Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002987.1 Hibiscus syriacus cultivar Beakdansim tig00006176_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: 63642
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31
Found at i:3975 original size:14 final size:14
Alignment explanation
Indices: 3937--3965 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3927 TTTCATTAAA
3937 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
3951 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
3965 A
1 A
3966 GAAGCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:7120 original size:19 final size:18
Alignment explanation
Indices: 7076--7111 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
7066 TATGATTTCA
* *
7076 AAAATAAAAATTAGACTT
1 AAAATAAAAAATAAACTT
7094 AAAATAAAAAATAAACTT
1 AAAATAAAAAATAAACTT
7112 TATAATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.25
Consensus pattern (18 bp):
AAAATAAAAAATAAACTT
Found at i:11978 original size:2 final size:2
Alignment explanation
Indices: 11971--11999 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11961 TAAATCTCAT
11971 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12000 TTTGGCTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:12231 original size:120 final size:120
Alignment explanation
Indices: 12017--12247 Score: 345
Period size: 120 Copynumber: 1.9 Consensus size: 120
12007 CAATTGAGAT
* * *
12017 TGCAATTTGAACAAAAGATAACCAGAAAAGATTGCATATTTTAAGATTAAAATGCAAACATGCTA
1 TGCAACTTGAACAAAAGATAACCAGAAAAGATAGCAGATTTTAAGATTAAAATGCAAACATGCTA
* * *
12082 TATGTTACCACTAGATATGGATCAAGAACACTCTGGAACTTCATTTGATGAAACA
66 AATGTTACAACTAGATATGGATCAAGAACACTCTAGAACTTCATTTGATGAAACA
* * * * *
12137 TGCAACTTGAACAAAGGATAACTAGAAAAGATAGTAGATTTTAAGTTTCAAATGCAAACATGCTA
1 TGCAACTTGAACAAAAGATAACCAGAAAAGATAGCAGATTTTAAGATTAAAATGCAAACATGCTA
* *
12202 AATGTTACAACTAGATATGGATCATGAACACTCTAGAGCTTCATTT
66 AATGTTACAACTAGATATGGATCAAGAACACTCTAGAACTTCATTT
12248 TAAGAAGAGT
Statistics
Matches: 98, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
120 98 1.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.28
Consensus pattern (120 bp):
TGCAACTTGAACAAAAGATAACCAGAAAAGATAGCAGATTTTAAGATTAAAATGCAAACATGCTA
AATGTTACAACTAGATATGGATCAAGAACACTCTAGAACTTCATTTGATGAAACA
Found at i:17435 original size:21 final size:21
Alignment explanation
Indices: 17411--17450 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
17401 AGTAAAAAAT
*
17411 TACCTAAAATATTATTATTTC
1 TACCGAAAATATTATTATTTC
**
17432 TACCGAATTTATTATTATT
1 TACCGAAAATATTATTATT
17451 GGACGTTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (21 bp):
TACCGAAAATATTATTATTTC
Found at i:18123 original size:13 final size:14
Alignment explanation
Indices: 18091--18124 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
18081 GTTTTAGGGT
*
18091 TTAGGGTTTATAAT
1 TTAGGGTTTATAAG
18105 TTAGGGTTT-TAAG
1 TTAGGGTTTATAAG
18118 TTAGGGT
1 TTAGGGT
18125 AAAGTATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (14 bp):
TTAGGGTTTATAAG
Found at i:41075 original size:31 final size:31
Alignment explanation
Indices: 41034--41092 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
41024 CAGTAAAAGG
*
41034 AGAGTGGTTCTAGT-TTAGCC-TTAGAAAAACT
1 AGAGTAGTTCTA-TCTTAGCCATT-GAAAAACT
41065 AGAGTAGTTCTATCTTAGCCATTGAAAA
1 AGAGTAGTTCTATCTTAGCCATTGAAAA
41093 GTTATAGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 1 0.04
31 22 0.88
32 2 0.08
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (31 bp):
AGAGTAGTTCTATCTTAGCCATTGAAAAACT
Found at i:44157 original size:23 final size:23
Alignment explanation
Indices: 44131--44198 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
44121 ATTATTATAT
44131 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
44154 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
44177 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
44199 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:46876 original size:17 final size:17
Alignment explanation
Indices: 46841--46880 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
46831 GGTAATTAAA
46841 GATTGA-TAAGGAATTT
1 GATTGATTAAGGAATTT
* *
46857 GATTGATTAATGATTTT
1 GATTGATTAAGGAATTT
46874 GATTGAT
1 GATTGAT
46881 AAGAACTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.45
Consensus pattern (17 bp):
GATTGATTAAGGAATTT
Found at i:49286 original size:23 final size:23
Alignment explanation
Indices: 49221--49286 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
49211 TATTATATGA
*
49221 CACTTCGGTGCATTTCTACACGG
1 CACTTCGGTGCATTTCTACGCGG
* * * *
49244 CACTACGGTGTAATTCTACGTGG
1 CACTTCGGTGCATTTCTACGCGG
*
49267 CACTTCGGTGCATTTATACG
1 CACTTCGGTGCATTTCTACG
49287 AGCTGTGGTG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.32
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGCGG
Found at i:51452 original size:22 final size:21
Alignment explanation
Indices: 51427--51467 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
51417 TTGAACCTAG
*
51427 GAATTTCATTGTGAATGAGTAA
1 GAATTTCAGT-TGAATGAGTAA
*
51449 GAATTTGAGTTGAATGAGT
1 GAATTTCAGTTGAATGAGT
51468 CAAATAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.37
Consensus pattern (21 bp):
GAATTTCAGTTGAATGAGTAA
Found at i:51953 original size:17 final size:17
Alignment explanation
Indices: 51918--51957 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
51908 GGTAATTAAA
51918 GATTGA-TAAGGAATTT
1 GATTGATTAAGGAATTT
* *
51934 GATTGATTAATGATTTT
1 GATTGATTAAGGAATTT
51951 GATTGAT
1 GATTGAT
51958 AAGAACTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.45
Consensus pattern (17 bp):
GATTGATTAAGGAATTT
Found at i:54386 original size:23 final size:23
Alignment explanation
Indices: 54321--54386 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
54311 TATTATATGA
*
54321 CACTTCGGTGCATTTCTACACGG
1 CACTTCGGTGCATTTCTACGCGG
* * *
54344 CACTACGGTGCAATTCTACGTGG
1 CACTTCGGTGCATTTCTACGCGG
*
54367 CACTTCGGTGCATTTATACG
1 CACTTCGGTGCATTTCTACG
54387 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGCGG
Done.