Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005119.1 Hibiscus syriacus cultivar Beakdansim tig00011506_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: 71109
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:9550 original size:62 final size:62
Alignment explanation
Indices: 9453--9578 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
9443 CTTACGTATC
9453 ATTAGGAAATGCATTAACATAAATACATCATTAAGAAGAGGTAATACAAAAGTGTGTAAACT
1 ATTAGGAAATGCATTAACATAAATACATCATTAAGAAGAGGTAATACAAAAGTGTGTAAACT
9515 ATTAGGAAATGCATTAACATAAATACATCATTAAGAAGAGGTAATACAAAAGTGTGTAAACT
1 ATTAGGAAATGCATTAACATAAATACATCATTAAGAAGAGGTAATACAAAAGTGTGTAAACT
9577 AT
1 AT
9579 AAAAACGGGT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (62 bp):
ATTAGGAAATGCATTAACATAAATACATCATTAAGAAGAGGTAATACAAAAGTGTGTAAACT
Found at i:12280 original size:22 final size:22
Alignment explanation
Indices: 12252--12306 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
12242 AAAAATAGAC
12252 GGATCAAGAAGTAAACATTCAA
1 GGATCAAGAAGTAAACATTCAA
12274 GGATCAAGAAGTAAACATTCAA
1 GGATCAAGAAGTAAACATTCAA
12296 GGATCAAGAAG
1 GGATCAAGAAG
12307 GCTTTACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.49, C:0.13, G:0.22, T:0.16
Consensus pattern (22 bp):
GGATCAAGAAGTAAACATTCAA
Found at i:13797 original size:38 final size:40
Alignment explanation
Indices: 13732--13837 Score: 135
Period size: 41 Copynumber: 2.6 Consensus size: 40
13722 ATCCAAAACA
*
13732 TGCGGCGTTTGTATTTAAAAACACCACT-T-CACTAACTTAT
1 TGCGGCGTTTG--TTTAAAAACGCCACTATGCACTAACTTAT
* *
13772 TGCGGCGTTTGTTTAAAAACGCCACTACTGCACTGATTTAT
1 TGCGGCGTTTGTTTAAAAACGCCACTA-TGCACTAACTTAT
*
13813 TGCGGCGTTTGTTTAAAAGCGCCAC
1 TGCGGCGTTTGTTTAAAAACGCCAC
13838 AAAAGACAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
38 14 0.24
40 12 0.20
41 33 0.56
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (40 bp):
TGCGGCGTTTGTTTAAAAACGCCACTATGCACTAACTTAT
Found at i:14164 original size:83 final size:81
Alignment explanation
Indices: 14077--14302 Score: 240
Period size: 83 Copynumber: 2.7 Consensus size: 81
14067 TGCTAAAGAA
* * * * *
14077 CCCTATTACGGTGTTTATATAAAAACACCATTAAAGTACTACTCTATCGCGACATTTGTTGGAAA
1 CCCTATTA-GGAGTTTGTATAAAAAC-CCATTAAAGTACTACTCTATCGCGGCGTTTGTTAGAAA
* * *
14142 AATGCCAATATAAATGAT
64 AATACCAACATAAACGAT
* *
14160 CCCTATTGAGGAGTTTGTATAAAAACGCCGA-TAAAGTACTACTCTATCACGGCGTTTATTAGAA
1 CCCTATT-AGGAGTTTGTATAAAAAC-CC-ATTAAAGTACTACTCTATCGCGGCGTTTGTTAGAA
* *
14224 AAGTACCACCATAAACGAT
63 AAATACCAACATAAACGAT
* *
14243 CCCTATTTTGGCA-TTTGTATAAAAACGCAGTTAAAGTACTACTCTATCGCGGCGTTTGTT
1 CCCTA-TTAGG-AGTTTGTATAAAAACCCA-TTAAAGTACTACTCTATCGCGGCGTTTGTT
14303 TAAGAAACAT
Statistics
Matches: 120, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
81 1 0.01
82 1 0.01
83 113 0.94
84 5 0.04
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (81 bp):
CCCTATTAGGAGTTTGTATAAAAACCCATTAAAGTACTACTCTATCGCGGCGTTTGTTAGAAAAA
TACCAACATAAACGAT
Found at i:28763 original size:62 final size:62
Alignment explanation
Indices: 28666--28791 Score: 234
Period size: 62 Copynumber: 2.0 Consensus size: 62
28656 CTTACGTATC
*
28666 ATTAGGAAATGCATTAACATAAATACATTATTAAGAAGAGGTAATACAAAACTGTGTAAACT
1 ATTAGGAAATGCATTAACATAAATACATAATTAAGAAGAGGTAATACAAAACTGTGTAAACT
*
28728 ATTAGGAAATGCATTAACATAAATACATAATTAAGAAGAGGTAATACAAAAGTGTGTAAACT
