Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005532.1 Hibiscus syriacus cultivar Beakdansim tig00012796_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: 51393
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:659 original size:58 final size:58
Alignment explanation
Indices: 554--664 Score: 127
Period size: 58 Copynumber: 1.9 Consensus size: 58
544 AGTTCAAACA
* * * * * *
554 TTCAAAAGTTTGAGATCAATTTAGAATGAGAGTTATAGTTTGAGGATGGAATTAAATT
1 TTCAAAAGTTTGAAATCAATTTAGAATGAAAGATATAATATGAGGATGAAATTAAATT
*
612 TTCAAAAGTTT-AAATGCAAATTTAGAATGAAAGATA-AATATGGGGATGAAATT
1 TTCAAAAGTTTGAAAT-C-AATTTAGAATGAAAGATATAATATGAGGATGAAATT
665 GCAGCACTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
57 3 0.07
58 25 0.57
59 16 0.36
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.33
Consensus pattern (58 bp):
TTCAAAAGTTTGAAATCAATTTAGAATGAAAGATATAATATGAGGATGAAATTAAATT
Found at i:17300 original size:19 final size:20
Alignment explanation
Indices: 17263--17300 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
17253 ATCTAGATAT
*
17263 TATTCAAATAAAAATAAATC
1 TATTCAAATAAAAACAAATC
*
17283 TATT-AAATATAAACAAAT
1 TATTCAAATAAAAACAAAT
17301 ATCCAATTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (20 bp):
TATTCAAATAAAAACAAATC
Found at i:18303 original size:3 final size:3
Alignment explanation
Indices: 18295--18328 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
18285 AGAGTGTGTG
18295 AGA AGA AGA AGAA AGA AGGA AGA AGA AGA AGA AG
1 AGA AGA AGA AG-A AGA A-GA AGA AGA AGA AGA AG
18329 CTGCCAGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 23 0.79
4 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:21854 original size:6 final size:6
Alignment explanation
Indices: 21843--21868 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
21833 CTCAGCTCTC
21843 CAATCT CAATCT CAATCT CAATCT CA
1 CAATCT CAATCT CAATCT CAATCT CA
21869 TCACTCCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (6 bp):
CAATCT
Found at i:37992 original size:23 final size:23
Alignment explanation
Indices: 37964--38019 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
37954 ATAACTGCTC
37964 CTAACAGCTTCCTAACTACACAA
1 CTAACAGCTTCCTAACTACACAA
37987 CTAACAGCTTCCTAACTACACAA
1 CTAACAGCTTCCTAACTACACAA
*
38010 CTAACTGCTT
1 CTAACAGCTT
38020 ACATCAGCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.36, C:0.34, G:0.05, T:0.25
Consensus pattern (23 bp):
CTAACAGCTTCCTAACTACACAA
Found at i:38323 original size:19 final size:18
Alignment explanation
Indices: 38295--38347 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
38285 ATATTATTCT
38295 CTAAAAATTATAATTTAA
1 CTAAAAATTATAATTTAA
* *
38313 CTAAAATATTATTATAT-A
1 CTAAAA-ATTATAATTTAA
38331 -TAAAAAATTATAATTTA
1 CT-AAAAATTATAATTTA
38348 CATCCCACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 9 0.32
18 11 0.39
19 8 0.29
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
CTAAAAATTATAATTTAA
Found at i:38745 original size:2 final size:2
Alignment explanation
Indices: 38738--38782 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
38728 CTTTTGAGTT
38738 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
38780 TA T
1 TA T
38783 GAAGAGTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45359 original size:3 final size:3
Alignment explanation
Indices: 45351--45386 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
45341 TTCAAAGCTT
45351 TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
45387 GTACCCTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:45528 original size:20 final size:20
Alignment explanation
Indices: 45505--45549 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
45495 TATTTAAATT
45505 ATAATATTTATAATTAAAAA
1 ATAATATTTATAATTAAAAA
* * *
45525 ATAAAATTTTTATTTAAAAA
1 ATAATATTTATAATTAAAAA
*
45545 TTAAT
1 ATAAT
45550 TTTTTAAATT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAATATTTATAATTAAAAA
Found at i:49801 original size:32 final size:33
Alignment explanation
Indices: 49739--49812 Score: 116
Period size: 32 Copynumber: 2.3 Consensus size: 33
49729 AAACCCGAAC
*
49739 CCGACCCGAATATCACACTTAAAAAAACCTGA-
1 CCGACCCGAATATCAAACTTAAAAAAACCTGAT
49771 CCTGACCCGAATATCAAACTT-AAAAAACCTGAT
1 CC-GACCCGAATATCAAACTTAAAAAAACCTGAT
49804 CCGACCCGA
1 CCGACCCGA
49813 TTTTTTTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
32 20 0.51
33 19 0.49
ACGTcount: A:0.41, C:0.32, G:0.11, T:0.16
Consensus pattern (33 bp):
CCGACCCGAATATCAAACTTAAAAAAACCTGAT
Found at i:49876 original size:33 final size:33
Alignment explanation
Indices: 49814--49876 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
49804 CCGACCCGAT
* *
49814 TTTTTTTAAAAAATCCGACCCGATCCCAAAATA
1 TTTTTTTAAAAAATCCAACCCGATACCAAAATA
*
49847 TTTTTTT-AAAATTCCAACCCGAATACCAAA
1 TTTTTTTAAAAAATCCAACCCG-ATACCAAA
49877 GATTGATGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 12 0.46
33 14 0.54
ACGTcount: A:0.40, C:0.24, G:0.05, T:0.32
Consensus pattern (33 bp):
TTTTTTTAAAAAATCCAACCCGATACCAAAATA
Found at i:50341 original size:21 final size:21
Alignment explanation
Indices: 50316--50360 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
50306 ACCGAAATAT
*
50316 TAAAAATATTAATATTTTAAA
1 TAAAAATAATAATATTTTAAA
50337 TAAAAATAATAATATTTTAAA
1 TAAAAATAATAATATTTTAAA
50358 TAA
1 TAA
50361 TTTTTACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAA
Done.