Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004639.1 Hibiscus syriacus cultivar Beakdansim tig00010388_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: 49866
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Found at i:4098 original size:25 final size:26
Alignment explanation
Indices: 4056--4109 Score: 92
Period size: 25 Copynumber: 2.1 Consensus size: 26
4046 TCTTAATTTA
4056 TTATGAGAAAAAACATAATCTCTAAC
1 TTATGAGAAAAAACATAATCTCTAAC
*
4082 TTATGAGAAAAAA-ATAATCTTTAAC
1 TTATGAGAAAAAACATAATCTCTAAC
4107 TTA
1 TTA
4110 GAAAAACACT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.31
Consensus pattern (26 bp):
TTATGAGAAAAAACATAATCTCTAAC
Found at i:5044 original size:39 final size:39
Alignment explanation
Indices: 5000--5075 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
4990 CAAATATCTA
5000 AAATATATATTAATTTAACAATTTTAAAAGAGTCCAAAC
1 AAATATATATTAATTTAACAATTTTAAAAGAGTCCAAAC
5039 AAATATATATTAATTTAACAATTTTAAAAGAGTCCAA
1 AAATATATATTAATTTAACAATTTTAAAAGAGTCCAA
5076 CGCTACTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.34
Consensus pattern (39 bp):
AAATATATATTAATTTAACAATTTTAAAAGAGTCCAAAC
Found at i:8424 original size:2 final size:2
Alignment explanation
Indices: 8417--8456 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
8407 TTAAATTATG
8417 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8457 GCATCATACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10182 original size:5 final size:5
Alignment explanation
Indices: 10172--10222 Score: 102
Period size: 5 Copynumber: 10.2 Consensus size: 5
10162 TCATGATTCA
10172 AACTC AACTC AACTC AACTC AACTC AACTC AACTC AACTC AACTC AACTC
1 AACTC AACTC AACTC AACTC AACTC AACTC AACTC AACTC AACTC AACTC
10222 A
1 A
10223 CTGAGTGCCC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (5 bp):
AACTC
Found at i:14505 original size:20 final size:20
Alignment explanation
Indices: 14431--14510 Score: 60
Period size: 20 Copynumber: 4.0 Consensus size: 20
14421 TTTAATTAAA
*
14431 AATTAAAATTTTAAATTATTT
1 AATTAAAA-TATAAATTATTT
*
14452 -A--AAAATATAGAACTTTTTT
1 AATTAAAATATA-AA-TTATTT
* *
14471 CATTATAAAT-CAAATTATTT
1 AATTA-AAATATAAATTATTT
14491 AATTAAAATATAAATTATTT
1 AATTAAAATATAAATTATTT
14511 TAACTTTATT
Statistics
Matches: 46, Mismatches: 6, Indels: 15
0.69 0.09 0.22
Matches are distributed among these distances:
17 3 0.07
18 6 0.13
19 9 0.20
20 20 0.43
21 2 0.04
22 2 0.04
23 4 0.09
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (20 bp):
AATTAAAATATAAATTATTT
Found at i:14570 original size:22 final size:23
Alignment explanation
Indices: 14527--14574 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
14517 TATTTTATAT
14527 TTTTAAAAATAAATATTAAATTA
1 TTTTAAAAATAAATATTAAATTA
*
14550 TTTTAAAAATAAA-ATTGAATTA
1 TTTTAAAAATAAATATTAAATTA
14572 TTT
1 TTT
14575 ATTTATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TTTTAAAAATAAATATTAAATTA
Found at i:15286 original size:151 final size:151
Alignment explanation
Indices: 15012--15315 Score: 581
Period size: 151 Copynumber: 2.0 Consensus size: 151
15002 AATTGGTTCA