1 ATTAGGAAATGCATTAACATAAATACATAATTAAGAAGAGGTAATACAAAACTGTGTAAACT
28790 AT
1 AT
28792 AAAAACGGGT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.27
Consensus pattern (62 bp):
ATTAGGAAATGCATTAACATAAATACATAATTAAGAAGAGGTAATACAAAACTGTGTAAACT
Found at i:31498 original size:22 final size:22
Alignment explanation
Indices: 31470--31524 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
31460 AAAAATAGAC
31470 GGATCAAGAAGTAAACATTCAA
1 GGATCAAGAAGTAAACATTCAA
31492 GGATCAAGAAGTAAACATTCAA
1 GGATCAAGAAGTAAACATTCAA
31514 GGATCAAGAAG
1 GGATCAAGAAG
31525 GCTTTACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.49, C:0.13, G:0.22, T:0.16
Consensus pattern (22 bp):
GGATCAAGAAGTAAACATTCAA
Found at i:33474 original size:83 final size:83
Alignment explanation
Indices: 33267--33477 Score: 273
Period size: 83 Copynumber: 2.5 Consensus size: 83
33257 CTATTACAGT
* * * * *
33267 GTTTATATAAAAACGCA-ATTAAAGTACTACTCTATCGCGACATTTGTTGGAAAAATACCAATAT
1 GTTTGTATAAAAACGCAGA-TAAAGTACTACTCTATCGCGGCGTTTATTAGAAAAATACCAATAT
*
33331 AAACGATCCCTATTGAGGA
65 AAACGATCCCTATTCAGGA
* * *
33350 GTTTGTATAAAAACGCCGATAAAGTACTACTCTATCGCGGCGTTTATTAGAAAAATGCCACTATA
1 GTTTGTATAAAAACGCAGATAAAGTACTACTCTATCGCGGCGTTTATTAGAAAAATACCAATATA
*
33415 AACGATCCCTATTCTGGCA
66 AACGATCCCTATTCAGG-A
* * *
33434 -TTTGTATAAAAATGCAGCTAAAGTACTACTCTATCACGGCGTTT
1 GTTTGTATAAAAACGCAGATAAAGTACTACTCTATCGCGGCGTTT
33478 GTTTAAGAAA
Statistics
Matches: 112, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
83 110 0.98
84 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (83 bp):
GTTTGTATAAAAACGCAGATAAAGTACTACTCTATCGCGGCGTTTATTAGAAAAATACCAATATA
AACGATCCCTATTCAGGA
Found at i:33479 original size:41 final size:40
Alignment explanation
Indices: 33350--33479 Score: 95
Period size: 41 Copynumber: 3.1 Consensus size: 40
33340 CTATTGAGGA
* * *
33350 GTTTGTATAAAAACGCCGATAAAGTACTACTCTATCGCGGC
1 GTTTGTATAAAAATGCAGCTAAAGTACTACTCTATC-CGGC
* * * * *
33391 GTTTATTAGAAAAATGCCA-CTATAA--ACGATCCCTATTCTGGC
1 GTTT-GTATAAAAATG-CAGCTA-AAGTACTA-CTCTA-TCCGGC
*
33433 ATTTGTATAAAAATGCAGCTAAAGTACTACTCTATCACGGC
1 GTTTGTATAAAAATGCAGCTAAAGTACTACTCTATC-CGGC
33474 GTTTGT
1 GTTTGT
33480 TTAAGAAACT
Statistics
Matches: 65, Mismatches: 15, Indels: 18
0.66 0.15 0.18
Matches are distributed among these distances:
40 6 0.09
41 31 0.48
42 23 0.35
43 5 0.08
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (40 bp):
GTTTGTATAAAAATGCAGCTAAAGTACTACTCTATCCGGC
Found at i:40963 original size:14 final size:14
Alignment explanation
Indices: 40944--40976 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
40934 TCTAATGATA
40944 GTGATGAAGCATCC
1 GTGATGAAGCATCC
40958 GTGATGAAGCATCC
1 GTGATGAAGCATCC
40972 GTGAT
1 GTGAT
40977 TCAAGGGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (14 bp):
GTGATGAAGCATCC
Found at i:44320 original size:62 final size:62
Alignment explanation
Indices: 44223--44348 Score: 234
Period size: 62 Copynumber: 2.0 Consensus size: 62
44213 CTTACGTATC
*
44223 ATTAGGAAATGCATTAACATAAATACATCATTAAGAAGAGGTAATACAAAAGTGTGTAAACT
1 ATTAGGAAATGAATTAACATAAATACATCATTAAGAAGAGGTAATACAAAAGTGTGTAAACT
*
44285 ATTAGGAAATGAATTAACGTAAATACATCATTAAGAAGAGGTAATACAAAAGTGTGTAAACT
1 ATTAGGAAATGAATTAACATAAATACATCATTAAGAAGAGGTAATACAAAAGTGTGTAAACT
