Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000279.1 Hibiscus syriacus cultivar Beakdansim tig00000518_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: 85373
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:3995 original size:14 final size:14
Alignment explanation
Indices: 3972--4009 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3962 TCTGTCTATA
*
3972 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
3985 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
4000 TGCAGGGATT
1 TGCAGGGATT
4010 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:7004 original size:12 final size:12
Alignment explanation
Indices: 6987--7011 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6977 ACAAAGCACC
6987 ATTTGGTGCCTA
1 ATTTGGTGCCTA
6999 ATTTGGTGCCTA
1 ATTTGGTGCCTA
7011 A
1 A
7012 ATTATTTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:17517 original size:27 final size:27
Alignment explanation
Indices: 17482--17550 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
17472 AATTACCATG
17482 GGAAATGTGGAAGTGATCATGTTTCAT
1 GGAAATGTGGAAGTGATCATGTTTCAT
17509 GGAAATGTGGAAGTGATCATGTTTCAT
1 GGAAATGTGGAAGTGATCATGTTTCAT
*
17536 GGAAATGGGGAAGTG
1 GGAAATGTGGAAGTG
17551 CATTACTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.30, C:0.06, G:0.35, T:0.29
Consensus pattern (27 bp):
GGAAATGTGGAAGTGATCATGTTTCAT
Found at i:25649 original size:23 final size:21
Alignment explanation
Indices: 25608--25654 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
25598 ATCCTTCTAA
*
25608 AATCCTAGAAATACTAAAGAT
1 AATCCTAGAAATACCAAAGAT
25629 AATCCTAAGAAAATACCAAAGAT
1 AATCCT-AG-AAATACCAAAGAT
25652 AAT
1 AAT
25655 TATTTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.26
22 2 0.09
23 15 0.65
ACGTcount: A:0.55, C:0.15, G:0.09, T:0.21
Consensus pattern (21 bp):
AATCCTAGAAATACCAAAGAT
Found at i:26660 original size:21 final size:21
Alignment explanation
Indices: 26635--26677 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
26625 ACTAGGAACA
26635 AATTTATGATTTTATATTAAG
1 AATTTATGATTTTATATTAAG
26656 AATTTATGATTTTATATTAAG
1 AATTTATGATTTTATATTAAG
26677 A
1 A
26678 GAATGAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (21 bp):
AATTTATGATTTTATATTAAG
Found at i:39353 original size:23 final size:23
Alignment explanation
Indices: 39323--39370 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
39313 TTCTATTTAT
*
39323 CAAACTACACTTTTATCCATACA
1 CAAACTACACTCTTATCCATACA
*
39346 CAAACTACACTCTTATCCGTACA
1 CAAACTACACTCTTATCCATACA
39369 CA
1 CA
39371 TTACAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.33, G:0.02, T:0.27
Consensus pattern (23 bp):
CAAACTACACTCTTATCCATACA
Found at i:43803 original size:30 final size:31
Alignment explanation
Indices: 43748--43864 Score: 120
Period size: 30 Copynumber: 3.9 Consensus size: 31
43738 GCGATCTAGT
*
43748 AAAAACATG-AACTT-AAAGGATTAAAAT-GAC
1 AAAAACA-GAAACTTAAAAGGACTAAAATAG-C
43778 AAAAACAGAAACTTAAAAGG-CTAAAATAGC
1 AAAAACAGAAACTTAAAAGGACTAAAATAGC
* * *
43808 GAAAATAGAAA-TTTAAAGGACTAAAATAGC
1 AAAAACAGAAACTTAAAAGGACTAAAATAGC
* *
43838 AAAAACACAAACTT-AAGGGACTAAAAT
1 AAAAACAGAAACTTAAAAGGACTAAAAT
43865 GGTATTAACA
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
29 8 0.11
30 58 0.78
31 8 0.11
ACGTcount: A:0.58, C:0.11, G:0.14, T:0.17
Consensus pattern (31 bp):
AAAAACAGAAACTTAAAAGGACTAAAATAGC
Found at i:45076 original size:3 final size:3
Alignment explanation
Indices: 45068--45113 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
45058 GTAATATAGT
45068 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
45114 TATTTTTTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:46652 original size:24 final size:24
Alignment explanation
Indices: 46625--46711 Score: 113
Period size: 24 Copynumber: 3.7 Consensus size: 24
