Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005917.1 Hibiscus syriacus cultivar Beakdansim tig00013895_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: 64311
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4401 original size:2 final size:2
Alignment explanation
Indices: 4394--4436 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
4384 CTCTTCACAT
4394 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4436 T
1 T
4437 AATGCTTTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:8876 original size:39 final size:39
Alignment explanation
Indices: 8817--8906 Score: 162
Period size: 39 Copynumber: 2.3 Consensus size: 39
8807 TATAATGAGG
8817 TGAATGATGGTGGTAATGAAGAAGCCTTTGACTTGCATCA
1 TGAA-GATGGTGGTAATGAAGAAGCCTTTGACTTGCATCA
*
8857 TGAGGATGGTGGTAATGAAGAAGCCTTTGACTTGCATCA
1 TGAAGATGGTGGTAATGAAGAAGCCTTTGACTTGCATCA
8896 TGAAGATGGTG
1 TGAAGATGGTG
8907 AGAGTGAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 45 0.94
40 3 0.06
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (39 bp):
TGAAGATGGTGGTAATGAAGAAGCCTTTGACTTGCATCA
Found at i:19710 original size:24 final size:24
Alignment explanation
Indices: 19683--19798 Score: 110
Period size: 24 Copynumber: 4.8 Consensus size: 24
19673 TTCGATTTGA
* *
19683 ATTCTAATCTGATAATTGACATGG
1 ATTCTGATATGATAATTGACATGG
19707 ATTCTGATATGAT-ATCTGACATGG
1 ATTCTGATATGATAAT-TGACATGG
* * *
19731 ATTATGATATGATACTTGACTTGG
1 ATTCTGATATGATAATTGACATGG
* * *
19755 ATTCTGATCTGATACTTGATC-TAG
1 ATTCTGATATGATAATTGA-CATGG
* *
19779 ATTTTGATATGATACTTGAC
1 ATTCTGATATGATAATTGAC
19799 CTGATTTATG
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
23 3 0.04
24 74 0.94
25 2 0.03
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (24 bp):
ATTCTGATATGATAATTGACATGG
Found at i:19756 original size:48 final size:48
Alignment explanation
Indices: 19692--19798 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
19682 AATTCTAATC
* *
19692 TGATAATTGACATGGATTCTGATATGATA-TCTGA-CATGGATTATGATA
1 TGATACTTGACATGGATTCTGATATGATACT-TGATC-TAGATTATGATA
* * *
19740 TGATACTTGACTTGGATTCTGATCTGATACTTGATCTAGATTTTGATA
1 TGATACTTGACATGGATTCTGATATGATACTTGATCTAGATTATGATA
19788 TGATACTTGAC
1 TGATACTTGAC
19799 CTGATTTATG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
48 50 0.96
49 2 0.04
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (48 bp):
TGATACTTGACATGGATTCTGATATGATACTTGATCTAGATTATGATA
Found at i:32534 original size:10 final size:10
Alignment explanation
Indices: 32519--32543 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
32509 TGTATGCTGC
32519 AAAAAAAAGA
1 AAAAAAAAGA
32529 AAAAAAAAGA
1 AAAAAAAAGA
32539 AAAAA
1 AAAAA
32544 GCAAAGGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:36661 original size:20 final size:21
Alignment explanation
Indices: 36636--36689 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
36626 TGTTATACAA
36636 GGGGGGAATCGGTA-CCCCCT
1 GGGGGGAATCGGTACCCCCCT
*
36656 GGGGGGAATCGATACCCCCCT
1 GGGGGGAATCGGTACCCCCCT
36677 GGGGGGAATCGGT
1 GGGGGGAATCGGT
36690 TCCCTCCGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.17, C:0.26, G:0.43, T:0.15
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCCT
Found at i:42319 original size:22 final size:23
Alignment explanation
Indices: 42293--42335 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
42283 AAACTGTTTA
42293 GGGGGAATCGGTT-CCTCCTATG
1 GGGGGAATCGGTTCCCTCCTATG
42315 GGGGGAATCGGTTCCCTCCTA
1 GGGGGAATCGGTTCCCTCCTA
42336 GCATTCTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.14, C:0.26, G:0.35, T:0.26
