Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003041.1 Hibiscus syriacus cultivar Beakdansim tig00006325_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: 42429
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:937 original size:18 final size:16
Alignment explanation
Indices: 905--935 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
895 AATATTGAAA
905 CTTGAACTCAAAAAAG
1 CTTGAACTCAAAAAAG
921 CTTGAACTCAAAAAA
1 CTTGAACTCAAAAAA
936 AAATTAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
CTTGAACTCAAAAAAG
Found at i:12896 original size:28 final size:27
Alignment explanation
Indices: 12835--12899 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 27
12825 CGAACCCGAC
12835 CCGACCCGAATATCACACTTAAAAAAA
1 CCGACCCGAATATCACACTTAAAAAAA
*
12862 CCTGACCCGAATATTACACTTAAAAAAA
1 CC-GACCCGAATATCACACTTAAAAAAA
*
12890 TTCGACCCGA
1 -CCGACCCGA
12900 CTCGACCCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.06
28 31 0.91
29 1 0.03
ACGTcount: A:0.43, C:0.29, G:0.09, T:0.18
Consensus pattern (27 bp):
CCGACCCGAATATCACACTTAAAAAAA
Found at i:12934 original size:37 final size:38
Alignment explanation
Indices: 12865--12936 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
12855 AAAAAAACCT
* *
12865 GACCCGAATATTACACTTAAAAAAATTCGACCCGACTC
1 GACCCGAATATCACACTTAAAAAAACTCGACCCGACTC
12903 GACCCGAATATCACACTT-AAAAAACTCGACCCGA
1 GACCCGAATATCACACTTAAAAAAACTCGACCCGA
12937 ACAAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
37 15 0.47
38 17 0.53
ACGTcount: A:0.40, C:0.31, G:0.11, T:0.18
Consensus pattern (38 bp):
GACCCGAATATCACACTTAAAAAAACTCGACCCGACTC
Found at i:14590 original size:30 final size:30
Alignment explanation
Indices: 14554--14618 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
14544 ACCAGGTGCT
14554 GGATAACCAGTTGGAGGGTACTGAGCAGGA
1 GGATAACCAGTTGGAGGGTACTGAGCAGGA
14584 GGATAACCAGTTGGAGGGTACTGAGCAGGA
1 GGATAACCAGTTGGAGGGTACTGAGCAGGA
14614 GGATA
1 GGATA
14619 TCCGGATGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.31, C:0.12, G:0.40, T:0.17
Consensus pattern (30 bp):
GGATAACCAGTTGGAGGGTACTGAGCAGGA
Found at i:14633 original size:30 final size:30
Alignment explanation
Indices: 14554--14633 Score: 115
Period size: 30 Copynumber: 2.7 Consensus size: 30
14544 ACCAGGTGCT
*
14554 GGATAACCAGTTGGAGGGTACTGAGCAGGA
1 GGATAACCAGATGGAGGGTACTGAGCAGGA
*
14584 GGATAACCAGTTGGAGGGTACTGAGCAGGA
1 GGATAACCAGATGGAGGGTACTGAGCAGGA
* * *
14614 GGATATCCGGATGGCGGGTA
1 GGATAACCAGATGGAGGGTA
14634 ACCTTGAGGC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.28, C:0.14, G:0.41, T:0.17
Consensus pattern (30 bp):
GGATAACCAGATGGAGGGTACTGAGCAGGA
Found at i:17678 original size:158 final size:164
Alignment explanation
Indices: 17470--17910 Score: 514
Period size: 158 Copynumber: 2.7 Consensus size: 164
17460 CTCCTTCATC
* *
17470 TTAAGTCCATTTTTTTACCAAATTTGAA-CCACATGCTCCTAAACCATAGTAGAATACATGTTTA
1 TTAAGTCCA-TGTTTTACCAAATTT-AAGTCACATGCTCCTAAACCATAGTAGAATACATGTTTA
*
17534 CTTTCAATTCCTCTTTTTGATAACAAATTTTATTTTTTTAATTTAGTCCTTCAATTTTTCATAAT
64 CTTTCAATTCCTCTTTTTGATAACAAATTTTATTTTTTCAATTTAGTCCTTCAATTTTTCATAAT
17599 CTTC-TTT-TTTTAT-TCAATT-C-G-TCATT-TAT-T
129 CTTCATTTGTTTT-TGTCAATTACAGTTCATTCT-TCT
* ** *
17629 TTAAGTCCATGTTTTACCAAATTTAAGTCACATGATCCTAATA-TGTAGTAGAATACATGTTTAA
1 TTAAGTCCATGTTTTACCAAATTTAAGTCACATGCTCCTAA-ACCATAGTAGAATACATGTTTAC
*
17693 TTTCAATTCCTCTTTTTGATAACAAGCTTTTA--TTTTCAATTTAGTCCTTCAATTTTTCATAAT
65 TTTCAATTCCTCTTTTTGATAACAA-ATTTTATTTTTTCAATTTAGTCCTTCAATTTTTCATAAT
*** *
17756 CTTCAATTTGTTTTTGTTTTTTACATGTTTATTCTTCT
129 CTTC-ATTTGTTTTTGTCAATTACA-GTTCATTCTTCT
* *
17794 TTTAGTCC-TCCGTTTTTACCAAATTTGAGTCACATGCTCCTAAACCATAGTAGAATACAT-TTA
1 TTAAGTCCAT--G-TTTTACCAAATTTAAGTCACATGCTCCTAAACCATAGTAGAATACATGTT-
*
17857 TACTTACAATTCCTCTTTTTGATAACAAATTTTTTTATTTTTTCAATTTAGTCC
62 TACTTTCAATTCCTCTTTTTGATAACAAA---TTTTATTTTTTCAATTTAGTCC
17911 CTTACCTTTG
