Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002964.1 Hibiscus syriacus cultivar Beakdansim tig00006132_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: 57180
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:5755 original size:25 final size:25
Alignment explanation
Indices: 5722--5770 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
5712 TAGTTAATTA
* *
5722 TATTCAATTAATTTAAATTTATATG
1 TATTCAATTAATTCAAAATTATATG
*
5747 TATTTAATTAATTCAAAATTATAT
1 TATTCAATTAATTCAAAATTATAT
5771 ACATAGTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (25 bp):
TATTCAATTAATTCAAAATTATATG
Found at i:7791 original size:26 final size:27
Alignment explanation
Indices: 7736--7798 Score: 103
Period size: 26 Copynumber: 2.4 Consensus size: 27
7726 TATTGTATGA
7736 TATTTA-TATTTTATCTTACATTTAAAT
1 TATTTATTATTTTATCTTA-ATTTAAAT
7763 TATTTATTATTTTATCTT-ATTTAAAT
1 TATTTATTATTTTATCTTAATTTAAAT
7789 TATTTATTAT
1 TATTTATTAT
7799 AATGATCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 18 0.51
27 6 0.17
28 11 0.31
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (27 bp):
TATTTATTATTTTATCTTAATTTAAAT
Found at i:14680 original size:23 final size:23
Alignment explanation
Indices: 14646--14689 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
14636 ATCTCAAGTC
* *
14646 CATCTACTGTTTGTTGACTGGAT
1 CATCTACCGTTTATTGACTGGAT
14669 CATCTACCGTTTATTGACTGG
1 CATCTACCGTTTATTGACTGG
14690 TTCAGCTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.41
Consensus pattern (23 bp):
CATCTACCGTTTATTGACTGGAT
Found at i:18819 original size:25 final size:25
Alignment explanation
Indices: 18785--18836 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
18775 AGTGAGCATT
18785 ACTATAATTTACCCTAAAATAAAAC
1 ACTATAATTTACCCTAAAATAAAAC
18810 ACTATAATTTACCCTAAAATAAAAC
1 ACTATAATTTACCCTAAAATAAAAC
18835 AC
1 AC
18837 GGAAATGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (25 bp):
ACTATAATTTACCCTAAAATAAAAC
Found at i:28151 original size:42 final size:42
Alignment explanation
Indices: 28092--28185 Score: 152
Period size: 42 Copynumber: 2.2 Consensus size: 42
28082 GTTGATTTGA
*
28092 CCGGTGCCGGTGCTGCTGATATCATCCATGAAAGTACCGGTG
1 CCGGTGCCGGTGCTGCTGATATCATCCATGAAAGTACCAGTG
* *
28134 CCGGTGCCGGTGCTGCTGATATTATCCATGAAAGTAGCAGTG
1 CCGGTGCCGGTGCTGCTGATATCATCCATGAAAGTACCAGTG
*
28176 CCGGTTCCGG
1 CCGGTGCCGG
28186 ATGAAGCACA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.24
Consensus pattern (42 bp):
CCGGTGCCGGTGCTGCTGATATCATCCATGAAAGTACCAGTG
Found at i:29508 original size:14 final size:16
Alignment explanation
Indices: 29474--29517 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 16
29464 AAATTAAAAA
29474 TTTAAATACTAAATAG
1 TTTAAATACTAAATAG
*
29490 ATTAAA-ACT-AATAG
1 TTTAAATACTAAATAG
*
29504 TTTAAGTACTAAAT
1 TTTAAATACTAAAT
29518 GTGTAGTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 9 0.39
15 6 0.26
16 8 0.35
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (16 bp):
TTTAAATACTAAATAG
Found at i:30418 original size:15 final size:15
Alignment explanation
Indices: 30398--30430 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
30388 TTAGCTGGAT
*
30398 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
30413 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
30428 GGG
1 GGG
30431 TAATGTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.15, G:0.70, T:0.09
