Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005960.1 Hibiscus syriacus cultivar Beakdansim tig00014004_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: 221916
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
File 2 of 2
Found at i:197150 original size:51 final size:51
Alignment explanation
Indices: 197090--197192 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
197080 TTAATTGTCA
*
197090 CTTAATTCATTGAATATTATTCTTGTCATCAGTACTATTTATACTGTTCTT
1 CTTAATTCATTGAATATTATTCTTGTCATCACTACTATTTATACTGTTCTT
197141 CTTAATTCATTGAATATTATTCTTGTCATCACTACTATTTATACTGTTCTT
1 CTTAATTCATTGAATATTATTCTTGTCATCACTACTATTTATACTGTTCTT
197192 C
1 C
197193 CCTTGCACAG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.50
Consensus pattern (51 bp):
CTTAATTCATTGAATATTATTCTTGTCATCACTACTATTTATACTGTTCTT
Found at i:197512 original size:2 final size:2
Alignment explanation
Indices: 197505--197529 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
197495 TTTTCAACCT
197505 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
197530 GTATGTATGT
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:198550 original size:11 final size:11
Alignment explanation
Indices: 198534--198559 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
198524 AAATGTCTTA
198534 AATCTCGACTG
1 AATCTCGACTG
198545 AATCTCGACTG
1 AATCTCGACTG
198556 AATC
1 AATC
198560 ATTTCATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (11 bp):
AATCTCGACTG
Found at i:198937 original size:16 final size:17
Alignment explanation
Indices: 198904--198937 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
198894 ACCTTCTAAT
*
198904 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
198921 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
198937 T
1 T
198938 AATAATAAAA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:201088 original size:185 final size:185
Alignment explanation
Indices: 200697--201072 Score: 630
Period size: 185 Copynumber: 2.0 Consensus size: 185
200687 ATAAAATTTT
* * *
200697 AAATTTTAAATATATTATATATAACATATGAGCTCAGCCCAAACTATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATAAATAACATATGAGCTCAGCCCAAACCATTTAAAACTCAATTAATAA
*
200762 TTTAAGATCCAATAACTTTTAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTTT
66 TTTAAGATCCAATAACTTTTAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTT
* * *
200827 TATTTTATAATTATATATTATTTAAATTAATTGTAAATTGTTTTTCTGAATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTCTGAATTAAA
*
200882 AAATATTAAATATATTATAAATAACATATGGGCTCAGCCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATAAATAACATATGAGCTCAGCCCAAACCATTTAAAACTCAATTAATAA
200947 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATAT-AAATTT
66 TTTAAGATCCAATAACTTTT-AACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
* * *
201011 TTATTTTATAATTGTATATTATTTAAATTAATTATAAACTATTTTT-TTAATTATA
130 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTCTGAATTAAA
201066 AAATATT
1 AAATATT
201073 TAATTTTTAT
Statistics
Matches: 179, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
184 14 0.08
185 129 0.72
186 36 0.20
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (185 bp):
AAATATTAAATATATTATAAATAACATATGAGCTCAGCCCAAACCATTTAAAACTCAATTAATAA
TTTAAGATCCAATAACTTTTAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTCTGAATTAAA
Found at i:203007 original size:19 final size:18
Alignment explanation
Indices: 202956--203011 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
202946 TATAAGTAGA
202956 TTTTTCTCTATACT-TACGT
1 TTTTTCTCTATACTGT--GT
202975 TTTTTCTCTATACTTGTGT
1 TTTTTCTCTATAC-TGTGT
* *
202994 TTTTTCTTTTTACTGTGT
1 TTTTTCTCTATACTGTGT
203012 GAGCACCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 5 0.15
19 26 0.79
20 1 0.03
21 1 0.03
ACGTcount: A:0.11, C:0.16, G:0.09, T:0.64
Consensus pattern (18 bp):
TTTTTCTCTATACTGTGT
Found at i:203011 original size:18 final size:19
Alignment explanation
Indices: 202956--203000 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
202946 TATAAGTAGA
**
202956 TTTTTCTCTATACTTACGT
1 TTTTTCTCTATACTTGTGT
202975 TTTTTCTCTATACTTGTGT
1 TTTTTCTCTATACTTGTGT
202994 TTTTTCT
1 TTTTTCT
203001 TTTTACTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.11, C:0.18, G:0.07, T:0.64
Consensus pattern (19 bp):
TTTTTCTCTATACTTGTGT
Found at i:205068 original size:19 final size:19
Alignment explanation
Indices: 205020--205068 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
205010 TTTTTTGTGT
205020 TCTTTTTTTCTTTCGAACAG
1 TCTTTTTTT-TTTCGAACAG
* *
205040 TCTCTCTTTTTTCGAACAG
1 TCTTTTTTTTTTCGAACAG
*
205059 -CTATTTTTTT
1 TCTTTTTTTTT
205069 CATTCAACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 8 0.32
19 10 0.40
20 7 0.28
ACGTcount: A:0.14, C:0.20, G:0.08, T:0.57
Consensus pattern (19 bp):
TCTTTTTTTTTTCGAACAG
Found at i:211624 original size:21 final size:21
Alignment explanation
Indices: 211595--211634 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
211585 CATGGTGTTA
* *
211595 TGACGATCCATAGTGCTGACG
1 TGACAATCCACAGTGCTGACG
211616 TGACAATCCACAGTGCTGA
1 TGACAATCCACAGTGCTGA
211635 TGACATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (21 bp):
TGACAATCCACAGTGCTGACG
Found at i:213104 original size:13 final size:15
Alignment explanation
Indices: 213077--213108 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
213067 ATTAAAATTT
213077 ATTATCAAAAGAATA
1 ATTATCAAAAGAATA
213092 ATTA-CAAAA-AATA
1 ATTATCAAAAGAATA
213105 ATTA
1 ATTA
213109 ATACTTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 5 0.29
15 4 0.24
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.28
Consensus pattern (15 bp):
ATTATCAAAAGAATA
Found at i:214093 original size:29 final size:30
Alignment explanation
Indices: 214039--214110 Score: 69
Period size: 29 Copynumber: 2.4 Consensus size: 30
214029 CACTCTCTCA
* * * *
214039 TATTTTGCTTACCGTACTTTCAATTT-TTC
1 TATTTTGCTCACTGAACTTTCAATTTAATC
214068 TATTTTGCTCACTGAACTTT-ATATTTGAATC
1 TATTTTGCTCACTGAACTTTCA-ATTT-AATC
214099 -ATTTTGCTCACT
1 TATTTTGCTCACT
214111 CTGCCTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 1 0.03
29 21 0.58
30 12 0.33
31 2 0.06
ACGTcount: A:0.21, C:0.19, G:0.08, T:0.51
Consensus pattern (30 bp):
TATTTTGCTCACTGAACTTTCAATTTAATC
Found at i:221070 original size:16 final size:17
Alignment explanation
Indices: 221049--221081 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
221039 CCGTTTAGAG
221049 AATAAAAATA-GTCATT
1 AATAAAAATACGTCATT
*
221065 AATAAAACTACGTCATT
1 AATAAAAATACGTCATT
221082 TAATGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (17 bp):
AATAAAAATACGTCATT
Done.