Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002086.1 Hibiscus syriacus cultivar Beakdansim tig00004258_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: 473624
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 3 of 3
Found at i:449340 original size:13 final size:13
Alignment explanation
Indices: 449302--449340 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
449292 TAACCAGTCT
* *
449302 TAGTTGACTCAGT
1 TAGTTAACTCAGC
449315 TAGTTAACTCAGC
1 TAGTTAACTCAGC
449328 TAGTTAACTCAGC
1 TAGTTAACTCAGC
449341 CAACCAGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (13 bp):
TAGTTAACTCAGC
Found at i:451076 original size:16 final size:16
Alignment explanation
Indices: 451055--451085 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
451045 GTTTGATATT
451055 TATTTCAATCATAATA
1 TATTTCAATCATAATA
451071 TATTTCAATCATAAT
1 TATTTCAATCATAAT
451086 CTAAATGAAC
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:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (16 bp):
TATTTCAATCATAATA
Found at i:452555 original size:15 final size:15
Alignment explanation
Indices: 452535--452587 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
452525 CATGATACAT
452535 AACTTTTGAAAATTA
1 AACTTTTGAAAATTA
****
452550 AACTTTTGGTCCTTA
1 AACTTTTGAAAATTA
452565 AACTTTT-AGAAATTA
1 AACTTTTGA-AAATTA
452580 AACTTTTG
1 AACTTTTG
452588 GTATCTAAAC
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.43
Consensus pattern (15 bp):
AACTTTTGAAAATTA
Found at i:454192 original size:15 final size:15
Alignment explanation
Indices: 454172--454206 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
454162 AAGGTTCCAC
454172 TAATATTTCTTCAGG
1 TAATATTTCTTCAGG
454187 TAATATTTCTTCAGG
1 TAATATTTCTTCAGG
454202 TAATA
1 TAATA
454207 GACAAGAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (15 bp):
TAATATTTCTTCAGG
Found at i:459322 original size:19 final size:19
Alignment explanation
Indices: 459298--459342 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
459288 AAAAATCAAC
*
459298 TTAAATCTAATTATCCATA
1 TTAAATCTAATGATCCATA
459317 TTAAATCTAATGATCCATA
1 TTAAATCTAATGATCCATA
459336 TTAAATC
1 TTAAATC
459343 CTACCAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (19 bp):
TTAAATCTAATGATCCATA
Found at i:459600 original size:30 final size:29
Alignment explanation
Indices: 459555--459637 Score: 82
Period size: 28 Copynumber: 2.9 Consensus size: 29
459545 ATACATAACA
* *
459555 TTTTAAAA-GTATACTTTGGTCC-CTAAACT
1 TTTTAAAATTTATACTTT-GACCACTAAA-T
*
459584 TTTTAAACTTTATACTTT-ACCACTAAAT
1 TTTTAAAATTTATACTTTGACCACTAAAT
* *
459612 TTTTAAAATTTATATTTTGATCACTA
1 TTTTAAAATTTATACTTTGACCACTA
459638 GCCAAAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
28 19 0.42
29 18 0.40
30 8 0.18
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.47
Consensus pattern (29 bp):
TTTTAAAATTTATACTTTGACCACTAAAT
Found at i:459636 original size:29 final size:30
Alignment explanation
Indices: 459555--459637 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 30
459545 ATACATAACA
* * *
459555 TTTTAAAA-GTATACTTTGGTCCCTAAACT
1 TTTTAAAATTTATACTTTGATCACTAAACT
* *
459584 TTTTAAACTTTATACTTT-ACCACTAAA-T
1 TTTTAAAATTTATACTTTGATCACTAAACT
*
459612 TTTTAAAATTTATATTTTGATCACTA
1 TTTTAAAATTTATACTTTGATCACTA
459638 GCCAAAATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
28 17 0.39
29 19 0.43
30 8 0.18
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.47
Consensus pattern (30 bp):
TTTTAAAATTTATACTTTGATCACTAAACT
Found at i:460999 original size:56 final size:54
Alignment explanation
Indices: 460925--461030 Score: 142
Period size: 53 Copynumber: 1.9 Consensus size: 54
460915 GCTCATAAGC
460925 TTATTTTTACCAAAATACTTACCATTTAAATTCCATAAGCTCATAAGCTTATTATTA
1 TTATTTTTACCAAAATACTTACCA-TT--ATTCCATAAGCTCATAAGCTTATTATTA
* * * *
460982 TTATTTTT-TCAATATACTTGCCATTATTCCGTAAGCTCATAAGCTTATT
1 TTATTTTTACCAAAATACTTACCATTATTCCATAAGCTCATAAGCTTATT
461031 TGCATGGTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
53 23 0.51
55 2 0.04
56 12 0.27
57 8 0.18
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (54 bp):
TTATTTTTACCAAAATACTTACCATTATTCCATAAGCTCATAAGCTTATTATTA
Done.