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:30698 original size:52 final size:51
Alignment explanation
Indices: 30640--30856 Score: 121
Period size: 52 Copynumber: 4.2 Consensus size: 51
30630 TATAATACTA
*
30640 TTTTATAATAAAAAATATTAAATTATTTA-TGATTTAGTATGTGTGTTAGT
1 TTTTATAATAAAAAATATTAAATTATTTACTAATTTAGTATGTGTGTTAGT
** * * *
30690 TTAATTATAATATAAATTTTATTATATATATCTTATTAAATTT-TTAT-T-T-TTA-T
1 TT--TTATAATA-AAA-AATATTAAAT-TAT-TTACT-AATTTAGTATGTGTGTTAGT
* * * * *
30743 TCTTTATAATAAATTTAATTTTATATTATATACAAATTTAAGTATGTGTGTTAG-
1 T-TTTATAATAAA--AAATATTAAATTATTTACTAATTT-AGTATGTGTGTTAGT
* * *
30797 -TTTACAATAAAGAATATTAAATTATTTA-TGATTTAGTATGTG-GTTAGT
1 TTTTATAATAAAAAATATTAAATTATTTACTAATTTAGTATGTGTGTTAGT
30845 TTAATTATAATA
1 TT--TTATAATA
30857 TAAATTTAGC
Statistics
Matches: 125, Mismatches: 21, Indels: 41
0.67 0.11 0.22
Matches are distributed among these distances:
47 5 0.04
48 8 0.06
49 10 0.08
50 17 0.14
51 15 0.12
52 34 0.27
53 6 0.05
54 14 0.11
55 4 0.03
56 4 0.03
57 4 0.03
58 4 0.03
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (51 bp):
TTTTATAATAAAAAATATTAAATTATTTACTAATTTAGTATGTGTGTTAGT
Found at i:32907 original size:6 final size:6
Alignment explanation
Indices: 32896--32920 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
32886 CTTCGAGTTA
32896 TAAATT TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT T
32921 TAACATCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:33983 original size:42 final size:42
Alignment explanation
Indices: 33919--34017 Score: 180
Period size: 42 Copynumber: 2.3 Consensus size: 42
33909 GTTGAGCAAC
*
33919 TTGATCTCGACTCAATCAAAACTTGATAAAAGCTACATTCGGG
1 TTGA-CTCGACTCGATCAAAACTTGATAAAAGCTACATTCGGG
33962 TTGACTCGACTCGATCAAAACTTGATAAAAGCTACATTCGGG
1 TTGACTCGACTCGATCAAAACTTGATAAAAGCTACATTCGGG
34004 TTGACTCGACTCGA
1 TTGACTCGACTCGA
34018 CTTGAGACCT
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 51 0.93
43 4 0.07
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.27
Consensus pattern (42 bp):
TTGACTCGACTCGATCAAAACTTGATAAAAGCTACATTCGGG
Found at i:36872 original size:38 final size:38
Alignment explanation
Indices: 36830--36947 Score: 95
Period size: 38 Copynumber: 3.2 Consensus size: 38
36820 CTTCCAAGAC
36830 AGAGATCAGATAAATATATGCAATGAATTGCAAATTGA
1 AGAGATCAGATAAATATATGCAATGAATTGCAAATTGA
* * * * ** *
36868 AGAGAT-TGATTAACAAACT-TACGA-GGCTT-CCAA--GA
1 AGAGATCAGA-TAA-ATA-TATGCAATGAATTGCAAATTGA
36903 CAGAGATCAGATAAATATATGCAATGAATTGCAAATTGA
1 -AGAGATCAGATAAATATATGCAATGAATTGCAAATTGA
36942 AGAGAT
1 AGAGAT
36948 TGAAGACAAT
Statistics
Matches: 56, Mismatches: 14, Indels: 20
0.62 0.16 0.22
Matches are distributed among these distances:
34 1 0.02
35 7 0.12
36 12 0.21
37 10 0.18
38 18 0.32
39 7 0.12
40 1 0.02
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.25
Consensus pattern (38 bp):
AGAGATCAGATAAATATATGCAATGAATTGCAAATTGA
Found at i:36891 original size:74 final size:74
Alignment explanation
Indices: 36803--36950 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
36793 TCGGAACAAG
36803 TTAACAAACTTACGAGGCTTCCAAGACAGAGATCAGATAAATATATGCAATGAATTGCAAATTGA
1 TTAACAAACTTACGAGGCTTCCAAGACAGAGATCAGATAAATATATGCAATGAATTGCAAATTGA
36868 AGAGATTGA
66 AGAGATTGA
36877 TTAACAAACTTACGAGGCTTCCAAGACAGAGATCAGATAAATATATGCAATGAATTGCAAATTGA
1 TTAACAAACTTACGAGGCTTCCAAGACAGAGATCAGATAAATATATGCAATGAATTGCAAATTGA
36942 AGAGATTGA
66 AGAGATTGA
36951 AGACAATTTA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (74 bp):