15012 TTTTATTATTCCAATGGACCCTATTGGTTAATTATTTTATTTCAATAGCATGGTGACAAATGTCA
1 TTTTATTATTCCAATGGACCCTATTGGTTAATTATTTTATTTCAATAGCATGGTGACAAATGTCA
15077 CTATCTAATTGGTTAATTAAAAATAATTAAGATATCTTATTTGATTGTTGACGTGGAATTTGAAA
66 CTATCTAATTGGTTAATTAAAAATAATTAAGATATCTTATTTGATTGTTGACGTGGAATTTGAAA
15142 AAAATATTAAAAAGCATTACG
131 AAAATATTAAAAAGCATTACG
* *
15163 TTTTATTATTCCAATGGACCCTATTGGTTAATTATTTTATTTCAATAGCGTGGTGACACATGTCA
1 TTTTATTATTCCAATGGACCCTATTGGTTAATTATTTTATTTCAATAGCATGGTGACAAATGTCA
*
15228 CTATCTTATTGGTTAATTAAAAATAATTAAGATATCTTATTTGATTGTTGACGTGGAATTTGAAA
66 CTATCTAATTGGTTAATTAAAAATAATTAAGATATCTTATTTGATTGTTGACGTGGAATTTGAAA
15293 AAAATATTAAAAAGCATTACG
131 AAAATATTAAAAAGCATTACG
15314 TT
1 TT
15316 GTACGACATC
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
151 150 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.40
Consensus pattern (151 bp):
TTTTATTATTCCAATGGACCCTATTGGTTAATTATTTTATTTCAATAGCATGGTGACAAATGTCA
CTATCTAATTGGTTAATTAAAAATAATTAAGATATCTTATTTGATTGTTGACGTGGAATTTGAAA
AAAATATTAAAAAGCATTACG
Found at i:18967 original size:20 final size:21
Alignment explanation
Indices: 18931--18973 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
18921 TTATAAACTC
*
18931 GTACCTTCAATATAAAATTAT
1 GTACCTTCAACATAAAATTAT
18952 GTACCTT-AACATAAAATTAT
1 GTACCTTCAACATAAAATTAT
18972 GT
1 GT
18974 GTATGTGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (21 bp):
GTACCTTCAACATAAAATTAT
Found at i:25388 original size:22 final size:22
Alignment explanation
Indices: 25346--25386 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
25336 AGGTACTGGT
25346 TCACTGGTTCAACCGGATTTAA
1 TCACTGGTTCAACCGGATTTAA
*
25368 TCAC-GGTTGAACCGGATTT
1 TCACTGGTTCAACCGGATTT
25387 TATATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (22 bp):
TCACTGGTTCAACCGGATTTAA
Found at i:25916 original size:24 final size:25
Alignment explanation
Indices: 25879--25925 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
25869 CTATTCTTTC
**
25879 GCTTCAATTTAAC-TCAAATTTTAG
1 GCTTCAATCGAACTTCAAATTTTAG
*
25903 GCTTCAATCGAACTTCTAATTTT
1 GCTTCAATCGAACTTCAAATTTT
25926 TTTTTGAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.43
Consensus pattern (25 bp):
GCTTCAATCGAACTTCAAATTTTAG
Found at i:27496 original size:15 final size:16
Alignment explanation
Indices: 27464--27496 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
27454 TTTGATTGTG
27464 TTATATCTTTAAATTTT
1 TTATATCTTT-AATTTT
27481 TTATATCTTT-ATTTT
1 TTATATCTTTAATTTT
27496 T
1 T
27497 AAAGAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATATCTTTAATTTT
Found at i:27767 original size:31 final size:31
Alignment explanation
Indices: 27729--27840 Score: 134
Period size: 31 Copynumber: 3.6 Consensus size: 31
27719 CTTTGGTTAG
*
27729 ATTTAAGGATTAAATTAATATTTTATCTAAA
1 ATTTAAAGATTAAATTAATATTTTATCTAAA
* * * * *
27760 ATTTAAGGATCAAATTGACATTTTATCAAAA
1 ATTTAAAGATTAAATTAATATTTTATCTAAA
* * *
27791 ATTCAAAGATTAACTTAATATTTTATATGAAA
1 ATTTAAAGATTAAATTAATATTTTATCT-AAA
27823 ATTTAAAGATTAAATTAA
1 ATTTAAAGATTAAATTAA
27841 GAATGAACTT
Statistics
Matches: 66, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
31 47 0.71
32 19 0.29
