Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006780.1 Hibiscus syriacus cultivar Beakdansim tig00017181_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: 62718
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:12268 original size:22 final size:22
Alignment explanation
Indices: 12240--12288 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
12230 CACGTTTTCA
12240 AAAGCTATTATTTTCCTATTCG
1 AAAGCTATTATTTTCCTATTCG
*
12262 AAAGCTATTATTTTTCTATTCG
1 AAAGCTATTATTTTCCTATTCG
12284 AAAGC
1 AAAGC
12289 AGTAAAACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (22 bp):
AAAGCTATTATTTTCCTATTCG
Found at i:12800 original size:82 final size:82
Alignment explanation
Indices: 12697--12866 Score: 227
Period size: 82 Copynumber: 2.1 Consensus size: 82
12687 TTTTTATAAC
** * *
12697 AAACGCCACTATTGATGAACCCTATT-ATGACATTTGTCTAAAAATGCCATTAAACTACTCTTTA
1 AAACGCCACTATAAATGAACCCTATTGA-GACATTTGTCTAAAAACGCCACTAAACTACTCTTTA
12761 TCGCGGCGTTTGTTGGAA
65 TCGCGGCGTTTGTTGGAA
* * * *
12779 AAACGCCACTATAAA-GTAACCCTATTGAGGCGTTTGTCTAAAAACGCCGCTAAAGTACTCTTTA
1 AAACGCCACTATAAATG-AACCCTATTGAGACATTTGTCTAAAAACGCCACTAAACTACTCTTTA
*
12843 TCGCGGCGTTTGTTGGTA
65 TCGCGGCGTTTGTTGGAA
12861 AAACGC
1 AAACGC
12867 AGCTAAAGTT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
81 1 0.01
82 75 0.97
83 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (82 bp):
AAACGCCACTATAAATGAACCCTATTGAGACATTTGTCTAAAAACGCCACTAAACTACTCTTTAT
CGCGGCGTTTGTTGGAA
Found at i:12855 original size:40 final size:40
Alignment explanation
Indices: 12729--12855 Score: 125
Period size: 41 Copynumber: 3.1 Consensus size: 40
12719 TATTATGACA
* * *
12729 TTTGTCTAAAAATGCCATTAAACTACTCTTTATCGCGGCG
1 TTTGTCTAAAAACGCCACTAAAGTACTCTTTATCGCGGCG
* * *
12769 TTTGT-TGGAAAAACGCCACTATAAAGTAAC-C-CTATTGAGGCG
1 TTTGTCT--AAAAACGCCAC--TAAAGT-ACTCTTTATCGCGGCG
*
12811 TTTGTCTAAAAACGCCGCTAAAGTACTCTTTATCGCGGCG
1 TTTGTCTAAAAACGCCACTAAAGTACTCTTTATCGCGGCG
12851 TTTGT
1 TTTGT
12856 TGGTAAAACG
Statistics
Matches: 69, Mismatches: 10, Indels: 16
0.73 0.11 0.17
Matches are distributed among these distances:
38 2 0.03
39 8 0.12
40 18 0.26
41 19 0.28
42 13 0.19
43 7 0.10
44 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (40 bp):
TTTGTCTAAAAACGCCACTAAAGTACTCTTTATCGCGGCG
Found at i:12864 original size:41 final size:41
Alignment explanation
Indices: 12747--12875 Score: 131
Period size: 41 Copynumber: 3.1 Consensus size: 41
12737 AAAATGCCAT
* *
12747 TAAACTACTCTTTATCGCGGCGTTTGTTGGAAAAACGCCAC
1 TAAAGTACTCTTTATCGCGGCGTTTGTTGGAAAAACGCCGC
* * *
12788 TATAAAGTAAC-C-CTATTGAGGCGTTTGTCT--AAAAACGCCGC
1 --TAAAGT-ACTCTTTATCGCGGCGTTTGT-TGGAAAAACGCCGC
* *
12829 TAAAGTACTCTTTATCGCGGCGTTTGTTGGTAAAACGCAGC
1 TAAAGTACTCTTTATCGCGGCGTTTGTTGGAAAAACGCCGC
12870 TAAAGT
1 TAAAGT
12876 TTCATTTTGT
Statistics
Matches: 70, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
38 2 0.03
39 8 0.11
40 13 0.19
41 25 0.36
42 13 0.19
43 7 0.10
44 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (41 bp):
TAAAGTACTCTTTATCGCGGCGTTTGTTGGAAAAACGCCGC
Found at i:13311 original size:15 final size:15
Alignment explanation
Indices: 13277--13318 Score: 59
Period size: 14 Copynumber: 2.7 Consensus size: 15
13267 TGGGTAGGTG
13277 AAAAATATTTTATGTT
1 AAAAATA-TTTATGTT
13293 AAAAATATTT-TGTT
1 AAAAATATTTATGTT
13307 AAAAATTATTTA
1 AAAAA-TATTTA
13319 ACAATAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 9 0.38
15 8 0.33
16 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (15 bp):
AAAAATATTTATGTT
Found at i:13661 original size:14 final size:14
Alignment explanation
Indices: 13642--13677 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
13632 TTTAGATGTT
13642 ATATAAAAGCATAA
1 ATATAAAAGCATAA
13656 ATATAAAAGCATAA
1 ATATAAAAGCATAA
*
13670 AAATAAAA
1 ATATAAAA
13678 ATACTGATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (14 bp):
ATATAAAAGCATAA
Found at i:15931 original size:29 final size:29
Alignment explanation
Indices: 15893--15952 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
15883 CCCGCATCCA
15893 ACCCTCTAAATCCATCTCTAATTCAAACC
1 ACCCTCTAAATCCATCTCTAATTCAAACC
