Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003442.1 Hibiscus syriacus cultivar Beakdansim tig00007259_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: 43612
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1674 original size:16 final size:17
Alignment explanation
Indices: 1641--1679 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
1631 TCCCATTTAT
1641 CATTTAAATTTAAAACA
1 CATTTAAATTTAAAACA
1658 CATTTAAATTT-AAACA
1 CATTTAAATTTAAAACA
1674 CATTTA
1 CATTTA
1680 CACTTCTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (17 bp):
CATTTAAATTTAAAACA
Found at i:7755 original size:22 final size:21
Alignment explanation
Indices: 7713--7752 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
7703 GAGTTTATTT
* *
7713 TCATTTTTCTATTTTGAAACA
1 TCATTTTTATATTTTAAAACA
7734 TCATTTTTATATTTTAAAA
1 TCATTTTTATATTTTAAAA
7753 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTATATTTTAAAACA
Found at i:14305 original size:18 final size:18
Alignment explanation
Indices: 14258--14308 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
14248 AGAGATTATC
* *
14258 AGTGGTCTTTCAGGACAT
1 AGTGGTCATTCGGGACAT
*
14276 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
*
14294 CGTGGTCATTCGGGA
1 AGTGGTCATTCGGGA
14309 TAAATATTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.18, C:0.20, G:0.33, T:0.29
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:15271 original size:3 final size:3
Alignment explanation
Indices: 15263--15310 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
15253 GTAAAGTCCT
* * * *
15263 ACA ACA ACA ACA ACA ACA ATA ATA ATA ATA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
15311 TGACGAAAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.25, G:0.00, T:0.08
Consensus pattern (3 bp):
ACA
Found at i:15765 original size:29 final size:29
Alignment explanation
Indices: 15719--15779 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
15709 TCGACGACGA
* *
15719 AGGGAGAGTTTTCTAATTGATAAGATGGG
1 AGGGAAAGTTTTCCAATTGATAAGATGGG
15748 AGGGAAAGTTTTCCAATTGATAAGATGGG
1 AGGGAAAGTTTTCCAATTGATAAGATGGG
15777 AGG
1 AGG
15780 AAATGAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.33, C:0.05, G:0.34, T:0.28
Consensus pattern (29 bp):
AGGGAAAGTTTTCCAATTGATAAGATGGG
Found at i:16046 original size:134 final size:134
Alignment explanation
Indices: 15806--16082 Score: 536
Period size: 134 Copynumber: 2.1 Consensus size: 134
15796 TCACTGCATC
*
15806 CATCTATCTGCATGTAATGTCGTGCAAAACACACAATGAATTTCACCATGTCGTCCATGGTTAGG
1 CATCTATATGCATGTAATGTCGTGCAAAACACACAATGAATTTCACCATGTCGTCCATGGTTAGG
15871 TGCCTTGTTACTACTACTTTCACAAGGTCTGAGAGTTGCCAAACAAAAGATAAATCATTTATACA
66 TGCCTTGTTACTACTACTTTCACAAGGTCTGAGAGTTGCCAAACAAAAGATAAATCATTTATACA
15936 CACA
131 CACA
*
15940 CATCTATATGCATGTAATGTCGTGCAAAACACACAATGAGTTTCACCATGTCGTCCATGGTTAGG
1 CATCTATATGCATGTAATGTCGTGCAAAACACACAATGAATTTCACCATGTCGTCCATGGTTAGG
16005 TGCCTTGTTACTACTACTTTCACAAGGTCTGAGAGTTGCCAAACAAAAGATAAATCATTTATACA
66 TGCCTTGTTACTACTACTTTCACAAGGTCTGAGAGTTGCCAAACAAAAGATAAATCATTTATACA
16070 CACA
131 CACA
16074 CATCTATAT
1 CATCTATAT
16083 AAAGTTTGCT
Statistics
Matches: 141, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 141 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (134 bp):
CATCTATATGCATGTAATGTCGTGCAAAACACACAATGAATTTCACCATGTCGTCCATGGTTAGG
TGCCTTGTTACTACTACTTTCACAAGGTCTGAGAGTTGCCAAACAAAAGATAAATCATTTATACA
CACA
Found at i:16727 original size:34 final size:34
Alignment explanation
Indices: 16684--16752 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
16674 ATTAATGTGT
*
16684 TAATGCAGACTGAAACCTTGGACTATGAACTTTC
1 TAATGCAGACTGAAACCTTGGAATATGAACTTTC
16718 TAATGCAGACTGAAACCTTGGAATATGAACTTTC
