:22526 original size:41 final size:42
Alignment explanation
Indices: 22464--22556 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 42
22454 TTAATCTCTC
* * *
22464 ATTTTTTTCTTTTTTTCTTTTTCGTTTTCTTTTTCTTTTTCT
1 ATTTTTTTCTTTTTCTCTTTTTCGTTTTCTTCTTCTGTTTCT
* **
22506 ATTTTTTT-TTTTTCTGTTTTTTTTTTTCTTCTTCTGTTTCT
1 ATTTTTTTCTTTTTCTCTTTTTCGTTTTCTTCTTCTGTTTCT
22547 -TTTTTTTCTT
1 ATTTTTTTCTT
22557 ATAATATATA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
40 7 0.16
41 29 0.66
42 8 0.18
ACGTcount: A:0.02, C:0.13, G:0.03, T:0.82
Consensus pattern (42 bp):
ATTTTTTTCTTTTTCTCTTTTTCGTTTTCTTCTTCTGTTTCT
Found at i:22532 original size:35 final size:33
Alignment explanation
Indices: 22467--22555 Score: 108
Period size: 35 Copynumber: 2.6 Consensus size: 33
22457 ATCTCTCATT
*
22467 TTTTTCTTTTTTTCTTTTTC-GTTTTCTTTTTC
1 TTTTTCTTTTTTTTTTTTTCTGTTTTCTTTTTC
*
22499 TTTTTCTATTTTTTTTTTTTCTGTTTTTTTTTTTC
1 TTTTTCT-TTTTTTTTTTTTCTG-TTTTCTTTTTC
* *
22534 TTCTTCTGTTTCTTTTTTTTCT
1 TTTTTCT-TTTTTTTTTTTTCT
22556 TATAATATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
32 7 0.14
33 12 0.24
34 1 0.02
35 29 0.59
ACGTcount: A:0.01, C:0.13, G:0.03, T:0.82
Consensus pattern (33 bp):
TTTTTCTTTTTTTTTTTTTCTGTTTTCTTTTTC
Found at i:22549 original size:21 final size:21
Alignment explanation
Indices: 22465--22556 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
22455 TAATCTCTCA
* *
22465 TTTTTTTCTTTTTTTCTTT-T
1 TTTTTTTCTTTTTCTGTTTCT
** *
22485 TCGTTTTCTTTTTCTTTTTCT
1 TTTTTTTCTTTTTCTGTTTCT
22506 ATTTTTTT-TTTTTCTGTTT-T
1 -TTTTTTTCTTTTTCTGTTTCT
*
22526 TTTTTTTCTTCTTCTGTTTCT
1 TTTTTTTCTTTTTCTGTTTCT
22547 TTTTTTTCTT
1 TTTTTTTCTT
22557 ATAATATATA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
19 7 0.12
20 26 0.43
21 22 0.37
22 5 0.08
ACGTcount: A:0.01, C:0.13, G:0.03, T:0.83
Consensus pattern (21 bp):
TTTTTTTCTTTTTCTGTTTCT
Found at i:26877 original size:18 final size:18
Alignment explanation
Indices: 26854--26889 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
26844 CTTCCATCCG
*
26854 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
26872 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
26890 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:28215 original size:18 final size:18
Alignment explanation
Indices: 28192--28232 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
28182 AACGGGTCAA
28192 CGGGTCGAGTCAACAGGT
1 CGGGTCGAGTCAACAGGT
* **
28210 CGGGTCGGGTCAATGGGT
1 CGGGTCGAGTCAACAGGT
28228 CGGGT
1 CGGGT
28233 AAACGGGTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.20, G:0.46, T:0.20
Consensus pattern (18 bp):
CGGGTCGAGTCAACAGGT
Found at i:28219 original size:31 final size:31
Alignment explanation
Indices: 28184--28250 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
28174 CGACGGTAAA
* *
28184 CGGGTCAACGGGTCGAGTCAACAGGTCGGGT
1 CGGGTCAACGGGTCGAGTAAACAGGTCAGGT
* * *
28215 CGGGTCAATGGGTCGGGTAAACGGGTCAGGT
1 CGGGTCAACGGGTCGAGTAAACAGGTCAGGT
28246 CGGGT
1 CGGGT
28251 TGTGACCGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.18, C:0.19, G:0.45, T:0.18
Consensus pattern (31 bp):
CGGGTCAACGGGTCGAGTAAACAGGTCAGGT
Found at i:32040 original size:18 final size:18
Alignment explanation
Indices: 32017--32051 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
32007 TTCCATCCGG
*
32017 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
32035 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
32052 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:33367 original size:18 final size:18
Alignment explanation
Indices: 33346--33386 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
33336 CGACGGTCAA
33346 CGGGTCGAGTCAACGGGT
1 CGGGTCGAGTCAACGGGT
*
33364 CGGGTCGGGTCAACGGGT
1 CGGGTCGAGTCAACGGGT
33382 CGGGT
1 CGGGT
33387 AAATGGGTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGAGTCAACGGGT
Found at i:33376 original size:31 final size:31
Alignment explanation
Indices: 33340--33404 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
33330 GGTCAACGAC
* *
33340 GGTCAACGGGTCGAGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGAGTAAACGGGTCGAGTCG
* *
33371 GGTCAACGGGTCGGGTAAATGGGTCGAGTCG
1 GGTCAACGGGTCGAGTAAACGGGTCGAGTCG
33402 GGT
1 GGT
33405 TGTGACCGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.17, C:0.18, G:0.46, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGAGTAAACGGGTCGAGTCG
Found at i:33386 original size:13 final size:13
Alignment explanation
Indices: 33340--33369 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
33330 GGTCAACGAC
33340 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
33353 AGTCAACGGGTCG
1 GGTCAACGGGTCG
33366 GGTC
1 GGTC
33370 GGGTCAACGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:34700 original size:30 final size:30
Alignment explanation
Indices: 34664--34720 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
34654 TAATATTATG
*
34664 CATCGATACACTATAGTAACTGCTACAATA
1 CATCGATACACTACAGTAACTGCTACAATA
** *
34694 CATCGATATGCTGCAGTAACTGCTACA
1 CATCGATACACTACAGTAACTGCTACA
34721 GTAAACTTCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (30 bp):
CATCGATACACTACAGTAACTGCTACAATA
Found at i:35172 original size:47 final size:45
Alignment explanation
Indices: 35102--35274 Score: 215
Period size: 47 Copynumber: 3.8 Consensus size: 45
35092 TATAAAATCT
*
35102 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
35147 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTCTACCAAAATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
35194 CTTACCATTTAGATTCCATAAGATCGTAAGCTTAATTTT-CCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTT-ATTTTACCAAAATA
* * * *
35241 CTTGCCA-TTATTCCGTAAGCTCATAAGATTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
35275 CCATGGTTAC
Statistics
Matches: 114, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
43 4 0.04
44 17 0.15
45 10 0.09
46 2 0.02
47 77 0.68
48 4 0.04
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:35424 original size:40 final size:40
Alignment explanation
Indices: 35378--35538 Score: 297
Period size: 40 Copynumber: 4.0 Consensus size: 40
35368 ACCGTAGTGC
35378 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
35418 TACACATAAGG-CGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
35457 TACACATAAGGTCGTGCCCACCATATACACAGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
35497 TACACATAAGGTCGTGCCCACCATATACATCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
35537 TA
1 TA
35539 TAAACCTACA
Statistics
Matches: 117, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
39 39 0.33
40 78 0.67
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Done.