Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004802.1 Hibiscus syriacus cultivar Beakdansim tig00010817_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: 58492
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:21103 original size:13 final size:15
Alignment explanation
Indices: 21074--21105 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
21064 AGCTATTGTA
21074 TTTTTTCTATTTGAT
1 TTTTTTCTATTTGAT
21089 TTTTTTCT-TTT-AT
1 TTTTTTCTATTTGAT
21102 TTTT
1 TTTT
21106 CAATCTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 3 0.18
15 8 0.47
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.81
Consensus pattern (15 bp):
TTTTTTCTATTTGAT
Found at i:24989 original size:75 final size:75
Alignment explanation
Indices: 24856--25002 Score: 204
Period size: 75 Copynumber: 2.0 Consensus size: 75
24846 AGAGGGTTCA
* * * * *
24856 GAACCATGAGGAGTTTCAGTTCCAGTTCCAGTTCCAGAGTCCTTAAGAGAGGAAACCTGAGCACT
1 GAACCATGAGGAGATACAGTTCCAATTCCAGTTCCAGAATCCTTAAGAGAGGAAACCTGAGAACT
24921 ATCATTTTCG
66 ATCATTTTCG
* * * * *
24931 GAACCCTGAGGAGATACATTTCCAATTCCAGTTCCAGAATCCTTAGGAGATGATACCTGAGAACT
1 GAACCATGAGGAGATACAGTTCCAATTCCAGTTCCAGAATCCTTAAGAGAGGAAACCTGAGAACT
24996 ATCATTT
66 ATCATTT
25003 GTAGTGTTCT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 62 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.27
Consensus pattern (75 bp):
GAACCATGAGGAGATACAGTTCCAATTCCAGTTCCAGAATCCTTAAGAGAGGAAACCTGAGAACT
ATCATTTTCG
Found at i:32281 original size:36 final size:36
Alignment explanation
Indices: 32234--32306 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
32224 AGTTAAATAC
*
32234 TTAATGATGTTATGATTAAACATTTTTGTAAAAAAT
1 TTAATGATGTTATGATTAAACATTTTTATAAAAAAT
*
32270 TTAATGATGTTATGATTAGACATTTTTATAAAAAAT
1 TTAATGATGTTATGATTAAACATTTTTATAAAAAAT
32306 T
1 T
32307 ATGAACATAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.45
Consensus pattern (36 bp):
TTAATGATGTTATGATTAAACATTTTTATAAAAAAT
Found at i:32594 original size:24 final size:24
Alignment explanation
Indices: 32577--32649 Score: 128
Period size: 24 Copynumber: 3.0 Consensus size: 24
32567 CGTTCGTGAA
32577 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
* *
32601 CGTTCGATTATGTTCATTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
32625 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
32649 C
1 C
32650 ATTCATTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.11, C:0.14, G:0.22, T:0.53
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATGTT
Found at i:32603 original size:10 final size:10
Alignment explanation
Indices: 32578--32649 Score: 54
Period size: 10 Copynumber: 6.4 Consensus size: 10
32568 GTTCGTGAAC
*
32578 GTTCGGTTAT
1 GTTCGTTTAT
32588 GTTCGTTTAT
1 GTTCGTTTAT
32598 GTTCGTTCGATTAT
1 GTTCG-T---TTAT
*
32612 GTTCATTTAT
1 GTTCGTTTAT
32622 GTTCGTTCGGTTAT
1 GTTCG-T---TTAT
32636 GTTCGTTTAT
1 GTTCGTTTAT
32646 GTTC
1 GTTC
32650 ATTCATTTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
10 30 0.59
11 2 0.04
13 2 0.04
14 17 0.33
ACGTcount: A:0.11, C:0.12, G:0.22, T:0.54
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:32605 original size:14 final size:14
Alignment explanation
Indices: 32588--32642 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 14
32578 GTTCGGTTAT
32588 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
32602 GTTCGATTA---T-
1 GTTCGTTTATGTTC
*
32612 GTTCATTTATGTTC
1 GTTCGTTTATGTTC
*
32626 GTTCGGTTATGTTC
1 GTTCGTTTATGTTC
32640 GTT
1 GTT
32643 TATGTTCATT
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
10 7 0.22
11 1 0.03
13 1 0.03
14 23 0.72
ACGTcount: A:0.11, C:0.13, G:0.22, T:0.55
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:32659 original size:24 final size:23
Alignment explanation
Indices: 32584--32662 Score: 104
Period size: 24 Copynumber: 3.3 Consensus size: 23
32574 GAACGTTCGG
32584 TTATGTTCGTTTATGTTCGTTCGA
1 TTATGTTCGTTTATGTTCGTTC-A
* *
32608 TTATGTTCATTTATGTTCGTTCGG
1 TTATGTTCGTTTATGTTCGTTC-A
*
32632 TTATGTTCGTTTATGTTCATTCA
1 TTATGTTCGTTTATGTTCGTTCA
32655 TTTATGTT
1 -TTATGTT
32663 TAACCCAATC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.14, C:0.11, G:0.18, T:0.57
Consensus pattern (23 bp):
TTATGTTCGTTTATGTTCGTTCA
Found at i:33764 original size:16 final size:16
Alignment explanation
Indices: 33739--33811 Score: 114
Period size: 16 Copynumber: 4.7 Consensus size: 16
33729 CCAACATTTA
*
33739 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
33755 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
