Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018659.1 Corchorus olitorius cultivar O-4 contig18692, 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: 4025
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28


Found at i:3129 original size:77 final size:77

Alignment explanation


    Indices: 3002--3223  Score: 362
    Period size: 77  Copynumber: 2.9  Consensus size: 77

       2992 CAGGGCAGAG

                  *                                                          
       3002 GCCCGACTGCCGCTGGGCGCCCAGGCAGAACGCCCAAGCGCCCAGGCGACAGGCATCCAGAGCCC
          1 GCCCGATTGCCGCTGGGCGCCCAGGCAGAACGCCCAAGCGCCCAGGCGACAGGCATCCAGAGCCC

                        
       3067 AGCTAGAGCAAA
         66 AGCTAGAGCAAA

                                                                             
       3079 GCCCGATTGCCGCTGGGCGCCCAGGCAGAACGCCCAAGCGCCCAGGCGACAGGCATCCAGAGCCC
          1 GCCCGATTGCCGCTGGGCGCCCAGGCAGAACGCCCAAGCGCCCAGGCGACAGGCATCCAGAGCCC

                        
       3144 AGCTAGAGCAAA
         66 AGCTAGAGCAAA

                                           *                               * 
       3156 GCCCGATTGCCGCTGGGCGCCCAGGC-GAAATGCCTC-AGCGCCCAGGCGACAAGGC-T-CAGCG
          1 GCCCGATTGCCGCTGGGCGCCCAGGCAG-AACGCC-CAAGCGCCCAGGCGAC-AGGCATCCAGAG

                   
       3217 CCCAGCT
         63 CCCAGCT

       3224 CGATCCCTGA


Statistics
Matches: 139,  Mismatches: 3, Indels: 7
        0.93            0.02        0.05

Matches are distributed among these distances:
  76   12  0.09
  77  122  0.88
  78    5  0.04

ACGTcount: A:0.23, C:0.39, G:0.32, T:0.07


Consensus pattern (77 bp):   
GCCCGATTGCCGCTGGGCGCCCAGGCAGAACGCCCAAGCGCCCAGGCGACAGGCATCCAGAGCCC
AGCTAGAGCAAA

Found at i:3196 original size:21 final size:21

Alignment explanation


    Indices: 3172--3221  Score: 75
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       3162 TTGCCGCTGG

                                  
       3172 GCGCCCAGGCGA-AATGCCTCA
          1 GCGCCCAGGCGACAA-GCCTCA

                            *    
       3193 GCGCCCAGGCGACAAGGCTCA
          1 GCGCCCAGGCGACAAGCCTCA

                    
       3214 GCGCCCAG
          1 GCGCCCAG

       3222 CTCGATCCCT


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  21   25  0.93
  22    2  0.07

ACGTcount: A:0.22, C:0.40, G:0.32, T:0.06


Consensus pattern (21 bp):   
GCGCCCAGGCGACAAGCCTCA
Done.