Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019123.1 Corchorus olitorius cultivar O-4 contig19156, 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: 22087
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29


Found at i:1813 original size:51 final size:51

Alignment explanation


    Indices: 1737--1843  Score: 205
    Period size: 51  Copynumber: 2.1  Consensus size: 51

       1727 ATCTGGTATT

                                              *                
       1737 GGAAACACTGGCTCAAAAGGAAAGTTATTGAATGGAAGCGGTTTTTCAGGA
          1 GGAAACACTGGCTCAAAAGGAAAGTTATTGAATGAAAGCGGTTTTTCAGGA

                                                               
       1788 GGAAACACTGGCTCAAAAGGAAAGTTATTGAATGAAAGCGGTTTTTCAGGA
          1 GGAAACACTGGCTCAAAAGGAAAGTTATTGAATGAAAGCGGTTTTTCAGGA

                 
       1839 GGAAA
          1 GGAAA

       1844 TCATGGCGAT


Statistics
Matches: 55,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  51   55  1.00

ACGTcount: A:0.37, C:0.11, G:0.29, T:0.22


Consensus pattern (51 bp):   
GGAAACACTGGCTCAAAAGGAAAGTTATTGAATGAAAGCGGTTTTTCAGGA

Found at i:4689 original size:16 final size:16

Alignment explanation


    Indices: 4668--4709  Score: 75
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       4658 ACTGTTTGGA

                            
       4668 AAAGCGAACAGTGCTG
          1 AAAGCGAACAGTGCTG

                            
       4684 AAAGCGAACAGTGCTG
          1 AAAGCGAACAGTGCTG

                 *    
       4700 AAAGCAAACA
          1 AAAGCGAACA

       4710 AGTGAAGGAC


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  16   25  1.00

ACGTcount: A:0.45, C:0.19, G:0.26, T:0.10


Consensus pattern (16 bp):   
AAAGCGAACAGTGCTG

Found at i:22042 original size:2 final size:2

Alignment explanation


    Indices: 22035--22082  Score: 89
    Period size: 2  Copynumber: 24.5  Consensus size: 2

      22025 TAAGGCAAGA

                                                                          
      22035 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

                      
      22077 AG -G AG A
          1 AG AG AG A

      22083 AGAAA


Statistics
Matches: 45,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
   1    1  0.02
   2   44  0.98

ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00


Consensus pattern (2 bp):   
AG

Done.