Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008385.1 Hibiscus syriacus cultivar Beakdansim tig00111148_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: 58498
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:13449 original size:4 final size:4
Alignment explanation
Indices: 13440--13477 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
13430 ACTAATTGAC
13440 AGTT AGTT AGTT AGTT AGTT AGTT AGTT AGTT AGTT AG
1 AGTT AGTT AGTT AGTT AGTT AGTT AGTT AGTT AGTT AG
13478 ATTGAAATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (4 bp):
AGTT
Found at i:14407 original size:59 final size:59
Alignment explanation
Indices: 14296--14409 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 59
14286 GATTGATTTA
* * *
14296 AAACCAATAACTCCAACCTATTACTATTTGTTTTATTAATTCAAATCATCCGTTTGACC
1 AAACCAATAACTCCAACCTATTACTATATGTTTTATTAATTAAAACCATCCGTTTGACC
* *
14355 AAACCAATAACTCCAACCTATTACT-TATGTTTTATTATTTAAAACCCTTCCGTTT
1 AAACCAATAACTCCAACCTATTACTATATGTTTTATTAATTAAAA-CCATCCGTTT
14410 CCTTTTAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
58 16 0.33
59 33 0.67
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (59 bp):
AAACCAATAACTCCAACCTATTACTATATGTTTTATTAATTAAAACCATCCGTTTGACC
Found at i:23638 original size:27 final size:27
Alignment explanation
Indices: 23600--23655 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
23590 TTTTGCCAAG
23600 AACTCTATCAGGCTGGCATGATTCGAC
1 AACTCTATCAGGCTGGCATGATTCGAC
23627 AACTCTATCAGGCTGGCATGATTCGAC
1 AACTCTATCAGGCTGGCATGATTCGAC
23654 AA
1 AA
23656 GATCTTAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (27 bp):
AACTCTATCAGGCTGGCATGATTCGAC
Found at i:29221 original size:13 final size:12
Alignment explanation
Indices: 29201--29255 Score: 65
Period size: 13 Copynumber: 4.3 Consensus size: 12
29191 ATGCTTGAAG
*
29201 AAAAAAAATGAA
1 AAAAAAAAAGAA
29213 AAAATAAAAAGAA
1 AAAA-AAAAAGAA
29226 GAAAAAAAAAGAA
1 -AAAAAAAAAGAA
*
29239 AGAAAAGAAAGAA
1 A-AAAAAAAAGAA
29252 AAAA
1 AAAA
29256 TGAAGAAGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
12 8 0.21
13 26 0.68
14 4 0.11
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.04
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:29232 original size:26 final size:26
Alignment explanation
Indices: 29197--29255 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
29187 TACTATGCTT
*
29197 GAAGAAAAAAAATGAAA-AAATAAAAA
1 GAAGAAAAAAAAAGAAAGAAA-AAAAA
*
29223 GAAGAAAAAAAAAGAAAGAAAAGAAA
1 GAAGAAAAAAAAAGAAAGAAAAAAAA
29249 GAA-AAAA
1 GAAGAAAA
29256 TGAAGAAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 4 0.13
26 23 0.77
27 3 0.10
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.03
Consensus pattern (26 bp):
GAAGAAAAAAAAAGAAAGAAAAAAAA
Found at i:29235 original size:19 final size:20
Alignment explanation
Indices: 29198--29262 Score: 71
Period size: 19 Copynumber: 3.2 Consensus size: 20
29188 ACTATGCTTG
*
29198 AAGAAAAAAAATGAAAAAATA
1 AAGAAAAGAAA-GAAAAAATA
*
29219 AA-AAGAAGAAA-AAAAAAGA
1 AAGAA-AAGAAAGAAAAAATA
*
29238 AAGAAAAGAAAGAAAAAATG
1 AAGAAAAGAAAGAAAAAATA
29258 AAGAA
1 AAGAA
29263 GGAGGGTTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
19 15 0.41
20 15 0.41
21 7 0.19
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (20 bp):
AAGAAAAGAAAGAAAAAATA
Found at i:30620 original size:271 final size:270
Alignment explanation
Indices: 30218--30708 Score: 797
Period size: 271 Copynumber: 1.8 Consensus size: 270
30208 AAAAAGAGGT
* *
30218 GGATCAGCATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTT
* *
30283 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
66 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCAAGACATTTCGAATCAGGGACACCTCG
** * * *
30348 CTTGAGGAATTGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAA
131 CTTGAGGAATCAACATTTCCAATGAAGAGTTCATAATGAGAAAAACTCATCC--AAAAGAGAGAA
*
30413 GAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGAC
194 GAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGAC
30478 ACCTCGCTTGAG
259 ACCTCGCTTGAG