44347 AT
1 AT
44349 AAAAACGGGT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (62 bp):
ATTAGGAAATGAATTAACATAAATACATCATTAAGAAGAGGTAATACAAAAGTGTGTAAACT
Found at i:47056 original size:22 final size:22
Alignment explanation
Indices: 47028--47082 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
47018 AAAAATAGAC
47028 GGATCAAGAAGTAAACATTCAA
1 GGATCAAGAAGTAAACATTCAA
47050 GGATCAAGAAGTAAACATTCAA
1 GGATCAAGAAGTAAACATTCAA
47072 GGATCAAGAAG
1 GGATCAAGAAG
47083 GCTTTACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.49, C:0.13, G:0.22, T:0.16
Consensus pattern (22 bp):
GGATCAAGAAGTAAACATTCAA
Found at i:48575 original size:38 final size:40
Alignment explanation
Indices: 48510--48615 Score: 126
Period size: 41 Copynumber: 2.6 Consensus size: 40
48500 ATCCAAAACA
*
48510 TGCGGCGTTTGTATTTAAAAACACCACT-T-CACTAACTTAT
1 TGCGGCGTTTG--TTTAAAAACGCCACTATGCACTAACTTAT
* *
48550 TGCGGCGTTTGTTTAAAAACGCCACTACTGCACTGATTTAT
1 TGCGGCGTTTGTTTAAAAACGCCACTA-TGCACTAACTTAT
* *
48591 TACGGCGTTTGTTTAAAAGCGCCAC
1 TGCGGCGTTTGTTTAAAAACGCCAC
48616 AAAAGACAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
38 14 0.24
40 12 0.21
41 32 0.55
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (40 bp):
TGCGGCGTTTGTTTAAAAACGCCACTATGCACTAACTTAT
Found at i:48942 original size:83 final size:82
Alignment explanation
Indices: 48855--49071 Score: 235
Period size: 83 Copynumber: 2.6 Consensus size: 82
48845 TGCTAAAGAA
* * * *
48855 CCCTATTACGGTGTTTATATAAAAACGCCATTAAAGTACTACTCTATCGTGACATTTGTTGGAAA
1 CCCTATTACGGAGTTTATATAAAAACGCCA-TAAAGTACTACTCTATCGCGACATTTATTAGAAA
* *
48920 AATGCCAATATAAATGAT
65 AATACCAATATAAACGAT
* * *
48938 CCCTATTGA-GGAGTTTGTATAAAAACGCCGATAAAGTACTACTCTATCACGTCATTTATTAGAA
1 CCCTATT-ACGGAGTTTATATAAAAACGCC-ATAAAGTACTACTCTATCGCGACATTTATTAGAA
* *
49002 AAGTACCACTATAAACGAT
64 AAATACCAATATAAACGAT
*
49021 CCCTATT-CTGGCA-TTTATATAAAAATG-CAGCTAAAGTACTACTCTATCGCG
1 CCCTATTAC-GG-AGTTTATATAAAAACGCCA--TAAAGTACTACTCTATCGCG
49072 GCGTTTGTTT
Statistics
Matches: 113, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
81 1 0.01
82 1 0.01
83 108 0.96
84 3 0.03
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.31
Consensus pattern (82 bp):
CCCTATTACGGAGTTTATATAAAAACGCCATAAAGTACTACTCTATCGCGACATTTATTAGAAAA
ATACCAATATAAACGAT
Found at i:54533 original size:13 final size:13
Alignment explanation
Indices: 54515--54560 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
54505 CGTTCCCATC
54515 TTCTTCTTCACTT
1 TTCTTCTTCACTT
*
54528 TTCTTCTTCATTTT
1 TTCTTCTTCA-CTT
54542 TTCTT-TTCACTT
1 TTCTTCTTCACTT
54554 TTCTTCT
1 TTCTTCT
54561 CCTCGCCACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 7 0.24
13 15 0.52
14 7 0.24
ACGTcount: A:0.07, C:0.26, G:0.00, T:0.67
Consensus pattern (13 bp):
TTCTTCTTCACTT
Found at i:70365 original size:20 final size:22
Alignment explanation
Indices: 70339--70391 Score: 92
Period size: 20 Copynumber: 2.5 Consensus size: 22
70329 AAAAATAGAC
70339 GGATCAAGAAGTAAAC-TTCAA
1 GGATCAAGAAGTAAACATTCAA
70360 -GATCAAGAAGTAAACATTCAA
1 GGATCAAGAAGTAAACATTCAA
70381 GGATCAAGAAG
1 GGATCAAGAAG
70392 GCTTTACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 15 0.50
21 5 0.17
22 10 0.33
ACGTcount: A:0.49, C:0.13, G:0.21, T:0.17
Consensus pattern (22 bp):
GGATCAAGAAGTAAACATTCAA
Done.