Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013011.1 Corchorus olitorius cultivar O-4 contig13044, 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: 11977
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:10631 original size:43 final size:43

Alignment explanation


    Indices: 10572--10817  Score: 315
    Period size: 41  Copynumber: 5.8  Consensus size: 43

      10562 CCAATAACCA

                                           *           
      10572 AAAGTCCCCAAACACATATATAACACAGGGGTATCTCTATTCC
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC

                   **                   *               
      10615 AAAGTCCTTAAACACATATATAACACAGAGGCA-C-CTATATCC
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTAT-TCC

                    *                        *       * 
      10657 -AAGTCCCAAAACACATATATAACACAGGGGCAACTCTATTAC
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC

                   *                    *               
      10699 AAAGTCCTCAAACACATATATAACACAGAGGCAT-T-TATAT-C
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTAT-TCC

                                                       *
      10740 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATT-CC

                   *                    *     
      10784 AAAGTCCTCAAACACATATATAACACAGAGGCAT
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAT

      10818 TTCTCCTTAT


Statistics
Matches: 177,  Mismatches: 17, Indels: 17
        0.84            0.08        0.08

Matches are distributed among these distances:
  41   69  0.39
  42   11  0.06
  43   65  0.37
  44   32  0.18

ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21


Consensus pattern (43 bp):   
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC

Found at i:10673 original size:84 final size:84

Alignment explanation


    Indices: 10572--10816  Score: 400
    Period size: 84  Copynumber: 2.9  Consensus size: 84

      10562 CCAATAACCA

                                           *                   *             
      10572 AAAGTCCCCAAACACATATATAACACAGGGGTATCTCTATTCCAAAGTCCTTAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA

                               
      10637 ACACAGAGGCACCTATATC
         66 ACACAGAGGCACCTATATC

            *       *                        *       *                       
      10656 CAAGTCCCAAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA

                       **      
      10721 ACACAGAGGCATTTATATC
         66 ACACAGAGGCACCTATATC

                                                       *                     
      10740 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATT-CCAAAGTCCTCAAACACATATAT

                        
      10805 AACACAGAGGCA
         65 AACACAGAGGCA

      10817 TTTCTCCTTA


Statistics
Matches: 147,  Mismatches: 13, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
  84  114  0.78
  85   33  0.22

ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21


Consensus pattern (84 bp):   
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
ACACAGAGGCACCTATATC
Done.