30490 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAC-GAGGGAGAAGAAGTT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTT
* *
30554 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAG-CATTTCGAGTCAGGGACGCCTC
66 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCA-AGACATTTCGAATCAGGGACACCTC
* * *
30618 GCTTGAGGGATCAACATTTTCAGTGAAGAGTTCATAATGAGAAAAACTCATCCAAAAGAGAGAAG
130 GCTTGAGGAATCAACATTTCCAATGAAGAGTTCATAATGAGAAAAACTCATCCAAAAGAGAGAAG
*
30683 AAGTTCATAATGCGAAGAACTTGTTC
195 AAGTTCATAATGAGAAGAACTTGTTC
30709 AATCTAACAA
Statistics
Matches: 202, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
269 35 0.17
271 119 0.59
272 48 0.24
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (270 bp):
GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTT
CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCAAGACATTTCGAATCAGGGACACCTCG
CTTGAGGAATCAACATTTCCAATGAAGAGTTCATAATGAGAAAAACTCATCCAAAAGAGAGAAGA
AGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACAC
CTCGCTTGAG
Found at i:30626 original size:135 final size:135
Alignment explanation
Indices: 30218--30708 Score: 779
Period size: 136 Copynumber: 3.6 Consensus size: 135
30208 AAAAAGAGGT
* *
30218 GGATCAGCATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACA-AGGGAGAAGAAGTT
30283 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
65 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
30348 CTTGAG
130 CTTGAG
* ** * *
30354 GAATTGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCC-AACAAGGGAGAAGAAGTT
30419 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
65 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
30484 CTTGAG
130 CTTGAG
*
30490 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTC
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTC
* * * *
30555 ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCA-CAGCATTTCGAGTCAGGGACGCCTCG
66 ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGA-CATTTCGAATCAGTGACACCTCG
30619 CTTGAG
130 CTTGAG
* * * *
30625 GGATCAACATTTTCAGTGAAGAGTTCATAATGAGAAAAACTCATCCAA-AAGAGAGAAGAAGTTC
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTC
* *
30689 ATAATGCGAAGAACTTGTTC
66 ATAATGAGAAGAGCTTGTTC
30709 AATCTAACAA
Statistics
Matches: 329, Mismatches: 24, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
134 33 0.10
135 126 0.38
136 168 0.51
137 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (135 bp):
GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTC
ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCGC
TTGAG
Found at i:32089 original size:2 final size:2
Alignment explanation
Indices: 32082--32133 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
32072 TAATGTTTCC
32082 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32124 TA TA TA TA TA
1 TA TA TA TA TA
32134 CAACAATTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:37612 original size:24 final size:22
Alignment explanation
Indices: 37585--37629 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
37575 GTAATAAAGT
37585 AATAATATACATTTTTAATTTTTG
1 AATAATATA-ATTTTT-ATTTTTG
*
37609 AATAATTTAATTTTTATTTTT
1 AATAATATAATTTTTATTTTT
37630 CGTATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 6 0.30
24 8 0.40
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
AATAATATAATTTTTATTTTTG
Found at i:54521 original size:13 final size:13
Alignment explanation
Indices: 54503--54567 Score: 57
Period size: 13 Copynumber: 5.1 Consensus size: 13
54493 ATATGATTTC
54503 ATAAGAATATGAA
1 ATAAGAATATGAA
54516 ATAAGAAGTATGAA
1 ATAAGAA-TATGAA
* *
54530 A-AGGACATA--AG
1 ATAAGA-ATATGAA
54541 A-AAGAATATGAA
1 ATAAGAATATGAA
54553 ATAAGAAGTATGAA
1 ATAAGAA-TATGAA
54567 A
1 A
54568 AGGACATAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
10 3 0.07
11 5 0.12
12 2 0.05
13 17 0.40
14 15 0.36
ACGTcount: A:0.60, C:0.02, G:0.20, T:0.18
Consensus pattern (13 bp):
ATAAGAATATGAA
Found at i:54541 original size:20 final size:20
Alignment explanation
Indices: 54516--54579 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
