Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022748.1 Corchorus olitorius cultivar O-4 contig22781, 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: 6773
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26


Found at i:5734 original size:35 final size:35

Alignment explanation


    Indices: 5688--6062  Score: 617
    Period size: 35  Copynumber: 10.7  Consensus size: 35

       5678 CTCAGGAATA

                                               
       5688 CAGATGACTCGGTGCAGCATCTTCAAAGACAAATT
          1 CAGATGACTCGGTGCAGCATCTTCAAAGACAAATT

                            *                 *
       5723 CAGATGACTCGGTGCAACATCTTCAAAGACAAATC
          1 CAGATGACTCGGTGCAGCATCTTCAAAGACAAATT

                                              *
       5758 CAGATGACTCGGTGCAGCATCTTCAAAGACAAATA
          1 CAGATGACTCGGTGCAGCATCTTCAAAGACAAATT

                            *                 *
       5793 CAGATGACTCGGTGCAACATCTTCAAAGACAAATC
          1 CAGATGACTCGGTGCAGCATCTTCAAAGACAAATT

                                *              
       5828 CAGATGACTCGGTGCAGCATTTTCAAAGACAAATT
          1 CAGATGACTCGGTGCAGCATCTTCAAAGACAAATT

                          *                    
       5863 CAGATGACTCGGTGTAGCATCTTCAAAGACAAATT
          1 CAGATGACTCGGTGCAGCATCTTCAAAGACAAATT

                                          *    
       5898 CAGATGACTCGGTGCAGCATCTTCAAAGACGAATT
          1 CAGATGACTCGGTGCAGCATCTTCAAAGACAAATT

                          *                    
       5933 CAGATGACTCGGTGTAGCATCTTCAAAGAC-AATT
          1 CAGATGACTCGGTGCAGCATCTTCAAAGACAAATT

                                          *    
       5967 CAGATGACTCGGTGCAGCATCTTCAAAGACGAATT
          1 CAGATGACTCGGTGCAGCATCTTCAAAGACAAATT

                          *                  * 
       6002 CAGATGACTCGGTGTAGCATCTTCAAAGACAAAGT
          1 CAGATGACTCGGTGCAGCATCTTCAAAGACAAATT

                       *  *           
       6037 CAGATGACTCGATGTAGCATCTTCAA
          1 CAGATGACTCGGTGCAGCATCTTCAA

       6063 TACGAACTCA


Statistics
Matches: 320,  Mismatches: 19, Indels: 2
        0.94            0.06        0.01

Matches are distributed among these distances:
  34   33  0.10
  35  287  0.90

ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23


Consensus pattern (35 bp):   
CAGATGACTCGGTGCAGCATCTTCAAAGACAAATT

Found at i:6413 original size:29 final size:29

Alignment explanation


    Indices: 6315--6410  Score: 167
    Period size: 29  Copynumber: 3.3  Consensus size: 29

       6305 TAGGGTCACT

                                         
       6315 CATCCAGGGGCATTTTGGTCATTTTTGCA
          1 CATCCAGGGGCATTTTGGTCATTTTTGCA

                                         
       6344 CATCCAGGGGCATTTTGGTCA-TTTTGCA
          1 CATCCAGGGGCATTTTGGTCATTTTTGCA

                      *                  
       6372 CATCCAGGGGTATTTTGGTCATTTTTGCA
          1 CATCCAGGGGCATTTTGGTCATTTTTGCA

                *     
       6401 CATCTAGGGG
          1 CATCCAGGGG

       6411 TATCTCAGTC


Statistics
Matches: 64,  Mismatches: 2, Indels: 2
        0.94            0.03        0.03

Matches are distributed among these distances:
  28   27  0.42
  29   37  0.58

ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36


Consensus pattern (29 bp):   
CATCCAGGGGCATTTTGGTCATTTTTGCA

Done.