Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005555.1 Hibiscus syriacus cultivar Beakdansim tig00012878_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: 188475
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:185711 original size:311 final size:311
Alignment explanation
Indices: 185125--186035 Score: 1275
Period size: 311 Copynumber: 2.9 Consensus size: 311
185115 CAAACATGAG
* * *
185125 CACGAAGAAAATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTT
1 CACGAAGAATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGA-CGCTGGTTGTC
* * ** *
185190 AATAAACAA-TTTTGCAATACTAGAGCCAATTTCAACTTCACA-CGAAGGATAGT-GA---CAGA
65 AACAAACAACTTCT-CAAT--TTCAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
* * * *
185249 CAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACACTTCCCAATTTCAGAG
127 CAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAAACTT-CCAATTTCAGAG
* *
185314 TCAATTTCAACTTCACAGCGAAGGATAGTAGACTCCAGACAA--CAAGTTCAACTTTCACGACGA
191 TCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC-TTCACGACGA
** * *
185377 AGGGATTGCTGGTTGTTAATAAACAACTTCCCAATTTCAGAGTCAATTTCAACTTCA
255 AGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCA
*
185434 -ACGAAGAATA-TGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGATCGATGGTTGTC
1 CACGAAGAATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGA-CGCTGGTTGTC
185497 AAACAAACAACTTCTCAATTTCAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA-A
65 -AACAAACAACTTCTCAATTTCAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACA
*
185561 ACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAACTTCTCAATTTTAGAGT
129 ACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAAAACTTC-CAATTTCAGAGT
* *
185626 CAATTTCAACTTCACAACGAAGGA-ATTGGACTCCAGACAACGCAAATTCAACTTCACGACGAAG
192 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
185690 GGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCA
257 GGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCA
*
185745 CAGCGAAGGATATTGGACTCCAGACAA-GCATG-TCAACTTCACGACGAAGGGACGCTGGTTGTC
1 CA-CGAAGAATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACGCTGGTTGTC
* *
185808 AAC-AATAACTTCTCAATATCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAC
65 AACAAACAACTTCTCAATTTC--AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAC
* * *
185872 AATGCATGTTCAACTTCACGACGAAGGGA---CTGGTTGTCAATAAATAATTTCCCATTTCAGAG
128 AACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAA-AACTTCCAATTTCAGAG
* *
185934 TCAATTTCAACTTCATAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAA
191 TCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
185999 GGGACCGCTGGTTGTCAATAAACAACTT-TCAATTTCA
256 GGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
186036 CGACGGAGGA
Statistics
Matches: 546, Mismatches: 37, Indels: 38
0.88 0.06 0.06
Matches are distributed among these distances:
306 20 0.04
307 59 0.11
308 23 0.04
309 72 0.13
310 129 0.24
311 158 0.29
312 58 0.11
313 13 0.02
314 14 0.03
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (311 bp):
CACGAAGAATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACGCTGGTTGTCA
ACAAACAACTTCTCAATTTCAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAAC
GCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAAACTTCCAATTTCAGAGTCAAT
TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
CGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCA
Found at i:185841 original size:102 final size:105
Alignment explanation
Indices: 185135--186035 Score: 1179
Period size: 104 Copynumber: 8.7 Consensus size: 105
185125 CACGAAGAAA
* *
185135 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAATAAACAA-
1 ATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAACAAC
* *
185199 TTTTGCAA-TACTAGAGCCAATTTCAACTTCACA-CGAAGGAT
65 TTCT-CAATTTC-AGAGCCAATTTCAACTTCACAGCGAAGGAT
* * * *
185240 AGT-GA---CAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAC-ACT
1 ATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAACAACT
* *
185300 TCCCAATTTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
66 TCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
* * * ** *
185340 AGTAGACTCCAGACAA--CAAGTTCAACTTTCACGACGAAGGGATTGCTGGTTGTTAATAAACAA
1 ATTGGACTCCAGACAACGCATGTTCAAC-TTCACGACGAAGGGACCGCTGGTTGTCAA-AAACAA
* * *
185403 CTTCCCAATTTCAGAGTCAATTTCAACTTCA-A-CGAAGAAT
64 CTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
* *
185443 A-TGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGATCGATGGTTGTCAAACAAACAA
1 ATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC-AA-AAACAA
185507 CTTCTCAATTTC--AGCCAATTTCAACTTCACAGCGAAGGAT
64 CTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
185547 ATTGGACTCCAGA-AACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA-AAC
1 ATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAACAAC
* * *
185610 TTCTCAATTTTAGAGTCAATTTCAACTTCACAACGAAGGA-
65 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
**
185650 ATTGGACTCCAGACAACGCAAATTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
1 ATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAACAAC
*
185715 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
65 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
* *
185756 ATTGGACTCCAGACAA-GCATG-TCAACTTCACGACGAAGGGA-CGCTGGTTGTCAACAATAACT
1 ATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAACAACT
*
185818 TCTCAATATCAGAGCCAATTTCAACTTCACAGCGAAGGAT
66 TCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
* * *
185858 ATTGGACTCCAGACAATGCATGTTCAACTTCACGACGAAGGGA---CTGGTTGTCAATAAATAAT
1 ATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAACAAC
* * *
185920 TTC-CCATTTCAGAGTCAATTTCAACTTCATAGCGAAGGAT
65 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
* *
185960 ATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
1 ATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAACAAC
186025 TT-TCAATTTCA
65 TTCTCAATTTCA
186036 CGACGGAGGA
Statistics
Matches: 716, Mismatches: 52, Indels: 56
0.87 0.06 0.07
Matches are distributed among these distances:
99 24 0.03
100 18 0.03
101 48 0.07
102 196 0.27
103 104 0.15
104 197 0.28
105 113 0.16
106 16 0.02
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (105 bp):
ATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAACAACT
TCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
Found at i:187602 original size:15 final size:14
Alignment explanation
Indices: 187572--187609 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
187562 TTTAGTCCTA
187572 ATTTAG-ATTGTTT
1 ATTTAGTATTGTTT
187585 ATTTAGTATTGTTTT
1 ATTTAGTATTG-TTT
*
187600 ATTTATTATT
1 ATTTAGTATT
187610 ATAATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.27
14 4 0.18
15 12 0.55
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.66
Consensus pattern (14 bp):
ATTTAGTATTGTTT
Found at i:187678 original size:2 final size:2
Alignment explanation
Indices: 187671--187695 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
187661 CATTCTCTAT
187671 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
187696 TTAGTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:187848 original size:19 final size:18
Alignment explanation
Indices: 187824--187860 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
187814 AACCTTTTTA
187824 TATATTATTTTACTTATTT
1 TATATTATTTTA-TTATTT
187843 TATATTATTTTATTATTT
1 TATATTATTTTATTATTT
187861 CTATTATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (18 bp):
TATATTATTTTATTATTT
Done.