Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005713.1 Hibiscus syriacus cultivar Beakdansim tig00013354_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: 74783
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:5409 original size:42 final size:42
Alignment explanation
Indices: 5348--5435 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
5338 TAAATTAAAC
*
5348 GGGATGGAGAAAAACCGTTTATGTTAAACGGGGACGGGGACG
1 GGGATGGAGAAAAACCGTTTATGCTAAACGGGGACGGGGACG
* **
5390 GGGATGGGGAAAATTCGTTTATGCTAAACGGGGACGGGGACG
1 GGGATGGAGAAAAACCGTTTATGCTAAACGGGGACGGGGACG
5432 GGGA
1 GGGA
5436 CGAGTTTGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.28, C:0.11, G:0.43, T:0.17
Consensus pattern (42 bp):
GGGATGGAGAAAAACCGTTTATGCTAAACGGGGACGGGGACG
Found at i:5592 original size:38 final size:37
Alignment explanation
Indices: 5504--5596 Score: 132
Period size: 38 Copynumber: 2.5 Consensus size: 37
5494 AAATAATAAT
5504 AATTATATATATATATAATATTAATAAATTTAATTTA
1 AATTATATATATATATAATATTAATAAATTTAATTTA
* * * *
5541 AATTAAAAAATATATATAATATTTATATATTTAATTTA
1 AATT-ATATATATATATAATATTAATAAATTTAATTTA
5579 AATATATATATATATATA
1 AAT-TATATATATATATA
5597 TACCTGGCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
37 4 0.08
38 43 0.90
39 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (37 bp):
AATTATATATATATATAATATTAATAAATTTAATTTA
Found at i:6966 original size:24 final size:23
Alignment explanation
Indices: 6938--6987 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
6928 GCTTAAAAAA
*
6938 CCAATTACTCCAACTACGAATGGC
1 CCAATTACTCCAACTAC-AATAGC
**
6962 CCAATTGGTCCAACTACAATAGC
1 CCAATTACTCCAACTACAATAGC
6985 CCA
1 CCA
6988 GCAGGCACCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.34, C:0.34, G:0.12, T:0.20
Consensus pattern (23 bp):
CCAATTACTCCAACTACAATAGC
Found at i:7052 original size:16 final size:17
Alignment explanation
Indices: 7027--7060 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
7017 CAAAGGGTGA
*
7027 TTGTTTTTCT-TCTTTT
1 TTGTTCTTCTCTCTTTT
7043 TTGTTCTTCTCTCTTTT
1 TTGTTCTTCTCTCTTTT
7060 T
1 T
7061 CCCTGTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.00, C:0.18, G:0.06, T:0.76
Consensus pattern (17 bp):
TTGTTCTTCTCTCTTTT
Found at i:10745 original size:17 final size:18
Alignment explanation
Indices: 10723--10756 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10713 TTGAAAGGTC
*
10723 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
10740 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
10757 ACAAAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:20748 original size:19 final size:20
Alignment explanation
Indices: 20712--20755 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
20702 TTATCCGGAA
*
20712 AAAAATCCGGTCTGGGGTTT
1 AAAAATCCGGTATGGGGTTT
20732 AAAAATCCGGTAT-GGGTTT
1 AAAAATCCGGTATGGGGTTT
20751 AAAAA
1 AAAAA
20756 ATTAGATGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGTATGGGGTTT
Found at i:21263 original size:16 final size:16
Alignment explanation
Indices: 21242--21284 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
21232 TTAAAATTTG
21242 AATTTATTTATAATAA
1 AATTTATTTATAATAA
21258 AATTTATTTATAATAA
1 AATTTATTTATAATAA
21274 AATTTATTTAT
1 AATTTATTTAT
21285 TATATCCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTTATTTATAATAA
Found at i:21268 original size:20 final size:20
Alignment explanation
Indices: 21233--21285 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 20
21223 GTTTGAATTT
21233 TAAAATTTGAATTTATTTATAA
1 TAAAATTT--ATTTATTTATAA
21255 T-AAA---ATTTATTTATAA
1 TAAAATTTATTTATTTATAA
21271 TAAAATTTATTTATT
1 TAAAATTTATTTATT
21286 ATATCCAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
16 13 0.48
17 3 0.11
20 7 0.26
21 3 0.11
22 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TAAAATTTATTTATTTATAA