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (31 bp):
ATTTAAAGATTAAATTAATATTTTATCTAAA
Found at i:36106 original size:45 final size:45
Alignment explanation
Indices: 36042--36258 Score: 434
Period size: 45 Copynumber: 4.8 Consensus size: 45
36032 GCCCATATAC
36042 TTATTATGTTCATTATATTGCACGTCAATTACAATTAGTGTTAGT
1 TTATTATGTTCATTATATTGCACGTCAATTACAATTAGTGTTAGT
36087 TTATTATGTTCATTATATTGCACGTCAATTACAATTAGTGTTAGT
1 TTATTATGTTCATTATATTGCACGTCAATTACAATTAGTGTTAGT
36132 TTATTATGTTCATTATATTGCACGTCAATTACAATTAGTGTTAGT
1 TTATTATGTTCATTATATTGCACGTCAATTACAATTAGTGTTAGT
36177 TTATTATGTTCATTATATTGCACGTCAATTACAATTAGTGTTAGT
1 TTATTATGTTCATTATATTGCACGTCAATTACAATTAGTGTTAGT
36222 TTATTATGTTCATTATATTGCACGTCAATTACAATTA
1 TTATTATGTTCATTATATTGCACGTCAATTACAATTA
36259 TATTGCAAGA
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 172 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (45 bp):
TTATTATGTTCATTATATTGCACGTCAATTACAATTAGTGTTAGT
Found at i:40041 original size:13 final size:13
Alignment explanation
Indices: 39997--40041 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
39987 TTTAATATTT
39997 ATCGGGTCGGGT-
1 ATCGGGTCGGGTA
* *
40009 ATCGGGCCAGGTA
1 ATCGGGTCGGGTA
40022 ATCGGGTCGGGTA
1 ATCGGGTCGGGTA
40035 ATCGGGT
1 ATCGGGT
40042 AATCAGGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.16, C:0.18, G:0.44, T:0.22
Consensus pattern (13 bp):
ATCGGGTCGGGTA
Found at i:41170 original size:6 final size:6
Alignment explanation
Indices: 41159--41194 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
41149 ATTGTTTTAT
*
41159 ATATTA ATATTA ATATTA ATATTA TATTTTA ATATT
1 ATATTA ATATTA ATATTA ATATTA -ATATTA ATATT
41195 TTTTAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
ATATTA
Found at i:41174 original size:12 final size:13
Alignment explanation
Indices: 41155--41194 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
41145 AAATATTGTT
41155 TTATATATTAATA
1 TTATATATTAATA
41168 TTA-ATATTAATA
1 TTATATATTAATA
*
41180 TTATATTTTAATA
1 TTATATATTAATA
41193 TT
1 TT
41195 TTTTAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 12 0.48
13 13 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATATATTAATA
Found at i:41242 original size:20 final size:19
Alignment explanation
Indices: 41215--41252 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
41205 ATAATTATAA
41215 AATATTTAAAAATATTATC
1 AATATTTAAAAATATTATC
*
41234 AATACTTTAATAATATTAT
1 AATA-TTTAAAAATATTAT
41253 ATGTTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
AATATTTAAAAATATTATC
Found at i:46117 original size:45 final size:45
Alignment explanation
Indices: 46053--46179 Score: 254
Period size: 45 Copynumber: 2.8 Consensus size: 45
46043 GCCCATATAC
46053 TTATTATGTTCATTATATTGCACGTCAATTACAATTAGTGTTAGT
1 TTATTATGTTCATTATATTGCACGTCAATTACAATTAGTGTTAGT
46098 TTATTATGTTCATTATATTGCACGTCAATTACAATTAGTGTTAGT
1 TTATTATGTTCATTATATTGCACGTCAATTACAATTAGTGTTAGT
46143 TTATTATGTTCATTATATTGCACGTCAATTACAATTA
1 TTATTATGTTCATTATATTGCACGTCAATTACAATTA
46180 TATTGCAAGA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (45 bp):
TTATTATGTTCATTATATTGCACGTCAATTACAATTAGTGTTAGT
Done.