Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003348.1 Hibiscus syriacus cultivar Beakdansim tig00007048_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: 52239
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:8045 original size:22 final size:22
Alignment explanation
Indices: 8004--8045 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
7994 TTTTTTCATT
*
8004 ATGGTTTTGGTTAATGTTATCC
1 ATGGTTTTGATTAATGTTATCC
8026 ATGGTTTTGATCTAAT-TTAT
1 ATGGTTTTGAT-TAATGTTAT
8046 TTAAACATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.21, C:0.07, G:0.19, T:0.52
Consensus pattern (22 bp):
ATGGTTTTGATTAATGTTATCC
Found at i:16868 original size:37 final size:37
Alignment explanation
Indices: 16792--16868 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
16782 ATTTTTATAT
*
16792 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
16829 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
16866 TTT
1 TTT
16869 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:24303 original size:2 final size:2
Alignment explanation
Indices: 24296--24323 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24286 TCTGAAAAGA
24296 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
24324 TGATGAACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26346 original size:31 final size:34
Alignment explanation
Indices: 26295--26377 Score: 91
Period size: 34 Copynumber: 2.4 Consensus size: 34
26285 TTTTACATAG
26295 TTATTATATTTTATATATT-AAT-ATAATTATATAAA
1 TTATTAT-TTTT-T-TATTAAATAATAATTATATAAA
*
26330 -TATTATTTTTTTATTAAAATAATATTTATATAAA
1 TTATTATTTTTTTATT-AAATAATAATTATATAAA
*
26364 TTATTATTTATTTA
1 TTATTATTTTTTTA
26378 AATTTATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
31 4 0.10
32 1 0.02
33 7 0.17
34 18 0.43
35 12 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
TTATTATTTTTTTATTAAATAATAATTATATAAA
Found at i:26371 original size:16 final size:16
Alignment explanation
Indices: 26321--26386 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 16
26311 ATTAATATAA
26321 TTATATAAA-TATTATTT
1 TTATATAAATTATTA--T
* * *
26338 TTTTATTAAAATAATAT
1 TTATA-TAAATTATTAT
26355 TTATATAAATTATTAT
1 TTATATAAATTATTAT
*
26371 TTATTTAAATTTATTA
1 TTATATAAA-TTATTA
26387 ATTAATTATT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
16 17 0.43
17 15 0.38
18 4 0.10
19 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATATAAATTATTAT
Found at i:41799 original size:30 final size:30
Alignment explanation
Indices: 41765--41829 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
41755 GAACCAGAAT
41765 AACCGGCTGAAAACCAGG-AAAACCGGGGTG
1 AACCGGCTGAAAACC-GGCAAAACCGGGGTG
**
41795 AACCGGCTGAAAACCGGCAAAACCGGTTTG
1 AACCGGCTGAAAACCGGCAAAACCGGGGTG
41825 AACCG
1 AACCG
41830 CTGGTTCACT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 2 0.06
30 30 0.94
ACGTcount: A:0.35, C:0.26, G:0.29, T:0.09
Consensus pattern (30 bp):
AACCGGCTGAAAACCGGCAAAACCGGGGTG
Found at i:42066 original size:25 final size:24
Alignment explanation
Indices: 42038--42108 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
42028 AACTCAAAAA
* *
42038 AAAATTAGAAGTTCGATTGAAGCCT
1 AAAATTAG-AGCTCAATTGAAGCCT
*
42063 AAAATTTGAGCTCAATTGAAGCCT
1 AAAATTAGAGCTCAATTGAAGCCT
*
42087 AAAATTTGAGCTCAATTGAAGC
1 AAAATTAGAGCTCAATTGAAGC
42109 GAAAGAATAG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
24 36 0.84
25 7 0.16
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (24 bp):
AAAATTAGAGCTCAATTGAAGCCT
Found at i:42082 original size:24 final size:24
Alignment explanation
Indices: 42053--42108 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
42043 TAGAAGTTCG
42053 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
42077 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
42101 ATTGAAGC
1 ATTGAAGC
42109 GAAAGAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:46169 original size:32 final size:32
Alignment explanation
Indices: 46122--46222 Score: 118
Period size: 32 Copynumber: 3.2 Consensus size: 32
46112 GAATTAGCGG
* * * *
46122 GTTAGTTTGAGCAATAAAATAAATGTTAGTGA-
1 GTTAGTATGAACAATAAAATAAAAGTTAG-AAT
46154 GTTAGTATGAACAATAAAATAAAAGTTAGAAT
1 GTTAGTATGAACAATAAAATAAAAGTTAGAAT
46186 GTTAGTATGAACAA-ATAAATAAAAGTTAGCAA-
1 GTTAGTATGAACAATA-AAATAAAAGTTAG-AAT
46218 GTTAG
1 GTTAG
46223 CGGTTAAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
31 2 0.03
32 58 0.94
33 2 0.03
ACGTcount: A:0.48, C:0.04, G:0.19, T:0.30
Consensus pattern (32 bp):
GTTAGTATGAACAATAAAATAAAAGTTAGAAT
Found at i:51055 original size:13 final size:13
Alignment explanation
Indices: 51037--51062 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
51027 GAATTATTTT
51037 TTAAATATTTAAA
1 TTAAATATTTAAA
51050 TTAAATATTTAAA
1 TTAAATATTTAAA
51063 GTTGATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAAATATTTAAA
Done.