Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004157.1 Hibiscus syriacus cultivar Beakdansim tig00009095_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: 69464
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5872 original size:21 final size:21
Alignment explanation
Indices: 5826--5872 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
5816 TTTTCTTCTT
* *
5826 ATTTTATTTATTTTATTTATC
1 ATTTTATTTATGTTATTTACC
*
5847 TTTTTATTTACTGTT-TTTACC
1 ATTTTATTTA-TGTTATTTACC
5868 ATTTT
1 ATTTT
5873 TCATTGCCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.70
Consensus pattern (21 bp):
ATTTTATTTATGTTATTTACC
Found at i:6604 original size:35 final size:35
Alignment explanation
Indices: 6558--6627 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
6548 CATTGCAATA
*
6558 ATGGTACCGATACT-TCCCCATTG-GTATCGATACCC
1 ATGGTACCGATACTAT-CAC-TTGAGTATCGATACCC
6593 ATGGTACCGATACTATCACTTGAGTATCGATACCC
1 ATGGTACCGATACTATCACTTGAGTATCGATACCC
6628 CATGACGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 3 0.09
35 28 0.88
36 1 0.03
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (35 bp):
ATGGTACCGATACTATCACTTGAGTATCGATACCC
Found at i:9963 original size:21 final size:21
Alignment explanation
Indices: 9939--9980 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
9929 TATTGGTACA
9939 CCAATATGGGGTATCGATACT
1 CCAATATGGGGTATCGATACT
*
9960 CCAATATGGGGTATCGGTACT
1 CCAATATGGGGTATCGATACT
9981 ACCTTTGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (21 bp):
CCAATATGGGGTATCGATACT
Found at i:10178 original size:64 final size:64
Alignment explanation
Indices: 10095--10226 Score: 237
Period size: 64 Copynumber: 2.1 Consensus size: 64
10085 ACTGTGCATA
* *
10095 GTATCGGTACCATTTCGTGGTTCTAGAATTTGAGCCTTTATGGTAGTATCGATACTACCTAGTG
1 GTATCGATACCATTTCGTGGTTCTAGAATTTGAGCCTTCATGGTAGTATCGATACTACCTAGTG
*
10159 GTATCGATACCATTTCGTGGTTTTAGAATTTGAGCCTTCATGGTAGTATCGATACTACCTAGTG
1 GTATCGATACCATTTCGTGGTTCTAGAATTTGAGCCTTCATGGTAGTATCGATACTACCTAGTG
10223 GTAT
1 GTAT
10227 TGGTACTACT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (64 bp):
GTATCGATACCATTTCGTGGTTCTAGAATTTGAGCCTTCATGGTAGTATCGATACTACCTAGTG
Found at i:15901 original size:21 final size:19
Alignment explanation
Indices: 15866--15917 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
15856 GAGAGAGAAT
15866 AAAAGTTAAAATGAAAGAG
1 AAAAGTTAAAATGAAAGAG
15885 ACAAAGTTAATAATGAAAGAG
1 A-AAAGTTAA-AATGAAAGAG
*
15906 AAAAGTAAAAAT
1 AAAAGTTAAAAT
15918 TTGGGAGGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 4 0.13
20 15 0.50
21 11 0.37
ACGTcount: A:0.63, C:0.02, G:0.17, T:0.17
Consensus pattern (19 bp):
AAAAGTTAAAATGAAAGAG
Found at i:16218 original size:24 final size:24
Alignment explanation
Indices: 16184--16231 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
16174 AATCAAATAA
16184 AAAAATCTACAAAATAAAATAAAAT
1 AAAAATCTACAAAA-AAAATAAAAT
* *
16209 AAAAAT-TACAGAAAAAATTAAAT
1 AAAAATCTACAAAAAAAATAAAAT
16232 TTAAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 6 0.29
25 6 0.29
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.21
Consensus pattern (24 bp):
AAAAATCTACAAAAAAAATAAAAT
Found at i:24592 original size:21 final size:21
Alignment explanation
Indices: 24560--24614 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
24550 GAGACTAAGT
24560 GTATCAGA-ACACTATCAAAGG
1 GTATC-GATACACTATCAAAGG
*
24581 GTATCGGTACACTATCAAAGG
1 GTATCGATACACTATCAAAGG
24602 GTATCGATACACT
1 GTATCGATACACT
24615 CAGTGTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (21 bp):
GTATCGATACACTATCAAAGG
Found at i:26819 original size:22 final size:19
Alignment explanation
Indices: 26776--26820 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 19
