Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008271.1 Hibiscus syriacus cultivar Beakdansim tig00110928_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: 134579
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 2 of 2
Found at i:129722 original size:19 final size:19
Alignment explanation
Indices: 129698--129737 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
129688 ACTTGGATTC
*
129698 AGATAGCTTTAAATCTTTA
1 AGATAGCTGTAAATCTTTA
* *
129717 AGATAGGTGTAACTCTTTA
1 AGATAGCTGTAAATCTTTA
129736 AG
1 AG
129738 TATTTTTGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (19 bp):
AGATAGCTGTAAATCTTTA
Found at i:129884 original size:17 final size:18
Alignment explanation
Indices: 129862--129895 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
129852 TGATGGATTC
129862 AGATAGCT-TAACTCTTA
1 AGATAGCTGTAACTCTTA
*
129879 AGATAGGTGTAACTCTT
1 AGATAGCTGTAACTCTT
129896 TAAGTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (18 bp):
AGATAGCTGTAACTCTTA
Found at i:130047 original size:18 final size:18
Alignment explanation
Indices: 130024--130061 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
130014 GACTGGATTC
*
130024 AGATAGCTTTAACTCTTA
1 AGATAGCTGTAACTCTTA
*
130042 AGATAGGTGTAACTCTTA
1 AGATAGCTGTAACTCTTA
130060 AG
1 AG
130062 TATTTTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (18 bp):
AGATAGCTGTAACTCTTA
Found at i:131592 original size:19 final size:19
Alignment explanation
Indices: 131568--131607 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
131558 AAAATGATTC
*
131568 AGATAGCTTTAACTCTTTA
1 AGATAGCTGTAACTCTTTA
*
131587 AGATAGGTGTAACTCTTTA
1 AGATAGCTGTAACTCTTTA
131606 AG
1 AG
131608 TATTTTGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (19 bp):
AGATAGCTGTAACTCTTTA
Found at i:131677 original size:19 final size:19
Alignment explanation
Indices: 131653--131692 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
131643 GACTGGATTC
*
131653 AGATAGCTTTAACTCTTTA
1 AGATAGCTGTAACTCTTTA
*
131672 AGATAGGTGTAACTCTTTA
1 AGATAGCTGTAACTCTTTA
131691 AG
1 AG
131693 TATTTTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (19 bp):
AGATAGCTGTAACTCTTTA
Found at i:132174 original size:18 final size:18
Alignment explanation
Indices: 132151--132188 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
132141 GACTGGATTC
*
132151 AGATAGCTTTAACTCTTA
1 AGATAGCTGTAACTCTTA
*
132169 AGATAGGTGTAACTCTTA
1 AGATAGCTGTAACTCTTA
132187 AG
1 AG
132189 TATTTTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (18 bp):
AGATAGCTGTAACTCTTA
Found at i:133147 original size:19 final size:19
Alignment explanation
Indices: 133123--133162 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
133113 GACTGGATTC
*
133123 AGATAGCTTTAACTCTTTA
1 AGATAGCTGTAACTCTTTA
*
133142 AGATAGGTGTAACTCTTTA
1 AGATAGCTGTAACTCTTTA
133161 AG
1 AG
133163 TATTTTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (19 bp):
AGATAGCTGTAACTCTTTA
Found at i:134043 original size:18 final size:18
Alignment explanation
Indices: 134020--134054 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
134010 AAATGGATTC
*
134020 AGATAGCTTTAACTCTTA
1 AGATAGCTGTAACTCTTA
*
134038 AGATAGGTGTAACTCTT
1 AGATAGCTGTAACTCTT
134055 TAAGTATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (18 bp):
AGATAGCTGTAACTCTTA
Found at i:134293 original size:19 final size:18
Alignment explanation
Indices: 134269--134307 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
134259 TGACTGATTC
*
134269 AGATAGCTTTAACTCTTTA
1 AGATAGCTGT-ACTCTTTA
*
134288 AGATAGGTGTACTCTTTA
1 AGATAGCTGTACTCTTTA
134306 AG
1 AG
134308 TTTTTTTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (18 bp):
AGATAGCTGTACTCTTTA
Done.