46615 AAACATAATT
*
46625 CAGGTCAAGTATCATATCACAATC
1 CAGGTCAAGTATCATATCAGAATC
* *
46649 CAGGTCATGTATCAAATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
* * *
46673 CATGTC-AGTATCAGATTAGAATC
1 CAGGTCAAGTATCATATCAGAATC
46696 CAGGTCAAGTATCATA
1 CAGGTCAAGTATCATA
46712 AAAAAATTCA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 19 0.36
24 34 0.64
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (24 bp):
CAGGTCAAGTATCATATCAGAATC
Found at i:50048 original size:22 final size:22
Alignment explanation
Indices: 50020--50066 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
50010 CCGATTTGAT
*
50020 CTGGAGTGTCACATTAGGGCCA
1 CTGGAGTATCACATTAGGGCCA
50042 CTGGAGTATCACATTAGGGCCA
1 CTGGAGTATCACATTAGGGCCA
50064 CTG
1 CTG
50067 AAGCGACCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.23
Consensus pattern (22 bp):
CTGGAGTATCACATTAGGGCCA
Found at i:50835 original size:23 final size:23
Alignment explanation
Indices: 50779--50856 Score: 84
Period size: 24 Copynumber: 3.3 Consensus size: 23
50769 ATTCAGGTCA
* * * *
50779 AGTATCATATTAGAATCTAGGTC
1 AGTATCAGATCAGAATCCAAGTC
*
50802 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAAGTC
*
50826 AGTATTAGATCAGAATCCAAGTC
1 AGTATCAGATCAGAATCCAAGTC
50849 AGGTATCA
1 A-GTATCA
50857 TAACATAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
23 22 0.48
24 24 0.52
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAAGTC
Found at i:51697 original size:16 final size:17
Alignment explanation
Indices: 51668--51703 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
51658 CAAAGTTCAT
51668 GTCAACGTCGGTCAACG
1 GTCAACGTCGGTCAACG
51685 GTCAACG-CGGTCAACG
1 GTCAACGTCGGTCAACG
51701 GTC
1 GTC
51704 TTTTTTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.22, C:0.31, G:0.31, T:0.17
Consensus pattern (17 bp):
GTCAACGTCGGTCAACG
Found at i:52042 original size:20 final size:21
Alignment explanation
Indices: 52017--52055 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
52007 AAACCAACGA
*
52017 AGATTGAGTTAAAA-CGACAG
1 AGATTGAGTGAAAATCGACAG
52037 AGATTGAGTGAAAATCGAC
1 AGATTGAGTGAAAATCGAC
52056 GATGCTTCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.44, C:0.10, G:0.26, T:0.21
Consensus pattern (21 bp):
AGATTGAGTGAAAATCGACAG
Found at i:53820 original size:23 final size:24
Alignment explanation
Indices: 53758--53842 Score: 136
Period size: 24 Copynumber: 3.6 Consensus size: 24
53748 AAACATAATT
*
53758 CAGGTCAAGTATCAGATCAGAATC
1 CAGGTCAGGTATCAGATCAGAATC
*
53782 CAGGTCATGTATCAGATCAGAATC
1 CAGGTCAGGTATCAGATCAGAATC
*
53806 CATGTCA-GTATCAGATCAGAATC
1 CAGGTCAGGTATCAGATCAGAATC
53829 CAGGTCAGGTATCA
1 CAGGTCAGGTATCA
53843 TAACATAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
23 22 0.39
24 35 0.61
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (24 bp):
CAGGTCAGGTATCAGATCAGAATC
Found at i:60356 original size:43 final size:43
Alignment explanation
Indices: 60308--60392 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
60298 GTCATAAATA
*
60308 CGGGTTATAAATACGGTTAAAAAATTTATTGACGAACAATGAG
1 CGGGTTATAAATACGGGTAAAAAATTTATTGACGAACAATGAG
* * *
60351 CGGGTTATAAATACGGGTCATAGATTTATTGACGAACAATGA
1 CGGGTTATAAATACGGGTAAAAAATTTATTGACGAACAATGA
60393 ACGTCATTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (43 bp):
CGGGTTATAAATACGGGTAAAAAATTTATTGACGAACAATGAG
Found at i:62070 original size:19 final size:20
Alignment explanation
Indices: 62048--62085 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
62038 CATGACATAA
62048 TTAAAGTTAAAATT-AAAAT
1 TTAAAGTTAAAATTGAAAAT
* *
62067 TTAATGTTATAATTGAAAA
1 TTAAAGTTAAAATTGAAAA
62086 AACTGAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (20 bp):
TTAAAGTTAAAATTGAAAAT
Found at i:70925 original size:33 final size:32
Alignment explanation