26766 CTTTAATTTG
*
26776 TTTATTTAATTATTTTTCT
1 TTTATTTAATTATTTTTAT
26795 TTTATTTAATTCTAATTTTTAT
1 TTTATTTAA-T-T-ATTTTTAT
26817 TTTA
1 TTTA
26821 AAACCCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 1 0.05
21 1 0.05
22 11 0.50
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTATTTAATTATTTTTAT
Found at i:26891 original size:16 final size:18
Alignment explanation
Indices: 26859--26892 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
26849 ATATGTATTA
26859 TTATATTATTTTCATTTT
1 TTATATTATTTTCATTTT
26877 TTAT-TTATTTT-ATTTT
1 TTATATTATTTTCATTTT
26893 AATATATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 7 0.44
18 4 0.25
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATATTATTTTCATTTT
Found at i:29815 original size:18 final size:19
Alignment explanation
Indices: 29779--29816 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
29769 AGCAACAATT
**
29779 TTAAAACAAATTTTGAAAA
1 TTAAAACAAATTTAAAAAA
29798 TTAAAA-AAATTTAAAAAA
1 TTAAAACAAATTTAAAAAA
29816 T
1 T
29817 CTTGTGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (19 bp):
TTAAAACAAATTTAAAAAA
Found at i:42579 original size:17 final size:16
Alignment explanation
Indices: 42537--42584 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
42527 CTTTTCTTGT
*
42537 TTATTTTAATTATATAA
1 TTATTTT-ATTATTTAA
42554 TTATATTTATTATTTAA
1 TTAT-TTTATTATTTAA
42571 TATATTTTA-TATTT
1 T-TATTTTATTATTT
42585 TTACTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 5 0.18
17 17 0.61
18 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTTTATTATTTAA
Found at i:44081 original size:234 final size:234
Alignment explanation
Indices: 43668--44134 Score: 898
Period size: 234 Copynumber: 2.0 Consensus size: 234
43658 GACGAGGCGC
43668 CTGTGATAAACAATAACAACGGCGACGGTGACAATAAGAATAAGAAACAGCGGGCGCAGGGGGGC
1 CTGTGATAAACAATAACAACGGCGACGGTGACAATAAGAATAAGAAACAGCGGGCGCAGGGGGGC
*
43733 AATGACAAGTTAACTGTCGCGGTGGCAGTTGGGGAGGAGGAGAATAACAACAACAACAATAACAA
66 AATGACAAGTTAACTGTCGCGGCGGCAGTTGGGGAGGAGGAGAATAACAACAACAACAATAACAA
*
43798 TAGGGTTTTAGTGGAAAGGGATCGAGTGGAGAAAGAGGAAATTGGGGATAAGGAGATGGATGAGT
131 TAGGGTTTTAGTGGAAAGGGATCGAGTGGAGAAAGAGGAAATAGGGGATAAGGAGATGGATGAGT
43863 TCGATAACGGAGGAAGGCGGAGCAATGATAAGGGGAATG
196 TCGATAACGGAGGAAGGCGGAGCAATGATAAGGGGAATG
43902 CTGTGATAAACAATAACAACGGCGACGGTGACAATAAGAATAAGAAACAGCGGGCGCAGGGGGGC
1 CTGTGATAAACAATAACAACGGCGACGGTGACAATAAGAATAAGAAACAGCGGGCGCAGGGGGGC
*
43967 AATGACAAGTTAGCTGTCGCGGCGGCAGTTGGGGAGGAGGAGAATAACAACAACAACAATAACAA
66 AATGACAAGTTAACTGTCGCGGCGGCAGTTGGGGAGGAGGAGAATAACAACAACAACAATAACAA
44032 TAGGGTTTTAGTGGAAAGGGATCGAGTGGAGAAAGAGGAAATAGGGGATAAGGAGATGGATGAGT
131 TAGGGTTTTAGTGGAAAGGGATCGAGTGGAGAAAGAGGAAATAGGGGATAAGGAGATGGATGAGT
*
44097 TCGATAACGGAGGAAGGCGGAGTAATGATAAGGGGAAT
196 TCGATAACGGAGGAAGGCGGAGCAATGATAAGGGGAAT
44135 ACTGGTGACG
Statistics
Matches: 229, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
234 229 1.00
ACGTcount: A:0.38, C:0.12, G:0.36, T:0.15
Consensus pattern (234 bp):
CTGTGATAAACAATAACAACGGCGACGGTGACAATAAGAATAAGAAACAGCGGGCGCAGGGGGGC
AATGACAAGTTAACTGTCGCGGCGGCAGTTGGGGAGGAGGAGAATAACAACAACAACAATAACAA
TAGGGTTTTAGTGGAAAGGGATCGAGTGGAGAAAGAGGAAATAGGGGATAAGGAGATGGATGAGT
TCGATAACGGAGGAAGGCGGAGCAATGATAAGGGGAATG
Found at i:53444 original size:36 final size:34
Alignment explanation
Indices: 53375--53445 Score: 81
Period size: 34 Copynumber: 2.0 Consensus size: 34
53365 AAGAATTAAT
* * *
53375 TTTTATTTAATATTAAAAAATTAAATTATTTTGA
1 TTTTATTCAATATTAAAAAAATAAATTAATTTGA
53409 TTTTATTCAAT-TTGAAAGAAAATAAATTTAATTTGA
1 TTTTATTCAATATT-AAA-AAAATAAA-TTAATTTGA
53445 T
1 T
53446 AACTCAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
33 2 0.06