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCTCCTATG
Found at i:42378 original size:76 final size:76
Alignment explanation
Indices: 42218--42415 Score: 265
Period size: 75 Copynumber: 2.6 Consensus size: 76
42208 TTGTACAAGG
* * * **
42218 GGGGGAATCGGTACCCCCT-TGGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAGC
1 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAACCTCGGAGC
**
42282 AAAACTGTTTA
66 AAAACCATTTA
* * *
42293 GGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCTAGCATTCTGGAAACCTCGGGGC
1 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAACCTCGGAG-
42357 CAAAACCATTTA
65 CAAAACCATTTA
* *
42369 GGGGGAATCGGATCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCA
42416 ATCTGTAATT
Statistics
Matches: 107, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
75 53 0.50
76 31 0.29
77 23 0.21
ACGTcount: A:0.20, C:0.25, G:0.33, T:0.23
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAACCTCGGAGC
AAAACCATTTA
Found at i:43038 original size:17 final size:17
Alignment explanation
Indices: 43016--43059 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
43006 TTCATAAATC
*
43016 CAAAATCCAACAATCCA
1 CAAAATCAAACAATCCA
43033 CAAAATCAAACAATCCA
1 CAAAATCAAACAATCCA
43050 -AAATATCAAA
1 CAAA-ATCAAA
43060 AGTTTTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 3 0.12
17 22 0.88
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCAAACAATCCA
Found at i:45065 original size:20 final size:20
Alignment explanation
Indices: 44989--45073 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 20
44979 AACAGAACCC
*
44989 CAGGGGGGTATCGATTCCC-
1 CAGGGGGGAATCGATTCCCT
* *
45008 CTGTGGGAGGAATCGGTTCCCCTT
1 CAG-GGG-GGAATCGATT-CCC-T
* *
45032 CAAAGGGGGAATCGGTTCCCT
1 C-AGGGGGGAATCGATTCCCT
*
45053 CAGGGGGGGATCGATTCCCT
1 CAGGGGGGAATCGATTCCCT
45073 C
1 C
45074 TGCACCAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
19 2 0.04
20 20 0.38
21 10 0.19
22 6 0.12
23 10 0.19
24 4 0.08
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.22
Consensus pattern (20 bp):
CAGGGGGGAATCGATTCCCT
Found at i:48924 original size:22 final size:21
Alignment explanation
Indices: 48882--48921 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
48872 GAGTTTGTTT
*
48882 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
48903 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
48922 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:51034 original size:76 final size:76
Alignment explanation
Indices: 50846--51035 Score: 280
Period size: 75 Copynumber: 2.5 Consensus size: 76
50836 GTTGTACAAG
* * *
50846 GGGGGAATCGGTACCCCCT-TGGGGGGG-ATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAGC
1 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGC
**
50909 AAAACTGTTTA
66 AAAACCATTTA
* *
50920 GGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGC
1 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG-
50984 CAAAACCATTTA
65 CAAAACCATTTA
50996 -GGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTC
1 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTC
51036 TAAGCAATCT
Statistics
Matches: 105, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
74 23 0.22
75 53 0.50
76 29 0.28
ACGTcount: A:0.19, C:0.25, G:0.33, T:0.24
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGC
AAAACCATTTA
Found at i:55106 original size:12 final size:12
Alignment explanation
Indices: 55089--55113 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55079 ATAATTTAGA
55089 TAAAATATTATT
1 TAAAATATTATT
55101 TAAAATATTATT
1 TAAAATATTATT