Statistics
Matches: 239, Mismatches: 20, Indels: 34
0.82 0.07 0.12
Matches are distributed among these distances:
157 36 0.15
158 69 0.29
159 19 0.08
160 7 0.03
161 1 0.00
163 1 0.00
164 6 0.03
165 9 0.04
166 4 0.02
167 67 0.28
169 5 0.02
171 15 0.06
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.48
Consensus pattern (164 bp):
TTAAGTCCATGTTTTACCAAATTTAAGTCACATGCTCCTAAACCATAGTAGAATACATGTTTACT
TTCAATTCCTCTTTTTGATAACAAATTTTATTTTTTCAATTTAGTCCTTCAATTTTTCATAATCT
TCATTTGTTTTTGTCAATTACAGTTCATTCTTCT
Found at i:21345 original size:24 final size:24
Alignment explanation
Indices: 21309--21354 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
21299 ATTTAAGATA
21309 GAAAAAATATGTCAACTGAGAGCT
1 GAAAAAATATGTCAACTGAGAGCT
*
21333 GAAAAAATGTGTCAACTGAGAG
1 GAAAAAATATGTCAACTGAGAG
21355 ATTTTAACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.20
Consensus pattern (24 bp):
GAAAAAATATGTCAACTGAGAGCT
Found at i:36041 original size:3 final size:3
Alignment explanation
Indices: 36035--36101 Score: 72
Period size: 3 Copynumber: 23.7 Consensus size: 3
36025 ATAATAATAA
36035 TAT TAT TAT TAT TA- TAT T-T TA- TAT ATAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
* *
36077 TAT TAT TAT TAA TAA TA- TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
36102 CATACCCCAA
Statistics
Matches: 57, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
2 10 0.18
3 44 0.77
4 3 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:36061 original size:11 final size:12
Alignment explanation
Indices: 36034--36101 Score: 60
Period size: 11 Copynumber: 6.1 Consensus size: 12
36024 AATAATAATA
36034 ATAT-TATTATT
1 ATATATATTATT
36045 AT-TATATT-TT
1 ATATATATTATT
36055 ATATATATTA-T
1 ATATATATTATT
36066 AT-TATTATTATT
1 ATATA-TATTATT
*
36078 AT-TATTATTAAT
1 ATATA-TATTATT
36090 A-ATATATTATT
1 ATATATATTATT
36101 A
1 A
36102 CATACCCCAA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
10 7 0.14
11 27 0.55
12 15 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATATATATTATT
Found at i:37481 original size:30 final size:31
Alignment explanation
Indices: 37446--37517 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
37436 ATTTAGTCAC
* *
37446 TAGTTTTAATATTTTCATTTA-TTTAATTATA
1 TAGTTTTAAT-TTTTCATATATTTTAAATATA
*
37477 -AGTTTT-ATTTTTTATATATTTTAAATATA
1 TAGTTTTAATTTTTCATATATTTTAAATATA
37506 TAGTTTTAATTT
1 TAGTTTTAATTT
37518 CATTGTTTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 8 0.23
29 11 0.31
30 12 0.34
31 4 0.11
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (31 bp):
TAGTTTTAATTTTTCATATATTTTAAATATA
Found at i:37532 original size:25 final size:25
Alignment explanation
Indices: 37504--37551 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
37494 ATTTTAAATA
37504 TATAGTTTTAATTTCAT-TGTTTAGT
1 TATA-TTTTAATTTCATATGTTTAGT
*
37529 TATATTTTAATTTTATATGTTTA
1 TATATTTTAATTTCATATGTTTA
37552 TTTTAATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.62
Consensus pattern (25 bp):
TATATTTTAATTTCATATGTTTAGT
Found at i:38475 original size:28 final size:27
Alignment explanation
Indices: 38443--38496 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
38433 TAATTCTTTC
*
38443 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATA-TTATTA
**
38471 TTTTCCTAATATTTATATATATTATT
1 TTTTCAAAATATTTATATATATTATT
38497 TTATTAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATATTATTA
Found at i:38504 original size:24 final size:22
Alignment explanation
Indices: 38465--38519 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 22
38455 TTATATATAC
*
38465 TTATTATTTTCCTAATATTTATA
1 TTATTATTTTACTAATATTT-TA
* *
38488 TATATTATTTTATTAATGTTTTA
1 T-TATTATTTTACTAATATTTTA
38511 TT-TTATTTT
1 TTATTATTTT
38520 TAATGTATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 7 0.25
22 1 0.04
23 4 0.14
24 16 0.57
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATTATTTTACTAATATTTTA
Done.