Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011289.1 Corchorus olitorius cultivar O-4 contig11322, 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: 6045
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:2017 original size:23 final size:24

Alignment explanation


    Indices: 1985--2035  Score: 79
    Period size: 23  Copynumber: 2.2  Consensus size: 24

       1975 TATTGAAAGG

                       *            
       1985 GAGA-GGTGAGGGCTTGGTAG-GA
          1 GAGAGGGTGAGAGCTTGGTAGAGA

                                    
       2007 GAGAGGGTGAGAGCTTGGTAGAGA
          1 GAGAGGGTGAGAGCTTGGTAGAGA

                 
       2031 GAGAG
          1 GAGAG

       2036 CTTGTGTGTC


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  22    4  0.15
  23   15  0.58
  24    7  0.27

ACGTcount: A:0.27, C:0.04, G:0.53, T:0.16


Consensus pattern (24 bp):   
GAGAGGGTGAGAGCTTGGTAGAGA

Found at i:4153 original size:27 final size:27

Alignment explanation


    Indices: 4109--4181  Score: 67
    Period size: 26  Copynumber: 2.7  Consensus size: 27

       4099 GAGTGGACTT

                       ***            *
       4109 AAAATGACCAATGCGCCCCTGAATATG
          1 AAAATGACCAAAATGCCCCTGAATATA

                                * * *  
       4136 AAAATGACCAAAATG-CCCTTAGTGTA
          1 AAAATGACCAAAATGCCCCTGAATATA

                          *     
       4162 AAAATGACCAAAATACCCCT
          1 AAAATGACCAAAATGCCCCT

       4182 AAGTGACCCT


Statistics
Matches: 37,  Mismatches: 8, Indels: 2
        0.79            0.17        0.04

Matches are distributed among these distances:
  26   21  0.57
  27   16  0.43

ACGTcount: A:0.42, C:0.25, G:0.14, T:0.19


Consensus pattern (27 bp):   
AAAATGACCAAAATGCCCCTGAATATA
Done.