Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020011.1 Corchorus olitorius cultivar O-4 contig20044, 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: 14507
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:2425 original size:29 final size:29

Alignment explanation


    Indices: 2385--2452  Score: 127
    Period size: 29  Copynumber: 2.3  Consensus size: 29

       2375 GCAAATAATA

                                         
       2385 TTTTCAATTTGGTCCTAACATTTTTCAAT
          1 TTTTCAATTTGGTCCTAACATTTTTCAAT

                            *            
       2414 TTTTCAATTTGGTCCTTACATTTTTCAAT
          1 TTTTCAATTTGGTCCTAACATTTTTCAAT

                      
       2443 TTTTCAATTT
          1 TTTTCAATTT

       2453 CATATGTCTG


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  29   38  1.00

ACGTcount: A:0.22, C:0.16, G:0.06, T:0.56


Consensus pattern (29 bp):   
TTTTCAATTTGGTCCTAACATTTTTCAAT

Found at i:8855 original size:27 final size:27

Alignment explanation


    Indices: 8825--8947  Score: 176
    Period size: 27  Copynumber: 4.6  Consensus size: 27

       8815 GATCATCTAA

                             * *        
       8825 GGGCATTTTGGTCATTTTTACAC-CTAG
          1 GGGCATTTTGGTCATTTATGCACTC-AG

                                    *  
       8852 GGGCATTTTGGTCATTTATGCACTTAG
          1 GGGCATTTTGGTCATTTATGCACTCAG

                      *                
       8879 GGGCATTTTGTTCATTTATGCACTCAG
          1 GGGCATTTTGGTCATTTATGCACTCAG

                             *    *    
       8906 GGGCATTTTGGTCATTTGTGCATTCAG
          1 GGGCATTTTGGTCATTTATGCACTCAG

                           
       8933 GGGCATTTTGGTCAT
          1 GGGCATTTTGGTCAT

       8948 GCTCTAGGTT


Statistics
Matches: 87,  Mismatches: 8, Indels: 2
        0.90            0.08        0.02

Matches are distributed among these distances:
  27   87  1.00

ACGTcount: A:0.17, C:0.16, G:0.26, T:0.41


Consensus pattern (27 bp):   
GGGCATTTTGGTCATTTATGCACTCAG

Found at i:13693 original size:15 final size:15

Alignment explanation


    Indices: 13673--13704  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      13663 TACTCGGGTA

                        *  
      13673 CGAATTCTTGGTCCC
          1 CGAATTCTTGGTACC

                           
      13688 CGAATTCTTGGTACC
          1 CGAATTCTTGGTACC

              
      13703 CG
          1 CG

      13705 CTCCGAGACT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.16, C:0.31, G:0.22, T:0.31


Consensus pattern (15 bp):   
CGAATTCTTGGTACC
Done.