Found at i:21463 original size:18 final size:20
Alignment explanation
Indices: 21442--21490 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
21432 ACATATTATC
*
21442 AATATTAAG-TATATA-AAA
1 AATATTAAGATATAAAGAAA
21460 AATATCTAAGATATAAAGAAA
1 AATAT-TAAGATATAAAGAAA
21481 AATATTAAGA
1 AATATTAAGA
21491 GACTATTCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 5 0.19
19 4 0.15
20 10 0.37
21 8 0.30
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (20 bp):
AATATTAAGATATAAAGAAA
Found at i:23610 original size:15 final size:15
Alignment explanation
Indices: 23590--23622 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
23580 TTAGCTGGGT
*
23590 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
23605 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
23620 GGG
1 GGG
23623 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:25959 original size:31 final size:31
Alignment explanation
Indices: 25918--25976 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
25908 CTAATGATTA
* * *
25918 ATATATATTATTGATATGAAATTTATTATAT
1 ATATAAATTATTAATATGAAATATATTATAT
*
25949 ATATAAATTATTAATATGATATATATTA
1 ATATAAATTATTAATATGAAATATATTA
25977 CGTTATTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (31 bp):
ATATAAATTATTAATATGAAATATATTATAT
Found at i:29544 original size:37 final size:37
Alignment explanation
Indices: 29471--29544 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
29461 TTATATTTTA
*
29471 AATTTTGTAAAAAAAATTATATAAATATTGTGAATTT
1 AATTTTGTAAAAAAAATTATATAAATATTGTCAATTT
* * *
29508 AATTTTTTAAAGAAAA-TATATAAATATTTTACAATTT
1 AATTTTGTAAAAAAAATTATATAAATATTGT-CAATTT
29545 GTAATATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 13 0.41
37 19 0.59
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (37 bp):
AATTTTGTAAAAAAAATTATATAAATATTGTCAATTT
Found at i:33092 original size:16 final size:17
Alignment explanation
Indices: 33071--33105 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
33061 TTACTATTCA
33071 CGTGAATAGTG-AATTT
1 CGTGAATAGTGAAATTT
33087 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
33104 CG
1 CG
33106 GTCGGTGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:33874 original size:15 final size:16
Alignment explanation
Indices: 33856--33888 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
33846 GTGGCAGATC
33856 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
33871 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
33887 AA
1 AA
33889 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:41930 original size:41 final size:42
Alignment explanation
Indices: 41885--41983 Score: 112
Period size: 43 Copynumber: 2.4 Consensus size: 42
41875 TAATTTCAAT
*
41885 GTTTGTTCCAAAAACG-ATCTACAGA-TATCAACTTTTGCGGC
1 GTTTGTTCCAAAAACGCAGCTACAGACTAT-AACTTTTGCGGC
* * * * *
41926 GTTTGTTCTAAAAACGCCGCTATAGATCTATACCTTTTGCGGT
1 GTTTGTTCCAAAAACGCAGCTACAGA-CTATAACTTTTGCGGC
41969 GTTTGTTCCAAAAAC
1 GTTTGTTCCAAAAAC
41984 ACCGCTGTAG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 15 0.31
42 6 0.12
43 24 0.50
44 3 0.06
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.34
Consensus pattern (42 bp):
GTTTGTTCCAAAAACGCAGCTACAGACTATAACTTTTGCGGC
Found at i:41974 original size:43 final size:43
Alignment explanation
Indices: 41916--42012 Score: 133
Period size: 43 Copynumber: 2.3 Consensus size: 43
41906 CAGATATCAA
* *
41916 CTTTTGCGGCGTTTGTTCTAAAAACGCCGCTATAGATCTAT-AC
1 CTTTTGCGGCGTTTGTTCCAAAAACACCGCTATAGATCT-TGAC
* *
41959 CTTTTGCGGTGTTTGTTCCAAAAACACCGCTGTAGATCTTGAC
1 CTTTTGCGGCGTTTGTTCCAAAAACACCGCTATAGATCTTGAC
*
42002 CTATTGCGGCG
1 CTTTTGCGGCG
42013 GTTTTTGTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 1 0.02
43 46 0.98
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.34
Consensus pattern (43 bp):