34 13 0.42
35 7 0.23
36 9 0.29
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (34 bp):
TTTTATTCAATATTAAAAAAATAAATTAATTTGA
Found at i:54352 original size:3 final size:3
Alignment explanation
Indices: 54344--54377 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
54334 GATTTTAAAG
54344 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
54378 ATTTATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:58146 original size:13 final size:13
Alignment explanation
Indices: 58128--58152 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58118 GCATAAGGAG
58128 TGCATCGATGCAA
1 TGCATCGATGCAA
58141 TGCATCGATGCA
1 TGCATCGATGCA
58153 CTCCCTTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (13 bp):
TGCATCGATGCAA
Found at i:63094 original size:18 final size:18
Alignment explanation
Indices: 63071--63106 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
63061 AGGGATTATC
*
63071 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
63089 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
63107 TTCATAGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:63116 original size:23 final size:23
Alignment explanation
Indices: 63086--63158 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
63076 TCCTTTGGGA
63086 CATAGTGGTCCTTCGGGACATTT
1 CATAGTGGTCCTTCGGGACATTT
*
63109 CATAGTGGTCATTCGGGACATTT
1 CATAGTGGTCCTTCGGGACATTT
* *
63132 CATAGTAGTCCTTCGGGACAATT
1 CATAGTGGTCCTTCGGGACATTT
63155 CATA
1 CATA
63159 TGCCCCTAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (23 bp):
CATAGTGGTCCTTCGGGACATTT
Found at i:64656 original size:27 final size:25
Alignment explanation
Indices: 64626--64686 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 25
64616 GGATCAACAT
*
64626 TTTTGCATCTGCATTTGGATCTCTGCA
1 TTTTGCATCTGCATTTGAAT-TC-GCA
* *
64653 TTTTTCATTTGCATTTGAATTCGCA
1 TTTTGCATCTGCATTTGAATTCGCA
64678 TCTTTGCAT
1 T-TTTGCAT
64687 TTTTATGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 4 0.14
26 8 0.28
27 17 0.59
ACGTcount: A:0.16, C:0.20, G:0.15, T:0.49
Consensus pattern (25 bp):
TTTTGCATCTGCATTTGAATTCGCA
Found at i:64664 original size:33 final size:33
Alignment explanation
Indices: 64627--64690 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
64617 GATCAACATT
* * *
64627 TTTGCATCTGCATTTGGATCTCTGCATTTTTCA
1 TTTGCATCTGAATTCGCATCTCTGCATTTTTCA
* *
64660 TTTGCATTTGAATTCGCATCTTTGCATTTTT
1 TTTGCATCTGAATTCGCATCTCTGCATTTTT
64691 ATGTTTGTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.16, C:0.19, G:0.14, T:0.52
Consensus pattern (33 bp):
TTTGCATCTGAATTCGCATCTCTGCATTTTTCA
Found at i:67141 original size:14 final size:14
Alignment explanation
Indices: 67122--67186 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
67112 TCTATCAGAG
67122 AAAAAAGAAGAAAAA
1 AAAAAAGAAG-AAAA
*
67137 AAAAAAAAAGAAAA
1 AAAAAAGAAGAAAA
*
67151 AAGAAAA-AAG-AAG
1 AA-AAAAGAAGAAAA
*
67164 AAGAAAGAA-ATAAA
1 AAAAAAGAAGA-AAA
67178 AAAAAAGAA
1 AAAAAAGAA
67187 TTGAATCAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
12 3 0.07
13 6 0.15
14 19 0.46
15 13 0.32
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.02
Consensus pattern (14 bp):
AAAAAAGAAGAAAA
Found at i:67161 original size:32 final size:31
Alignment explanation
Indices: 67120--67186 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 31
67110 CATCTATCAG
67120 AGAAAAAAGAAGAAAAAAAAAAAAAAGAAAAA
1 AGAAAAAAGAAGAAAAAAAAAAAAAA-AAAAA
* * *
67152 AGAAAAAAGAAGAAGAAAGAAATAAAAAAAA
1 AGAAAAAAGAAGAAAAAAAAAAAAAAAAAAA
67183 AGAA
1 AGAA
67187 TTGAATCAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 9 0.28
32 23 0.72
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (31 bp):
AGAAAAAAGAAGAAAAAAAAAAAAAAAAAAA
Done.