Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004273.1 Hibiscus syriacus cultivar Beakdansim tig00009367_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: 49032
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2239 original size:4 final size:4
Alignment explanation
Indices: 2230--2331 Score: 52
Period size: 4 Copynumber: 26.0 Consensus size: 4
2220 GACAATATAC
** * * * *
2230 ATAA ATAA ATGG ATAA ATAA ATAA ACAA ATATGA GTAA ATAA ATCA A-AG
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA--A ATAA ATAA ATAA ATAA
* * * *
2279 ATAA A-GA A-AA ATAA A-GA A-AA ATAA ATAA ATAG ATAA CTAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
2323 ATAA GATAA
1 ATAA -ATAA
2332 GGGAAAAAAT
Statistics
Matches: 72, Mismatches: 20, Indels: 11
0.70 0.19 0.11
Matches are distributed among these distances:
3 9 0.12
4 56 0.78
5 4 0.06
6 3 0.04
ACGTcount: A:0.68, C:0.03, G:0.09, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:2294 original size:10 final size:10
Alignment explanation
Indices: 2279--2303 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2269 TAAATCAAAG
2279 ATAAAGAAAA
1 ATAAAGAAAA
2289 ATAAAGAAAA
1 ATAAAGAAAA
2299 ATAAA
1 ATAAA
2304 TAAATAGATA
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:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (10 bp):
ATAAAGAAAA
Found at i:2603 original size:2 final size:2
Alignment explanation
Indices: 2596--2625 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2586 ACAATAAAAG
2596 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
2626 GGTAATATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4682 original size:105 final size:105
Alignment explanation
Indices: 4494--5160 Score: 1172
Period size: 105 Copynumber: 6.3 Consensus size: 105
4484 TGTTTCGAGG
* * * * *
4494 CCAATATCTTTCGCTATGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAACCAG
*
4559 CGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGT
65 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
4600 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
*
4665 GGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
4705 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
*
4770 GGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
4810 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAATGTTTATTGACAACCAGT
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
*
4875 GGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
4915 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGA
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
4980 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
5020 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAATGTTTATTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
*
5085 GGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
5125 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
5161 GGTAAAACCT
Statistics
Matches: 539, Mismatches: 22, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
105 498 0.92
106 41 0.08
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (105 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:16485 original size:4 final size:4
Alignment explanation
Indices: 16476--16577 Score: 52
Period size: 4 Copynumber: 26.0 Consensus size: 4
16466 GACAATATAC
** * * * *
16476 ATAA ATAA ATGG ATAA ATAA ATAA ACAA ATATGA GTAA ATAA ATCA A-AG
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA--A ATAA ATAA ATAA ATAA
* * * *
16525 ATAA A-GA A-AA ATAA A-GA A-AA ATAA ATAA ATAG ATAA CTAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
16569 ATAA GATAA
1 ATAA -ATAA
16578 GGGAAAAATA
Statistics
Matches: 72, Mismatches: 20, Indels: 11
0.70 0.19 0.11
Matches are distributed among these distances:
3 9 0.12
4 56 0.78
5 4 0.06
6 3 0.04
ACGTcount: A:0.68, C:0.03, G:0.09, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:16540 original size:10 final size:10
Alignment explanation
Indices: 16525--16549 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
16515 TAAATCAAAG
16525 ATAAAGAAAA
1 ATAAAGAAAA
16535 ATAAAGAAAA
1 ATAAAGAAAA
16545 ATAAA
1 ATAAA
16550 TAAATAGATA
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:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (10 bp):
ATAAAGAAAA