Indices: 70871--70933 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 32
70861 TTTAAACTAA
70871 AATACCTAAAACAAATATAAAAATA-TAAAAAT
1 AATACCTAAAACAAATAT-AAAATACTAAAAAT
*
70903 AATATCCTAAAACTTAAT-TAAAATACTAAAA
1 AATA-CCTAAAAC-AAATATAAAATACTAAAA
70934 CTTATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 10 0.37
33 14 0.52
34 3 0.11
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.25
Consensus pattern (32 bp):
AATACCTAAAACAAATATAAAATACTAAAAAT
Found at i:76474 original size:73 final size:75
Alignment explanation
Indices: 76316--76501 Score: 245
Period size: 73 Copynumber: 2.5 Consensus size: 75
76306 AAATCCTAAT
* * * * * * *
76316 TAAAACC-ATTTAAACTAAAATAGCTAAAATAATA-ATAATATTTAAAACAATATTATAAATCCT
1 TAAAACCTATTTAAACTAAAATACCTAAAACAA-AGATAATAATAAAAAAAATATCATAAAACCT
76379 AATTAAAATAC
65 AATTAAAATAC
* *
76390 TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAA-AATAAAAAAAATATCCTAAAACTTA
1 TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAATAATAAAAAAAATATCATAAAACCTA
76454 A-TAAAATAC
66 ATTAAAATAC
*
76463 TAAAACTTATTTAAACTAAAATACCTAAAACAAAGATAA
1 TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAA
76502 CATATAATGT
Statistics
Matches: 100, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
73 46 0.46
74 27 0.27
75 27 0.27
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (75 bp):
TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAATAATAAAAAAAATATCATAAAACCTA
ATTAAAATAC
Found at i:80809 original size:20 final size:19
Alignment explanation
Indices: 80771--80810 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
80761 AACGTGTTTT
*
80771 TATGAATAATATTATACTG
1 TATGAATAATATGATACTG
*
80790 TATGAATAGTACTGATACTG
1 TATGAATAATA-TGATACTG
80810 T
1 T
80811 GCAAATAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (19 bp):
TATGAATAATATGATACTG
Found at i:81832 original size:31 final size:31
Alignment explanation
Indices: 81642--81830 Score: 272
Period size: 31 Copynumber: 6.1 Consensus size: 31
81632 ACCCGTATAA
* *
81642 TAATCTATCCATATGTCCCGAAGAACATAAG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
*
81673 TAATCTGTCCATATGTCCTGAAGAACATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
81704 TAATCTGTCCATATGTCCCGAAGAACATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
*
81735 TAATTTGTCCATATGTCCCGAAGAACATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
* * * *
81766 TATTCTGTTCATATATCCCGAAGAACATTGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
* *
81797 TAAAT-TGTCCATATGCCCCAAAGAACATAGG
1 T-AATCTGTCCATATGTCCCGAAGAACATAGG
81828 TAA
1 TAA
81831 ATCGTCGACT
Statistics
Matches: 141, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
30 2 0.01
31 137 0.97
32 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (31 bp):
TAATCTGTCCATATGTCCCGAAGAACATAGG
Found at i:82008 original size:33 final size:33
Alignment explanation
Indices: 81911--82011 Score: 168
Period size: 33 Copynumber: 3.1 Consensus size: 33
81901 AACAGTTCAC
* *
81911 ATCACT-TATATCATTCTTGTATGATCTCATAA
1 ATCACTGTATAACATTCTTGTATGATCTCATAG
*
81943 ATCATTGTATAACATTCTTGTATGATCTCATAG
1 ATCACTGTATAACATTCTTGTATGATCTCATAG
81976 ATCACTGTATAACATTCTTGTATGATCTCATAG
1 ATCACTGTATAACATTCTTGTATGATCTCATAG
82009 ATC
1 ATC
82012 TCTTTTCATA
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 5 0.08
33 59 0.92
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.42
Consensus pattern (33 bp):
ATCACTGTATAACATTCTTGTATGATCTCATAG
Found at i:82147 original size:10 final size:10
Alignment explanation
Indices: 82132--82156 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
82122 ATCATATGAC
82132 ACATAAAATA
1 ACATAAAATA
82142 ACATAAAATA
1 ACATAAAATA
82152 ACATA
1 ACATA
82157 TAAACTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (10 bp):
ACATAAAATA
Done.