CTTTTGCGGCGTTTGTTCCAAAAACACCGCTATAGATCTTGAC
Found at i:43631 original size:92 final size:93
Alignment explanation
Indices: 43473--43647 Score: 298
Period size: 92 Copynumber: 1.9 Consensus size: 93
43463 AACACAGGAA
* *
43473 TACTAGAGCGCAGCTGCAGGATGGTAGCATCGACAAGCAACACACTTAAAGATAGATGCCAGGCG
1 TACTAGAGCGCAGCCGCAGGATGGTAGCATCGACAAGCAAAACACTTAAAGATAGATGCCAGGCG
43538 AACACACCACAACCTACTAAATTGGGAG
66 AACACACCACAACCTACTAAATTGGGAG
* *
43566 TACTAGAGCGCA-CCGTAGGATGGTAGCATCGACAAGCAAAACATTTAAAGATAGATGCCAGGCG
1 TACTAGAGCGCAGCCGCAGGATGGTAGCATCGACAAGCAAAACACTTAAAGATAGATGCCAGGCG
*
43630 AACACACCACAGCCTACT
66 AACACACCACAACCTACT
43648 GAACTGGTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
92 65 0.84
93 12 0.16
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.15
Consensus pattern (93 bp):
TACTAGAGCGCAGCCGCAGGATGGTAGCATCGACAAGCAAAACACTTAAAGATAGATGCCAGGCG
AACACACCACAACCTACTAAATTGGGAG
Found at i:45619 original size:21 final size:22
Alignment explanation
Indices: 45592--45637 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
45582 ACGAATGCAC
*
45592 ATTATTAAAATAAATAAATAAAAT
1 ATTA-TAAATTAAATAAA-AAAAT
*
45616 ATTATAAATTATATAAAAAAAT
1 ATTATAAATTAAATAAAAAAAT
45638 CAAAAGCACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 11 0.55
24 4 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
ATTATAAATTAAATAAAAAAAT
Found at i:46204 original size:12 final size:13
Alignment explanation
Indices: 46176--46201 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46166 AAATTAATAG
46176 ATTATACAAAAAA
1 ATTATACAAAAAA
46189 ATTATACAAAAAA
1 ATTATACAAAAAA
46202 TTAAAGTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (13 bp):
ATTATACAAAAAA
Found at i:53769 original size:2 final size:2
Alignment explanation
Indices: 53762--53818 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
53752 ATTTGTTATC
53762 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
53804 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
53819 GATAGTTAGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54348 original size:23 final size:23
Alignment explanation
Indices: 54275--54349 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
54265 TCATAAATGC
* *
54275 TAAATGAACACGTTTGTGAATATA
1 TAAATGAATACGTTTGCGAATA-A
* * * * *
54299 TAAATAAATACGTTCGCGGACAT
1 TAAATGAATACGTTTGCGAATAA
*
54322 TAAATGAATATGTTTGCGAATAA
1 TAAATGAATACGTTTGCGAATAA
54345 TAAAT
1 TAAAT
54350 AAACGAACAC
Statistics
Matches: 38, Mismatches: 13, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
23 22 0.58
24 16 0.42
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (23 bp):
TAAATGAATACGTTTGCGAATAA
Found at i:55595 original size:13 final size:13
Alignment explanation
Indices: 55577--55603 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55567 TACGTCGTCA
55577 ATTATTAAAAAAT
1 ATTATTAAAAAAT
55590 ATTATTAAAAAAT
1 ATTATTAAAAAAT
55603 A
1 A
55604 CCACCACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTATTAAAAAAT
Found at i:63686 original size:2 final size:2
Alignment explanation
Indices: 63679--63738 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
63669 CAACAAAGGG
63679 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
63721 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
63739 CAATCACCAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73762 original size:21 final size:21
Alignment explanation
Indices: 73713--73762 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
73703 TGTAAGAATA
73713 ATTGAACATTCATTATCTAAT
1 ATTGAACATTCATTATCTAAT
73734 GATT-AACATTCATTATCTAAT
1 -ATTGAACATTCATTATCTAAT
73755 -TTAGAACA
1 ATT-GAACA
73763 GATACTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 2 0.08
21 21 0.81
22 3 0.12
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (21 bp):
ATTGAACATTCATTATCTAAT
Done.