Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005128.1 Hibiscus syriacus cultivar Beakdansim tig00011544_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: 60675
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:15530 original size:15 final size:16
Alignment explanation
Indices: 15492--15532 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
15482 TCAGAGTCTC
* *
15492 TGAATCATTCAACATT
1 TGAATCATTCAAAACT
15508 TGAATCATTCAAAACT
1 TGAATCATTCAAAACT
15524 T-AATCATTC
1 TGAATCATTC
15533 TGAAGTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAAAACT
Found at i:15847 original size:23 final size:23
Alignment explanation
Indices: 15778--15906 Score: 123
Period size: 24 Copynumber: 5.5 Consensus size: 23
15768 CATTTAAATT
* *
15778 ATAAACAAACACAATTGAACGAAC
1 ATAAACGAACACAA-TAAACGAAC
* *
15802 ATAAACGAACAGATGTAAACGAAC
1 ATAAACGAACACA-ATAAACGAAC
*
15826 ATAAACGAACACAATAAACGAAT
1 ATAAACGAACACAATAAACGAAC
* * *
15849 GTAAACAAACACAAATAAATGAAC
1 ATAAACGAACAC-AATAAACGAAC
* * *
15873 GTAAACGAACACGATAAATGAAC
1 ATAAACGAACACAATAAACGAAC
*
15896 GTAAACGAACA
1 ATAAACGAACA
15907 TAAATGAAAA
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
23 39 0.43
24 51 0.57
ACGTcount: A:0.57, C:0.18, G:0.12, T:0.12
Consensus pattern (23 bp):
ATAAACGAACACAATAAACGAAC
Found at i:15878 original size:47 final size:47
Alignment explanation
Indices: 15778--15911 Score: 133
Period size: 47 Copynumber: 2.8 Consensus size: 47
15768 CATTTAAATT
* * * * * **
15778 ATAAACAAACACAATTGAACGAACATAAACGAACAGATGTAAACGAAC
1 ATAAACGAACACAA-TAAACGAACGTAAACAAACACAAATAAACGAAC
* *
15826 ATAAACGAACACAATAAACGAATGTAAACAAACACAAATAAATGAAC
1 ATAAACGAACACAATAAACGAACGTAAACAAACACAAATAAACGAAC
* * * * *
15873 GTAAACGAACACGATAAATGAACGTAAACGAACATAAAT
1 ATAAACGAACACAATAAACGAACGTAAACAAACACAAAT
15912 GAAAATAGAT
Statistics
Matches: 71, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
47 58 0.82
48 13 0.18
ACGTcount: A:0.57, C:0.17, G:0.12, T:0.13
Consensus pattern (47 bp):
ATAAACGAACACAATAAACGAACGTAAACAAACACAAATAAACGAAC
Found at i:16118 original size:14 final size:14
Alignment explanation
Indices: 16081--16124 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
16071 GATTGGGCTA
16081 AACATAAATGAACG
1 AACATAAATGAACG
*
16095 CACAT--A--AACG
1 AACATAAATGAACG
16105 AACATAAATGAACG
1 AACATAAATGAACG
16119 AACATA
1 AACATA
16125 TTACCAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
10 8 0.33
12 2 0.08
14 14 0.58
ACGTcount: A:0.57, C:0.18, G:0.11, T:0.14
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:22044 original size:30 final size:28
Alignment explanation
Indices: 22023--22102 Score: 103
Period size: 25 Copynumber: 2.9 Consensus size: 28
22013 ATTAACGTTG
*
22023 AAAAGTAAAATTAAGAGAATATTGATATT
1 AAAA-TAAAATTAAGAGAATATTGACATT
22052 -AAA-AAAATT-AGAGAATATTGACATT
1 AAAATAAAATTAAGAGAATATTGACATT
22077 AAAAAATAAAATTAAGAGAATATTGA
1 --AAAATAAAATTAAGAGAATATTGA
22103 TGTTAGAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
25 15 0.33
26 6 0.13
28 6 0.13
29 6 0.13
30 12 0.27
ACGTcount: A:0.59, C:0.01, G:0.12, T:0.28
Consensus pattern (28 bp):
AAAATAAAATTAAGAGAATATTGACATT
Found at i:22260 original size:2 final size:2
Alignment explanation
Indices: 22253--22280 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22243 TTTCATTTTA
22253 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
22281 TTAATTGTTT
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:30095 original size:22 final size:22
Alignment explanation
Indices: 30067--30123 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
30057 TTTTTAAATT
*
30067 TAATGATCATTTTATAATATTG
1 TAATGATCATTTTATAACATTG
* * *
30089 TAGTGATTATTTTATAACATTT
1 TAATGATCATTTTATAACATTG
*
30111 TAATAATCATTTT
1 TAATGATCATTTT
30124 TGTTTTAGAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (22 bp):