15922 ACCCTCTAAATCCATCTCTAATTCAAACC
1 ACCCTCTAAATCCATCTCTAATTCAAACC
15951 AC
1 AC
15953 TTGTCTCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.27
Consensus pattern (29 bp):
ACCCTCTAAATCCATCTCTAATTCAAACC
Found at i:17652 original size:20 final size:20
Alignment explanation
Indices: 17627--17684 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
17617 TTTTTTGCTC
*
17627 AAAGGATCGATCCCTTGGTA
1 AAAGGATTGATCCCTTGGTA
17647 AAAGGATTGATACCCTT-GTA
1 AAAGGATTGAT-CCCTTGGTA
* *
17667 AAAAGATTGATCCTTTGG
1 AAAGGATTGATCCCTTGG
17685 ATTCTAGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 4 0.12
20 24 0.73
21 5 0.15
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (20 bp):
AAAGGATTGATCCCTTGGTA
Found at i:17782 original size:21 final size:21
Alignment explanation
Indices: 17716--17790 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 21
17706 ATCACTTTAC
* *
17716 AAAAGGATCAATCACTCGAGG
1 AAAAGGATCGATCACTCGACG
* * ** *
17737 AAAATGATCGATCCCTTTACA
1 AAAAGGATCGATCACTCGACG
* *
17758 AAAAGGATCGATCTCTCGATG
1 AAAAGGATCGATCACTCGACG
*
17779 AAAAGGGTCGAT
1 AAAAGGATCGAT
17791 TCCTTCCTTT
Statistics
Matches: 40, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (21 bp):
AAAAGGATCGATCACTCGACG
Found at i:17790 original size:42 final size:41
Alignment explanation
Indices: 17700--17795 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 41
17690 AGAAAGTTTG
* *
17700 GGATTGATCACTTTACAAAAGGATCAATCACTCGAGGAAAA
1 GGATCGATCCCTTTACAAAAGGATCAATCACTCGAGGAAAA
* * * *
17741 TGATCGATCCCTTTACAAAAAGGATCGATCTCTCGATGAAAA
1 GGATCGATCCCTTTAC-AAAAGGATCAATCACTCGAGGAAAA
* *
17783 GGGTCGATTCCTT
1 GGATCGATCCCTT
17796 CCTTTAAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 13 0.29
42 32 0.71
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (41 bp):
GGATCGATCCCTTTACAAAAGGATCAATCACTCGAGGAAAA
Found at i:19161 original size:23 final size:23
Alignment explanation
Indices: 19126--19169 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
19116 GTAAAGGAGG
* * *
19126 AAGAACAAGAAGAAGATGAAGAA
1 AAGAAAAACAAGAAGAAGAAGAA
19149 AAGAAAAACAAGAAGAAGAAG
1 AAGAAAAACAAGAAGAAGAAG
19170 GATGTTGGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.68, C:0.05, G:0.25, T:0.02
Consensus pattern (23 bp):
AAGAAAAACAAGAAGAAGAAGAA
Found at i:22089 original size:15 final size:15
Alignment explanation
Indices: 22066--22105 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
22056 AGAGCATAAG
*
22066 GATGAAGATGAGCAT
1 GATGGAGATGAGCAT
22081 GATGGAGATGAGCAT
1 GATGGAGATGAGCAT
22096 -ATGGATGATG
1 GATGGA-GATG
22106 CTCATGATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.35, C:0.05, G:0.38, T:0.23
Consensus pattern (15 bp):
GATGGAGATGAGCAT
Found at i:52077 original size:12 final size:12
Alignment explanation
Indices: 52057--52092 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
52047 AAAGAGATAT
52057 CAGAAATCAGAG
1 CAGAAATCAGAG
* *
52069 CAGAGATCAGAA
1 CAGAAATCAGAG
52081 CAGAAATCAGAG
1 CAGAAATCAGAG
52093 AAAACATCCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.17, G:0.25, T:0.08
Consensus pattern (12 bp):
CAGAAATCAGAG
Found at i:53044 original size:27 final size:28
Alignment explanation
Indices: 53009--53068 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
52999 TATTCCACGG
53009 TTTAGAGGG-ACTTTAGGTCATTTTACAC
1 TTTAGAGGGCA-TTTAGGTCATTTTACAC
*
53037 TTTA-AGGGCATTTTGGTCATTTTACAC
1 TTTAGAGGGCATTTAGGTCATTTTACAC
53064 TTTAG
1 TTTAG
53069 GGTAATTCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 24 0.83
28 5 0.17
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.43
Consensus pattern (28 bp):
TTTAGAGGGCATTTAGGTCATTTTACAC
Found at i:58136 original size:19 final size:20
Alignment explanation
Indices: 58102--58150 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
58092 TATTAATTTT
58102 TATTTTTAAA-AAAATCATTA
1 TATTTTTAAATAAAATC-TTA
*
58122 -A-TTTTAAATATAATCTTA
1 TATTTTTAAATAAAATCTTA
58140 TATTTTTAAAT
1 TATTTTTAAAT
58151 TATATAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 10 0.40
19 7 0.28
20 8 0.32
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTTTTAAATAAAATCTTA
Done.