Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000987.1 Hibiscus syriacus cultivar Beakdansim tig00001977_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: 59740
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:5499 original size:58 final size:58
Alignment explanation
Indices: 5437--5824 Score: 531
Period size: 58 Copynumber: 6.8 Consensus size: 58
5427 ATGGAACTAA
* *
5437 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATTGGGCATTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTC
* *
5495 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTATATGAATTTTCGTATTGTGCACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTC
* * * * *
5553 ATGTGCAAAAAGTTAATAAATTCATACTAAGTGTATGAATTTCCGCATTGGGCACTTA
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTC
*
5611 ATGTGCAAAAAGTTAAGAAATTCATA-T--GTGTATGAA-TTTCGTATTGGGCACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTC
* * * *
5665 GTGTG-GAAAAGTT-A-AAATTCATACTAACTGTAT-AATTTCCATATTGGGCACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTC
* * * *
5719 GTGTACAAAAAGTTAAGAAATTAATACTAAGTGTATGAATTTTCATATTGGACACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTC
* * *
5777 ATGTGCAAAAAGTTAAGAGATTCATACTAAGTGTATGAATTTCCGTAT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTAT
5825 GGGAAATGTG
Statistics
Matches: 290, Mismatches: 32, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
51 9 0.03
52 2 0.01
53 9 0.03
54 44 0.15
55 16 0.06
56 1 0.00
57 18 0.06
58 191 0.66
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (58 bp):
GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTC
Found at i:19074 original size:13 final size:13
Alignment explanation
Indices: 19056--19091 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
19046 CAGAACTGAA
19056 CTAAGGCTCAAAT
1 CTAAGGCTCAAAT
*
19069 CTAAGGCTCGAAT
1 CTAAGGCTCAAAT
*
19082 CAAAGGCTCA
1 CTAAGGCTCA
19092 TCTACTTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (13 bp):
CTAAGGCTCAAAT
Found at i:21219 original size:176 final size:175
Alignment explanation
Indices: 21009--21357 Score: 574
Period size: 176 Copynumber: 2.0 Consensus size: 175
20999 TGTATCATAT
*
21009 AATCAAATATAAAGCTAAAAAATTAAAATTAAATCAAGATAAATAAAT-AATAAACTTCTCATTC
1 AATCAAATATAAAACTAAAAAATTAAAATTAAATCAAGATAAATAAATAAATAAA-TTCTCATTC
* * * *
21073 AAAATCCACCACTGATTTTCATTAAGAAATCTCAAAGAAGGCTTGATTTATGAAGATCTAATTGA
65 AAAATCCACCACTGATTTTCATTAAGAAACCTCAAAGAAGGCTTAATTCATGAAAATCTAATTGA
*
21138 AAGCCTTTTCCTTATTCATTGGTTCTCTCATTCAATGGGATTTTAA
130 AAGCCTTTTCCTTATACATTGGTTCTCTCATTCAATGGGATTTTAA
** *
21184 AATCAAATATAAAACTCAAAATTTTAAAATTAAATCAAGATAAATAAATAAATAAATTTTCATTC
1 AATCAAATATAAAACT-AAAAAATTAAAATTAAATCAAGATAAATAAATAAATAAATTCTCATTC
* *
21249 AAAATCCACCACTGATTTTCATTGAGAAACCTCAAGGAAGGCTTAATTCATGAAAATCTAATTGA
65 AAAATCCACCACTGATTTTCATTAAGAAACCTCAAAGAAGGCTTAATTCATGAAAATCTAATTGA
21314 AAGCCTTTTCCTTATACATTGGTTCTCTCATTCAATGGGATTTT
130 AAGCCTTTTCCTTATACATTGGTTCTCTCATTCAATGGGATTTT
21358 CAAACAACAT
Statistics
Matches: 161, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
175 15 0.09
176 140 0.87
177 6 0.04
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (175 bp):