33771 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
33787 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
33803 T-TT-ATTTAT
1 TGTTCATTTAT
33812 TAAATGAACG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
14 6 0.11
15 2 0.04
16 46 0.85
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:33780 original size:32 final size:32
Alignment explanation
Indices: 33739--33803 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
33729 CCAACATTTA
33739 TGTTCGTTTATGTTCGTGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCGTGTTCATTTATGTTCG
33771 TGTTCGTTTATGTTCGTGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCGTGTTCATTTATGTTCG
33803 T
1 T
33804 TTATTTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.57
Consensus pattern (32 bp):
TGTTCGTTTATGTTCGTGTTCATTTATGTTCG
Found at i:33896 original size:16 final size:16
Alignment explanation
Indices: 33871--33911 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
33861 AAAAAAAATT
*
33871 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
*
33887 TGTTCATTTAAGTTCG
1 TGTTCATTTATGTTCG
33903 T-TT-ATTTAT
1 TGTTCATTTAT
33912 TAAATGAACG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 5 0.23
15 2 0.09
16 15 0.68
ACGTcount: A:0.15, C:0.10, G:0.17, T:0.59
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:35689 original size:16 final size:17
Alignment explanation
Indices: 35637--35693 Score: 66
Period size: 16 Copynumber: 3.4 Consensus size: 17
35627 CTAGAATGTT
35637 TCTG-AGGGAATTGAAA
1 TCTGAAGGGAATTGAAA
35653 TCTGTGAAGGGAATTGAAA
1 TC--TGAAGGGAATTGAAA
35672 TCTGAA-GGAATCTG-AA
1 TCTGAAGGGAAT-TGAAA
35688 TCTGAA
1 TCTGAA
35694 TCTAAAACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
16 15 0.41
17 6 0.16
18 2 0.05
19 14 0.38
ACGTcount: A:0.37, C:0.09, G:0.28, T:0.26
Consensus pattern (17 bp):
TCTGAAGGGAATTGAAA
Found at i:41345 original size:28 final size:28
Alignment explanation
Indices: 41312--41366 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
41302 AAAATTATAT
41312 TAAAAA-TAAAATATTTTTATTAAACAAA
1 TAAAAAGTAAAATATTTTTA-TAAACAAA
*
41340 TAAAAAGTACAATATTTTTATAAACAA
1 TAAAAAGTAAAATATTTTTATAAACAA
41367 TATCCATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (28 bp):
TAAAAAGTAAAATATTTTTATAAACAAA
Found at i:45072 original size:11 final size:11
Alignment explanation
Indices: 45056--45083 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
45046 TTAACTGGGC
45056 GGGCGGATGCG
1 GGGCGGATGCG
45067 GGGCGGATGCG
1 GGGCGGATGCG
45078 GGGCGG
1 GGGCGG
45084 GTAATGTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.18, G:0.68, T:0.07
Consensus pattern (11 bp):
GGGCGGATGCG
Found at i:47137 original size:24 final size:24
Alignment explanation
Indices: 47104--47159 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
47094 TGTTGATTTT
* *
47104 TTTTTATTTCAATTTGTGTAATTCCA
1 TTTTT-TTCCAATTTGTGTAA-TACA
* *
47130 TTTTTTTCCATTTTTTGTAATACA
1 TTTTTTTCCAATTTGTGTAATACA
47154 TTTTTT
1 TTTTTT
47160 GTTTAAACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 9 0.35
25 12 0.46
26 5 0.19
ACGTcount: A:0.20, C:0.11, G:0.05, T:0.64
Consensus pattern (24 bp):
TTTTTTTCCAATTTGTGTAATACA
Found at i:49809 original size:33 final size:33
Alignment explanation
Indices: 49751--49813 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
49741 GAGCACGAAA
49751 ATCCCTTCTTTATTCTATCAACTCTTCATATTTC
1 ATCCCTTCTTTATTCTATCAACTCTT-ATATTTC
*
49785 ATCCCTTTTTCTATTCT-T-AACTCTTATAT
1 ATCCCTTCTT-TATTCTATCAACTCTTATAT
49814 ATCTATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 4 0.15
33 7 0.26
34 10 0.37
35 6 0.22
ACGTcount: A:0.21, C:0.27, G:0.00, T:0.52
Consensus pattern (33 bp):
ATCCCTTCTTTATTCTATCAACTCTTATATTTC
Found at i:52955 original size:38 final size:38
Alignment explanation
Indices: 52901--52985 Score: 134
Period size: 38 Copynumber: 2.2 Consensus size: 38
52891 TCGTATAAAT
* * *
52901 TGTGTCCCGAATGACCTATCATCCCGAAGGATGTCATC
1 TGTGTCCCGAAAGACCTATCATCCCGAAGGATATAATC
*
52939 TGTGTCCCGAAAGACCTGTCATCCCGAAGGATATAATC
1 TGTGTCCCGAAAGACCTATCATCCCGAAGGATATAATC
52977 TGTGTCCCG
1 TGTGTCCCG
52986 TAGGACGTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (38 bp):
TGTGTCCCGAAAGACCTATCATCCCGAAGGATATAATC
Found at i:57160 original size:2 final size:2
Alignment explanation
Indices: 57153--57190 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
57143 TTCAATCAAT
57153 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
57191 ATGATATTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.