Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001540.1 Corchorus capsularis cultivar CVL-1 contig01540, 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: 5097
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:457 original size:26 final size:26

Alignment explanation


    Indices: 421--563  Score: 254
    Period size: 26  Copynumber: 5.6  Consensus size: 26

        411 ATGTGCCGTA

                                      
        421 TCATGGCAACCAAGTCCCCACATGGC
          1 TCATGGCAACCAAGTCCCCACATGGC

                                 *    
        447 TCATGGCAACCAAGTCCCCACTTGGC
          1 TCATGGCAACCAAGTCCCCACATGGC

                                      
        473 TCATGGCAACCAAGTCCCCACATGGC
          1 TCATGGCAACCAAGTCCCCACATGGC

                                      
        499 TCATGGCAACCAAGT-CCC-CATGGC
          1 TCATGGCAACCAAGTCCCCACATGGC

                 *                    
        523 TCATGACAACCAAGTCCCCACATGGC
          1 TCATGGCAACCAAGTCCCCACATGGC

                           
        549 TCATGGCAACCAAGT
          1 TCATGGCAACCAAGT

        564 TAGGTCTCAC


Statistics
Matches: 111,  Mismatches: 4, Indels: 4
        0.93            0.03        0.03

Matches are distributed among these distances:
  24   20  0.18
  25    6  0.05
  26   85  0.77

ACGTcount: A:0.27, C:0.37, G:0.19, T:0.17


Consensus pattern (26 bp):   
TCATGGCAACCAAGTCCCCACATGGC

Found at i:549 original size:76 final size:78

Alignment explanation


    Indices: 421--563  Score: 254
    Period size: 76  Copynumber: 1.9  Consensus size: 78

        411 ATGTGCCGTA

                                           *               *                 
        421 TCATGGCAACCAAGTCCCCACATGGCTCATGGCAACCAAGTCCCCACTTGGCTCATGGCAACCAA
          1 TCATGGCAACCAAGTCCCCACATGGCTCATGACAACCAAGTCCCCACATGGCTCATGGCAACCAA

                         
        486 GTCCCCACATGGC
         66 GTCCCCACATGGC

                                                                             
        499 TCATGGCAACCAAGT-CCC-CATGGCTCATGACAACCAAGTCCCCACATGGCTCATGGCAACCAA
          1 TCATGGCAACCAAGTCCCCACATGGCTCATGACAACCAAGTCCCCACATGGCTCATGGCAACCAA

              
        562 GT
         66 GT

        564 TAGGTCTCAC


Statistics
Matches: 63,  Mismatches: 2, Indels: 2
        0.94            0.03        0.03

Matches are distributed among these distances:
  76   45  0.71
  77    3  0.05
  78   15  0.24

ACGTcount: A:0.27, C:0.37, G:0.19, T:0.17


Consensus pattern (78 bp):   
TCATGGCAACCAAGTCCCCACATGGCTCATGACAACCAAGTCCCCACATGGCTCATGGCAACCAA
GTCCCCACATGGC
Done.