TTAACAAACTTACGAGGCTTCCAAGACAGAGATCAGATAAATATATGCAATGAATTGCAAATTGA
AGAGATTGA
Found at i:45535 original size:32 final size:31
Alignment explanation
Indices: 45499--45566 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
45489 TCAAAAAACA
*
45499 TAAGATATAATCACTTTCGT-TTTTTATTTAAT
1 TAAGATACAATCA-TTT-GTATTTTTATTTAAT
* * *
45531 TAAGATGCAGTCATTTTTATTTTTATTTAAT
1 TAAGATACAATCATTTGTATTTTTATTTAAT
45562 TAAGA
1 TAAGA
45567 CTTGGTCATC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 1 0.03
31 20 0.65
32 10 0.32
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.51
Consensus pattern (31 bp):
TAAGATACAATCATTTGTATTTTTATTTAAT
Found at i:45733 original size:15 final size:15
Alignment explanation
Indices: 45715--45744 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45705 AATGAAATAA
45715 AAATAAAATACATTT
1 AAATAAAATACATTT
*
45730 AAATAAAATATATTT
1 AAATAAAATACATTT
45745 TTTCTAACAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATAAAATACATTT
Found at i:47531 original size:20 final size:20
Alignment explanation
Indices: 47502--47553 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
47492 ACTTCGACTA
47502 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
47522 TCGTATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
47542 TCGCATTGCGAT
1 TCGCATTGCGAT
47554 AGTCCAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:47567 original size:21 final size:21
Alignment explanation
Indices: 47541--47615 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
47531 GATTTACATA
47541 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
47562 TTCGCATTGTGATTTATTCCAAA
1 TTCGCATTGCGA--TAGTCCAAG
* *
47585 TTTG--TTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
47604 TTCGCGTTGCGA
1 TTCGCATTGCGA
47616 ATCTGGAAAC
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
19 9 0.22
21 22 0.54
23 10 0.24
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:50332 original size:3 final size:3
Alignment explanation
Indices: 50324--50349 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
50314 CCTAACGGTG
50324 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
50350 AATTCTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:55384 original size:20 final size:22
Alignment explanation
Indices: 55350--55389 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
55340 TTATCTTTCA
55350 TTTACAGAATAAATT-TGAAAT
1 TTTACAGAATAAATTATGAAAT
*
55371 TTTACGGAAT-AATTATGAA
1 TTTACAGAATAAATTATGAA
55390 TTATCTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (22 bp):
TTTACAGAATAAATTATGAAAT
Found at i:55596 original size:78 final size:78
Alignment explanation
Indices: 55488--55643 Score: 208
Period size: 78 Copynumber: 2.0 Consensus size: 78
55478 TTAATATTTT
* *
55488 TTTAACATTTCCGGTAAAACGTTACCTAAAACATTA-TTTTTCTA-TCGGAAATGTTAATATTGG
1 TTTAACATTTCCGATAAAACGCTACCTAAAACATTATTTTTTCTACT-GGAAATG-TAATATTGG
*
55551 GCGCTACCTAAAATG
64 GCGCAACCTAAAATG
* * *
55566 TTTAACATTTTCGATAAAGCGCTAGCTAAAACATTATTTTTTTCTACTGGAAATGTAATATTGGG
1 TTTAACATTTCCGATAAAACGCTACCTAAAACATTA-TTTTTTCTACTGGAAATGTAATATTGGG
*
55631 TGCAACCTAAAAT
65 CGCAACCTAAAAT
55644 ATTGTTTTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
78 31 0.46
79 21 0.31
80 15 0.22
81 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (78 bp):
TTTAACATTTCCGATAAAACGCTACCTAAAACATTATTTTTTCTACTGGAAATGTAATATTGGGC
GCAACCTAAAATG
Done.