Found at i:16838 original size:2 final size:2
Alignment explanation
Indices: 16831--16883 Score: 97
Period size: 2 Copynumber: 26.0 Consensus size: 2
16821 ACAATAAAAG
16831 TA TA 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 TA TA
16873 TA TA TCA TA TA
1 TA TA T-A TA TA
16884 GGAAAAATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 48 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:32258 original size:64 final size:64
Alignment explanation
Indices: 32157--32284 Score: 195
Period size: 64 Copynumber: 2.0 Consensus size: 64
32147 CGTTTTGCAA
*
32157 TAAAACTGTTTTGAAAGTTAGCCTCCATATGTCCAAGATTGAAGTCTAAAAACCCATATCAACT
1 TAAAACTGTTTTGAAAGTTAGCCTCCATATGTCCAAGATTGAAGTATAAAAACCCATATCAACT
* * * *
32221 TAAAACT-TTTTCGGAAGTTAGCGTCCATATGTCCAAGATTGAAGTATGAAAATCCATATCAACT
1 TAAAACTGTTTT-GAAAGTTAGCCTCCATATGTCCAAGATTGAAGTATAAAAACCCATATCAACT
32285 AGAGGCATGC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
63 4 0.07
64 54 0.93
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (64 bp):
TAAAACTGTTTTGAAAGTTAGCCTCCATATGTCCAAGATTGAAGTATAAAAACCCATATCAACT
Found at i:37302 original size:16 final size:16
Alignment explanation
Indices: 37283--37320 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
37273 TAAGACACTT
37283 AAGATCGAGCTTTCTA
1 AAGATCGAGCTTTCTA
37299 AAGATCGAGCTTTCTA
1 AAGATCGAGCTTTCTA
37315 AAGATC
1 AAGATC
37321 CACTTGTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (16 bp):
AAGATCGAGCTTTCTA
Found at i:41915 original size:25 final size:24
Alignment explanation
Indices: 41882--41945 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
41872 TATTCTCCTT
* *
41882 TAAAGTTTAAATTTGTGTAAAATTA
1 TAAAATTT-AATTTCTGTAAAATTA
* *
41907 TAAAATTTATTCTTCTTTAAAATTA
1 TAAAATTTAAT-TTCTGTAAAATTA
41932 TAAAATTTTAATTT
1 TAAAA-TTTAATTT
41946 TCCTTCAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
24 2 0.06
25 25 0.78
26 5 0.16
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (24 bp):
TAAAATTTAATTTCTGTAAAATTA
Found at i:42864 original size:23 final size:23
Alignment explanation
Indices: 42791--42869 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 23
42781 TTGTAATAAA
*
42791 AATATTACATTTATAATAAAAAT
1 AATATTAAATTTATAATAAAAAT
* * *
42814 AATATAAAATTACTAAAACAAAGGAAAT
1 AATATTAAATT--TATAA-TAA--AAAT
*
42842 AATATTATATTTATAATAAAAAT
1 AATATTAAATTTATAATAAAAAT
42865 AATAT
1 AATAT
42870 AAGTTTACTT
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
23 18 0.42
25 6 0.14
26 6 0.14
28 13 0.30
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (23 bp):
AATATTAAATTTATAATAAAAAT
Found at i:42871 original size:28 final size:28
Alignment explanation
Indices: 42791--42871 Score: 66
Period size: 28 Copynumber: 3.1 Consensus size: 28
42781 TTGTAATAAA
*
42791 AATATTACATTTATAATAAAAATAATAT
1 AATATTATATTTATAATAAAAATAATAT
* * **
42819 AAAATTACTA---A-AA-CAAAGGAA-AT
1 AATATTA-TATTTATAATAAAAATAATAT
42842 AATATTATATTTATAATAAAAATAATAT
1 AATATTATATTTATAATAAAAATAATAT
42870 AA
1 AA
42872 GTTTACTTAT
Statistics
Matches: 37, Mismatches: 9, Indels: 14
0.62 0.15 0.23
Matches are distributed among these distances:
22 2 0.05
23 8 0.22
24 5 0.14
25 3 0.08
26 3 0.08
27 5 0.14
28 10 0.27
29 1 0.03
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (28 bp):
AATATTATATTTATAATAAAAATAATAT
Found at i:43339 original size:6 final size:6
Alignment explanation
Indices: 43328--43361 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
43318 ATTTGCCTTT
*
43328 ATCCTC ATCCTC ATCCTC ATCCTC AACCTC ATCC
1 ATCCTC ATCCTC ATCCTC ATCCTC ATCCTC ATCC
43362 CATGCAAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.21, C:0.50, G:0.00, T:0.29
Consensus pattern (6 bp):
ATCCTC
Found at i:45302 original size:2 final size:2
Alignment explanation
Indices: 45295--45328 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
45285 CAAATTTCTC
45295 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
45329 CACAGCAGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48041 original size:14 final size:13
Alignment explanation
Indices: 48021--48046 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48011 TTCTGGTAAT
48021 TTTAAAAATTTTA
1 TTTAAAAATTTTA
48034 TTTAAAAATTTTA
1 TTTAAAAATTTTA
48047 AAAATAAAAT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTAAAAATTTTA
Done.