55113 T
1 T
55114 TTTTATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:55131 original size:39 final size:43
Alignment explanation
Indices: 55043--55132 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 43
55033 ATATAAGGTT
**
55043 ATATAAATATATTATTAAAAATATTAATATTTTTTAATAATTT
1 ATATAAATATATTATTAAAAATATTAATATTTTTTAATAATAA
* * *
55086 AGATAAA-ATATTATTTAAAATATT-AT-TTTTTTATTAA-AA
1 ATATAAATATATTATTAAAAATATTAATATTTTTTAATAATAA
55125 ATATAAAT
1 ATATAAAT
55133 TTCGTTACCT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
39 6 0.15
40 10 0.25
41 2 0.05
42 16 0.40
43 6 0.15
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (43 bp):
ATATAAATATATTATTAAAAATATTAATATTTTTTAATAATAA
Found at i:56127 original size:29 final size:29
Alignment explanation
Indices: 56095--56160 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
56085 AACTCGCCTA
56095 AGTCAACCTAGACTGAGTCAGCTCGTCCG
1 AGTCAACCTAGACTGAGTCAGCTCGTCCG
56124 AGTCAACCTAGACTGAGTCAGCTCGTCCG
1 AGTCAACCTAGACTGAGTCAGCTCGTCCG
56153 AGTCAACC
1 AGTCAACC
56161 CGTTGACTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.26, C:0.32, G:0.23, T:0.20
Consensus pattern (29 bp):
AGTCAACCTAGACTGAGTCAGCTCGTCCG
Found at i:56128 original size:14 final size:14
Alignment explanation
Indices: 56109--56157 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
56099 AACCTAGACT
56109 GAGTCAGCTCGTCC
1 GAGTCAGCTCGTCC
* * * *
56123 GAGTCAACCTAGACT
1 GAGTC-AGCTCGTCC
56138 GAGTCAGCTCGTCC
1 GAGTCAGCTCGTCC
56152 GAGTCA
1 GAGTCA
56158 ACCCGTTGAC
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.22, C:0.31, G:0.27, T:0.20
Consensus pattern (14 bp):
GAGTCAGCTCGTCC
Found at i:56143 original size:15 final size:15
Alignment explanation
Indices: 56095--56143 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
56085 AACTCGCCTA
56095 AGTCAACCTAGACTG
1 AGTCAACCTAGACTG
* * * *
56110 AGTC-AGCTCGTCCG
1 AGTCAACCTAGACTG
56124 AGTCAACCTAGACTG
1 AGTCAACCTAGACTG
56139 AGTCA
1 AGTCA
56144 GCTCGTCCGA
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (15 bp):
AGTCAACCTAGACTG
Found at i:61162 original size:9 final size:10
Alignment explanation
Indices: 61138--61180 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
61128 TCATTTTTGT
61138 TAAAAATAAA
1 TAAAAATAAA
*
61148 TAAAAATGAA
1 TAAAAATAAA
* *
61158 TAAAATTCAA
1 TAAAAATAAA
61168 TAAAAATATAA
1 TAAAAATA-AA
61179 TA
1 TA
61181 TAAAGCTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 23 0.85
11 4 0.15
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:61618 original size:29 final size:29
Alignment explanation
Indices: 61570--61635 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 29
61560 TCATTAATTA
*
61570 TTATTTTTAACAACAGTTAATAATATT-TAT
1 TTATTTTTAACAACAATTAA-AAT-TTATAT
*
61600 TTATTTTTAATAA-AATTAAAATTTAATAT
1 TTATTTTTAACAACAATTAAAATTT-ATAT
61629 TTATTTT
1 TTATTTT
61636 ATATTTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 2 0.06
28 3 0.09
29 15 0.47
30 12 0.38
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (29 bp):
TTATTTTTAACAACAATTAAAATTTATAT
Found at i:61729 original size:10 final size:10
Alignment explanation
Indices: 61704--61751 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
61694 TTTACAATAT
*
61704 ATTTTTATTG
1 ATTTTTATTC
* *
61714 AATTTTGTTC
1 ATTTTTATTC
61724 ATTTTTAATTC
1 ATTTTT-ATTC
*
61735 ATTTTTATTT
1 ATTTTTATTC
61745 ATTTTTA
1 ATTTTTA
61752 AAAAAATTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
10 22 0.71
11 9 0.29
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (10 bp):
ATTTTTATTC
Done.