AATCAAATATAAAACTAAAAAATTAAAATTAAATCAAGATAAATAAATAAATAAATTCTCATTCA
AAATCCACCACTGATTTTCATTAAGAAACCTCAAAGAAGGCTTAATTCATGAAAATCTAATTGAA
AGCCTTTTCCTTATACATTGGTTCTCTCATTCAATGGGATTTTAA
Found at i:27086 original size:18 final size:18
Alignment explanation
Indices: 27063--27100 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
27053 CGTGAGGATT
27063 GGGCAGTGGTCCAGCATG
1 GGGCAGTGGTCCAGCATG
27081 GGGCAGTGGTCCAGCATG
1 GGGCAGTGGTCCAGCATG
27099 GG
1 GG
27101 CATCTGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.21, G:0.47, T:0.16
Consensus pattern (18 bp):
GGGCAGTGGTCCAGCATG
Found at i:30342 original size:19 final size:19
Alignment explanation
Indices: 30318--30355 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
30308 AATATTTTTA
30318 TATATTTAAAAATAAATTT
1 TATATTTAAAAATAAATTT
* *
30337 TATATTTTAAAATTAATTT
1 TATATTTAAAAATAAATTT
30356 AATTTAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATTTAAAAATAAATTT
Found at i:35776 original size:2 final size:2
Alignment explanation
Indices: 35769--35799 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35759 TTCCATTATT
35769 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35800 GGAGCATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36518 original size:5 final size:5
Alignment explanation
Indices: 36508--36541 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
36498 AAAGTTTCAT
36508 CCGAC CCGAC CCGAC CCGAC CCGAC CCGAC CCGA
1 CCGAC CCGAC CCGAC CCGAC CCGAC CCGAC CCGA
36542 ATATATGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.21, C:0.59, G:0.21, T:0.00
Consensus pattern (5 bp):
CCGAC
Found at i:36756 original size:33 final size:33
Alignment explanation
Indices: 36687--36759 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
36677 CCCTAAACAT
* * * *
36687 ACCCGAATATCATACTTAAAAAAATCCGACCTG
1 ACCCGAATATCAAACTTAAAAAAACCCAACCAG
*
36720 ACCCGAATATCAAACTTAAAAAAACCCAATCAG
1 ACCCGAATATCAAACTTAAAAAAACCCAACCAG
36753 ACCCGAA
1 ACCCGAA
36760 CCTGATTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.47, C:0.29, G:0.08, T:0.16
Consensus pattern (33 bp):
ACCCGAATATCAAACTTAAAAAAACCCAACCAG
Found at i:40343 original size:39 final size:39
Alignment explanation
Indices: 40300--40382 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
40290 AAAACTTTTC
* * *
40300 AATTCACAATAAAACACTCTAACACCCAAGATATTCTTA
1 AATTCACAATAAAACACTCTAACACCAAAGAGACTCTTA
* *
40339 AATTCACAATAAAACACTTTAACTCCAAAGAGACTCTTA
1 AATTCACAATAAAACACTCTAACACCAAAGAGACTCTTA
40378 AATTC
1 AATTC
40383 CCCCTTAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.46, C:0.24, G:0.04, T:0.27
Consensus pattern (39 bp):
AATTCACAATAAAACACTCTAACACCAAAGAGACTCTTA
Found at i:56576 original size:43 final size:43
Alignment explanation
Indices: 56515--56597 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
56505 TGTGAAGAAT
* *
56515 AAGGTTATCGTTGATCCAACTCCTTCTGTGAAGGATCGAGCGA
1 AAGGTTATCATTGATCCAACTCCTTATGTGAAGGATCGAGCGA
* *
56558 AAGGTTGTCATTGATCCAACTCCTTATGTGAATGATCGAG
1 AAGGTTATCATTGATCCAACTCCTTATGTGAAGGATCGAG
56598 TGATATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (43 bp):
AAGGTTATCATTGATCCAACTCCTTATGTGAAGGATCGAGCGA
Done.