54506 AGAATATGAA
54516 ATAAGAAGTATGAAAAGGAC
1 ATAAGAAGTATGAAAAGGAC
* * *
54536 ATAAGAA--A-GAATATGAA
1 ATAAGAAGTATGAAAAGGAC
54553 ATAAGAAGTATGAAAAGGAC
1 ATAAGAAGTATGAAAAGGAC
54573 ATAAGAA
1 ATAAGAA
54580 AGAATATGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 13 0.37
18 1 0.03
19 1 0.03
20 20 0.57
ACGTcount: A:0.59, C:0.03, G:0.22, T:0.16
Consensus pattern (20 bp):
ATAAGAAGTATGAAAAGGAC
Found at i:54549 original size:37 final size:37
Alignment explanation
Indices: 54505--54592 Score: 176
Period size: 37 Copynumber: 2.4 Consensus size: 37
54495 ATGATTTCAT
54505 AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
1 AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
54542 AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
1 AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
54579 AAGAATATGAAATA
1 AAGAATATGAAATA
54593 TACAGAATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.60, C:0.02, G:0.20, T:0.17
Consensus pattern (37 bp):
AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
Found at i:54957 original size:29 final size:30
Alignment explanation
Indices: 54869--55256 Score: 625
Period size: 29 Copynumber: 13.2 Consensus size: 30
54859 AAGGAACATA
54869 TGGATAGTTA-CGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
54898 TGGACAGTTACCGAGGA--TTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
54926 TGGATAGTTACCGAGGATC-TTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
* *
54955 TGGACAATTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
54985 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
55015 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
55045 TGGATAGTT-CCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
55074 TGGACAGTTA-CGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
55103 TGGACAGTTA-CGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
55132 TGGATAG-TACCGAGGATCTTTA-GACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
55160 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
55190 TGGATAGTTACCGAGGATCTTTTATGACCTC
1 TGGATAGTTACCGAGGATC-TTTATGACCTC
*
55221 TGGATGGTTA-CGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
55250 TGGATAG
1 TGGATAG
55257 GTCCTTCGGA
Statistics
Matches: 336, Mismatches: 14, Indels: 18
0.91 0.04 0.05
Matches are distributed among these distances:
28 41 0.12
29 162 0.48
30 113 0.34
31 20 0.06
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:55237 original size:205 final size:205
Alignment explanation
Indices: 54869--55256 Score: 676
Period size: 205 Copynumber: 1.9 Consensus size: 205
54859 AAGGAACATA
*
54869 TGGATAGTTACGAGGATCTTTATGACCTCTGGACAGTTACCGAGGATTTATGACCTCTGGATAGT
1 TGGACAGTTACGAGGATCTTTATGACCTCTGGACAGTTACCGAGGATTTATGACCTCTGGATAGT
54934 TACCGAGGATCTTATGACCTCTGGACAATTACCGAGGATCTTTATGACCTCTGGATAGTTACCGA
66 TACCGAGGATCTTATGACCTCTGGACAATTACCGAGGATCTTTATGACCTCTGGATAGTTACCGA
54999 GGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGATAGTTCCGAGGATCT
131 GGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGATAGTTCCGAGGATCT
55064 TTATGACCTC
196 TTATGACCTC
55074 TGGACAGTTACGAGGATCTTTATGACCTCTGGACAGTTA-CGAGGATCTTTATGACCTCTGGATA
1 TGGACAGTTACGAGGATCTTTATGACCTCTGGACAGTTACCGAGGA--TTTATGACCTCTGGATA
*
55138 G-TACCGAGGATCTT-TAGACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGATAGTTAC
64 GTTACCGAGGATCTTAT-GACCTCTGGACAATTACCGAGGATCTTTATGACCTCTGGATAGTTAC
**
55201 CGAGGATCTTTTATGACCTCTGGATGGTTA-CGAGGATCTTTATGACCTCTGGATAG
128 CGAGGATC-TTTATGACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGATAG
55257 GTCCTTCGGA
Statistics
Matches: 175, Mismatches: 4, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
204 7 0.04
205 131 0.75
206 37 0.21
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (205 bp):
TGGACAGTTACGAGGATCTTTATGACCTCTGGACAGTTACCGAGGATTTATGACCTCTGGATAGT
TACCGAGGATCTTATGACCTCTGGACAATTACCGAGGATCTTTATGACCTCTGGATAGTTACCGA
GGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGATAGTTCCGAGGATCT
TTATGACCTC
Done.