TAATGATCATTTTATAACATTG
Found at i:34862 original size:12 final size:12
Alignment explanation
Indices: 34845--34870 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
34835 TTAAAAAAGT
34845 TTAATATTTTTA
1 TTAATATTTTTA
34857 TTAATATTTTTA
1 TTAATATTTTTA
34869 TT
1 TT
34871 TTTTCTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTAATATTTTTA
Found at i:34891 original size:42 final size:41
Alignment explanation
Indices: 34822--34904 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 41
34812 ATAGATCATG
*
34822 TTTTTAATTTTTTTTAAAAAAGTTTAATATTTTTATTAATA
1 TTTTTAATTTTTTTTAAAAAAGTTTAATATTTCTATTAATA
* *
34863 TTTTTATTTTTTCTTTAATATAA-TTTAATATTTCTATTAATA
1 TTTTTAATTTTT-TTTAA-AAAAGTTTAATATTTCTATTAATA
34905 ATTTGAAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 11 0.30
42 23 0.62
43 3 0.08
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (41 bp):
TTTTTAATTTTTTTTAAAAAAGTTTAATATTTCTATTAATA
Found at i:34907 original size:20 final size:20
Alignment explanation
Indices: 34844--34908 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
34834 TTTAAAAAAG
* *
34844 TTTAATATTTTTATTAATATT
1 TTTAATATTTCTATTAATA-A
* *
34865 TTTATTTTTTCT-TTAATATAA
1 TTTAATATTTCTATT-A-ATAA
34886 TTTAATATTTCTATTAATAA
1 TTTAATATTTCTATTAATAA
34906 TTT
1 TTT
34909 GAAAGTCCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
20 9 0.26
21 21 0.60
22 5 0.14
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTAATATTTCTATTAATAA
Found at i:39299 original size:100 final size:100
Alignment explanation
Indices: 39126--39325 Score: 400
Period size: 100 Copynumber: 2.0 Consensus size: 100
39116 ATGCAAAGCA
39126 TAGGTTGGCATGAGATGGCATGTAAATGTACTGATCGAAGAAACTGGTGGTCTGTGACATGCATG
1 TAGGTTGGCATGAGATGGCATGTAAATGTACTGATCGAAGAAACTGGTGGTCTGTGACATGCATG
39191 CATGCCCCCAATGGGGTTCTCTCTTCATTTTTCTG
66 CATGCCCCCAATGGGGTTCTCTCTTCATTTTTCTG
39226 TAGGTTGGCATGAGATGGCATGTAAATGTACTGATCGAAGAAACTGGTGGTCTGTGACATGCATG
1 TAGGTTGGCATGAGATGGCATGTAAATGTACTGATCGAAGAAACTGGTGGTCTGTGACATGCATG
39291 CATGCCCCCAATGGGGTTCTCTCTTCATTTTTCTG
66 CATGCCCCCAATGGGGTTCTCTCTTCATTTTTCTG
39326 GGTTTTAAAC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (100 bp):
TAGGTTGGCATGAGATGGCATGTAAATGTACTGATCGAAGAAACTGGTGGTCTGTGACATGCATG
CATGCCCCCAATGGGGTTCTCTCTTCATTTTTCTG
Found at i:43032 original size:6 final size:6
Alignment explanation
Indices: 43021--43357 Score: 633
Period size: 6 Copynumber: 56.5 Consensus size: 6
43011 TCATGTCCCC
43021 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
* * *
43069 ATGTGT ATGTAT GTATGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
43117 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
43165 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
43213 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT A--TGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
43259 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
43307 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
43355 ATG
1 ATG
43358 CAATGGCTAA
Statistics
Matches: 323, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
4 4 0.01
6 319 0.99
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (6 bp):
ATGTGT
Found at i:46746 original size:33 final size:33
Alignment explanation
Indices: 46695--46910 Score: 109
Period size: 33 Copynumber: 6.5 Consensus size: 33
46685 AAAGCACGAG
* ** * *
46695 AACAGCAGCAACCTCAACTTCAGCATCAACAGC
1 AACAGCAGCAGCAGCAACTGCAGCAACAACAGC
*
46728 AACAGCAGCAGCAGCAACTGCAG-ATGCAACAGC
1 AACAGCAGCAGCAGCAACTGCAGCA-ACAACAGC
* ** *
46761 TTTTATTGCAG-AG--GCATGCT-CAGCAACAACAGC
1 ---AACAGCAGCAGCAGCA-ACTGCAGCAACAACAGC
* * *
46794 AGCAGCAGCAGCAGCAACAGCAGCAACAACAACAAC
1 AACAGCAGCAGCAGCAACTGCAG---CAACAACAGC
* * *
46830 AACAGCAGCAGCAGCAGCAGCAGCAACAACAAC
1 AACAGCAGCAGCAGCAACTGCAGCAACAACAGC
