Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000613.1 Corchorus olitorius cultivar O-4 contig00613, 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: 8661
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31


Found at i:5564 original size:31 final size:31

Alignment explanation


    Indices: 5459--5597  Score: 143
    Period size: 31  Copynumber: 4.5  Consensus size: 31

       5449 GGTGTCCGAC

                                     *     
       5459 GTGGCATGCCACGTGTACCAAAAAGCGACAT
          1 GTGGCATGCCACGTGTACCAAAAAGTGACAT

               *  *       *                
       5490 GTGACACGCCACGTATACCAAAAAGTGACAT
          1 GTGGCATGCCACGTGTACCAAAAAGTGACAT

              **  **   *                  *
       5521 GTATCACACCATGTGTACCAAAAAGTGACAA
          1 GTGGCATGCCACGTGTACCAAAAAGTGACAT

                *      *    **            *
       5552 GTGGTATGCCATGTGTTTCAAAAAGTGACAC
          1 GTGGCATGCCACGTGTACCAAAAAGTGACAT

                           
       5583 GTGGCATGCCACGTG
          1 GTGGCATGCCACGTG

       5598 CACAAAAGGA


Statistics
Matches: 88,  Mismatches: 20, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  31   88  1.00

ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20


Consensus pattern (31 bp):   
GTGGCATGCCACGTGTACCAAAAAGTGACAT

Found at i:6983 original size:54 final size:54

Alignment explanation


    Indices: 6884--6990  Score: 169
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       6874 TCTTCAGGTT

                *                  *                              
       6884 CAGGTCATTAGGCTCAATTTTATGAAAAGGAGCCCAATCAGAATAACAGGGAAA
          1 CAGGACATTAGGCTCAATTTTATCAAAAGGAGCCCAATCAGAATAACAGGGAAA

                     *                            * *            
       6938 CAGGACATTGGGCTCAATTTTATCAAAAGGAGCCCAATGATAATAACAGGGAA
          1 CAGGACATTAGGCTCAATTTTATCAAAAGGAGCCCAATCAGAATAACAGGGAA

       6991 GCAGTGAATA


Statistics
Matches: 48,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  54   48  1.00

ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21


Consensus pattern (54 bp):   
CAGGACATTAGGCTCAATTTTATCAAAAGGAGCCCAATCAGAATAACAGGGAAA
Done.