1 TAATGCAGACTGAAACCTTGGAATATGAACTTTC
16752 T
1 T
16753 TTTTCAAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (34 bp):
TAATGCAGACTGAAACCTTGGAATATGAACTTTC
Found at i:23665 original size:19 final size:18
Alignment explanation
Indices: 23633--23668 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
23623 TTTTTAAAGA
23633 TTTTTTTTAAAATAATAC
1 TTTTTTTTAAAATAATAC
*
23651 TTTTGTTTTATAATAATA
1 TTTT-TTTTAAAATAATA
23669 AAAGTTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTTTTTTAAAATAATAC
Found at i:24847 original size:2 final size:2
Alignment explanation
Indices: 24840--24885 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
24830 GTTTTTATTA
24840 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
24882 AT AT
1 AT AT
24886 TTGCATTACG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40499 original size:28 final size:28
Alignment explanation
Indices: 40444--40499 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
40434 TGTTCGATCT
* *
40444 GACCTGACCCGTCTGTTTGATCCGACTC
1 GACCTGACCCGTCTGGTTCATCCGACTC
40472 GACCTGACCCGTCTGGTTCAGTCC-ACTC
1 GACCTGACCCGTCTGGTTCA-TCCGACTC
40500 ACCGAGTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.14, C:0.38, G:0.21, T:0.27
Consensus pattern (28 bp):
GACCTGACCCGTCTGGTTCATCCGACTC
Found at i:40536 original size:14 final size:15
Alignment explanation
Indices: 40503--40569 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
40493 TCCACTCACC
*
40503 GAGTCAACTCAGTCT
1 GAGTCAACTCAGTAT
*
40518 GAGTCAAC-CTGTAT
1 GAGTCAACTCAGTAT
* *
40532 GAGTCAACTTAGTCT
1 GAGTCAACTCAGTAT
* *
40547 GAGTAAACTCAGTCT
1 GAGTCAACTCAGTAT
40562 GAGTCAAC
1 GAGTCAAC
40570 CCGTCTAAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
14 12 0.28
15 31 0.72
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (15 bp):
GAGTCAACTCAGTAT
Found at i:40580 original size:14 final size:14
Alignment explanation
Indices: 40562--40657 Score: 129
Period size: 14 Copynumber: 6.9 Consensus size: 14
40552 AACTCAGTCT
*
40562 GAGTCAACCCGTCT
1 GAGTCAACCCGTCC
* *
40576 AAGTCAACTCGTCC
1 GAGTCAACCCGTCC
* *
40590 AAGTCAACTCGTCC
1 GAGTCAACCCGTCC
40604 GAGTCAACCCGTCC
1 GAGTCAACCCGTCC
*
40618 GAGTTAACCCGTCC
1 GAGTCAACCCGTCC
*
40632 GAGTCAACCCGTCT
1 GAGTCAACCCGTCC
40646 GAGTCAACCCGT
1 GAGTCAACCCGT
40658 TGACTTTGAT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 74 1.00
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (14 bp):
GAGTCAACCCGTCC
Found at i:40614 original size:42 final size:43
Alignment explanation
Indices: 40501--40657 Score: 183
Period size: 42 Copynumber: 3.7 Consensus size: 43
40491 AGTCCACTCA
* * *
40501 CCGAGTCAACTCAGTCTGAGTCAACCTGTATGAGTCAACTTAGT
1 CCGAGTCAACTCAGTCTGAGTCAACCCGTCTGAGTCAAC-TCGT
* * *
40545 CTGAGTAAACTCAGTCTGAGTCAACCCGTCTAAGTCAACTCGT
1 CCGAGTCAACTCAGTCTGAGTCAACCCGTCTGAGTCAACTCGT
* * * * *
40588 CCAAGTCAACTC-GTCCGAGTCAACCCGTCCGAGTTAACCCGT
1 CCGAGTCAACTCAGTCTGAGTCAACCCGTCTGAGTCAACTCGT
*
40630 CCGAGTCAAC-CCGTCTGAGTCAACCCGT
1 CCGAGTCAACTCAGTCTGAGTCAACCCGT
40658 TGACTTTGAT
Statistics
Matches: 96, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
41 1 0.01
42 49 0.51
43 12 0.12
44 34 0.35
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (43 bp):
CCGAGTCAACTCAGTCTGAGTCAACCCGTCTGAGTCAACTCGT
Found at i:40673 original size:14 final size:14
Alignment explanation
Indices: 40656--40694 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
40646 GAGTCAACCC
*
40656 GTTGACTTTGATTT
1 GTTGACTTTGATAT
*
40670 GTTGCCTTTGATAT
1 GTTGACTTTGATAT
40684 GTTGACTTTGA
1 GTTGACTTTGA
40695 CCCGTGAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.15, C:0.10, G:0.23, T:0.51
Consensus pattern (14 bp):
GTTGACTTTGATAT
Done.