* * * * * * *
46863 AACAACAACAGCAGCAGCAGCAACAGCAACAAC
1 AACAGCAGCAGCAGCAACTGCAGCAACAACAGC
*
46896 AACAGCCGCAGCAGC
1 AACAGCAGCAGCAGC
46911 CGCCCCAGCA
Statistics
Matches: 144, Mismatches: 26, Indels: 26
0.73 0.13 0.13
Matches are distributed among these distances:
30 4 0.03
31 2 0.01
32 2 0.01
33 96 0.67
34 3 0.02
35 2 0.01
36 35 0.24
ACGTcount: A:0.42, C:0.32, G:0.19, T:0.06
Consensus pattern (33 bp):
AACAGCAGCAGCAGCAACTGCAGCAACAACAGC
Found at i:46796 original size:3 final size:3
Alignment explanation
Indices: 46790--46910 Score: 89
Period size: 3 Copynumber: 40.3 Consensus size: 3
46780 TCAGCAACAA
* * * * * *
46790 CAG CAG CAG CAG CAG CAG CAA CAG CAG CAA CAA CAA CAA CAA CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * * * * * *
46838 CAG CAG CAG CAG CAG CAA CAA CAA CAA CAA CAA CAG CAG CAG CAG CAA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * * *
46886 CAG CAA CAA CAA CAG CCG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG C
46911 CGCCCCAGCA
Statistics
Matches: 106, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 106 1.00
ACGTcount: A:0.45, C:0.35, G:0.20, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:46836 original size:36 final size:36
Alignment explanation
Indices: 46784--46899 Score: 187
Period size: 36 Copynumber: 3.2 Consensus size: 36
46774 GCATGCTCAG
* * *
46784 CAACAACAGCAGCAGCAGCAGCAGCAACAGCAGCAA
1 CAACAACAACAACAGCAGCAGCAGCAGCAGCAGCAA
46820 CAACAACAACAACAGCAGCAGCAGCAGCAGCAGCAA
1 CAACAACAACAACAGCAGCAGCAGCAGCAGCAGCAA
* *
46856 CAACAACAACAACAACAGCAGCAGCAGCAACAGCAA
1 CAACAACAACAACAGCAGCAGCAGCAGCAGCAGCAA
46892 CAACAACA
1 CAACAACA
46900 GCCGCAGCAG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 75 1.00
ACGTcount: A:0.49, C:0.34, G:0.17, T:0.00
Consensus pattern (36 bp):
CAACAACAACAACAGCAGCAGCAGCAGCAGCAGCAA
Found at i:54988 original size:24 final size:24
Alignment explanation
Indices: 54961--55011 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
54951 GAAAAAGATA
* * *
54961 AAAAAATGTGCAATAAAGGCAGAG
1 AAAAAACGTACAATAAAAGCAGAG
*
54985 -AAAAACGTACCATAAAAGCAGAG
1 AAAAAACGTACAATAAAAGCAGAG
55008 AAAA
1 AAAA
55012 CATACCAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.59, C:0.12, G:0.20, T:0.10
Consensus pattern (24 bp):
AAAAAACGTACAATAAAAGCAGAG
Found at i:55024 original size:21 final size:23
Alignment explanation
Indices: 54973--55027 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
54963 AAAATGTGCA
* *
54973 ATAAAGGCAGAGAAAAACGTACC
1 ATAAAAGCAGAGAAAAACATACC
54996 ATAAAAGCAGAG-AAAACATACC
1 ATAAAAGCAGAGAAAAACATACC
55018 A-AAAAGCAGA
1 ATAAAAGCAGA
55028 ATTTTTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 9 0.30
22 10 0.33
23 11 0.37
ACGTcount: A:0.58, C:0.16, G:0.18, T:0.07
Consensus pattern (23 bp):
ATAAAAGCAGAGAAAAACATACC
Found at i:57924 original size:27 final size:27
Alignment explanation
Indices: 57886--57939 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
57876 AATGACGAGT
* *
57886 TTTAATAAAAAATTATTTTTTTTTAGA
1 TTTAATAAAAAATTATATTTTATTAGA
57913 TTTAATAAAAAATTATATTTTATTAGA
1 TTTAATAAAAAATTATATTTTATTAGA
57940 ACTTGTTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (27 bp):
TTTAATAAAAAATTATATTTTATTAGA
Found at i:58803 original size:47 final size:46
Alignment explanation
Indices: 58730--58819 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 46
58720 CCATCAGTCA
*
58730 TTTCAATCAACCCTCTGTCACTACCGAGT-CACTGACTGGTCATTAT
1 TTTCAATCAACCCTCTGTCACTACCGA-TCCACTGACCGGTCATTAT
58776 TTTCAATCACACCCTCTGTCA-TCACCGATCCACTGACCGGTCAT
1 TTTCAATCA-ACCCTCTGTCACT-ACCGATCCACTGACCGGTCAT
58820 CGTTTTTGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
46 11 0.28
47 29 0.73
ACGTcount: A:0.23, C:0.34, G:0.12, T:0.30
Consensus pattern (46 bp):
TTTCAATCAACCCTCTGTCACTACCGATCCACTGACCGGTCATTAT
Done.