Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016160.1 Corchorus olitorius cultivar O-4 contig16193, 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: 18546
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30


Found at i:11 original size:2 final size:2

Alignment explanation


    Indices: 5--70  Score: 132
    Period size: 2  Copynumber: 33.0  Consensus size: 2

          1 TCTG

                                                                          
          5 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

                                               
         47 CT CT CT CT CT CT CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT

         71 AGTGTGGCTT


Statistics
Matches: 64,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   64  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
CT

Found at i:908 original size:21 final size:21

Alignment explanation


    Indices: 866--928  Score: 74
    Period size: 21  Copynumber: 3.0  Consensus size: 21

        856 AGGGAGATTA

                   *   *   *     
        866 ACAAAATCTCAGAGGGAGGTT
          1 ACAAAATATCATAGGAAGGTT

                                  
        887 ATCAAAA-ATCATAGGAAGGTT
          1 A-CAAAATATCATAGGAAGGTT

                   *             
        908 ACAAAATTTCATAGGAAGGTT
          1 ACAAAATATCATAGGAAGGTT

        929 TATTACAATT


Statistics
Matches: 36,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
  20    5  0.14
  21   26  0.72
  22    5  0.14

ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24


Consensus pattern (21 bp):   
ACAAAATATCATAGGAAGGTT

Found at i:960 original size:22 final size:22

Alignment explanation


    Indices: 867--1052  Score: 148
    Period size: 22  Copynumber: 8.5  Consensus size: 22

        857 GGGAGATTAA

                  *   *   *       
        867 CAAAATCTCAGAGGGAGGTTAT
          1 CAAAATTTCATAGGTAGGTTAT

                  *       *       
        889 CAAAA-ATCATAGGAAGGTTA-
          1 CAAAATTTCATAGGTAGGTTAT

                          *        
        909 CAAAATTTCATAGGAAGGTTTAT
          1 CAAAATTTCATAGGTAGG-TTAT

            * *          *        
        932 TACAATTTCATAGTTAGGTTAT
          1 CAAAATTTCATAGGTAGGTTAT

                              *    
        954 CAAAATTTCATATGG-AGTTTAT
          1 CAAAATTTCATA-GGTAGGTTAT

              *              *    
        976 CACAATTTCATAGGTA-ATTAT
          1 CAAAATTTCATAGGTAGGTTAT

                   *     * * *    
        997 CAAAATTCCATAGCTTGATTAT
          1 CAAAATTTCATAGGTAGGTTAT

                    *              
       1019 CAAAATTTAATAGGGTA-GTTAT
          1 CAAAATTTCATA-GGTAGGTTAT

            *           
       1041 GAAAATTTCATA
          1 CAAAATTTCATA

       1053 AAAATATTCA


Statistics
Matches: 132,  Mismatches: 25, Indels: 14
        0.77            0.15        0.08

Matches are distributed among these distances:
  20    5  0.04
  21   41  0.31
  22   69  0.52
  23   17  0.13

ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34


Consensus pattern (22 bp):   
CAAAATTTCATAGGTAGGTTAT

Found at i:17917 original size:12 final size:12

Alignment explanation


    Indices: 17900--17924  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      17890 AGTTGTAATA

                        
      17900 TTTATTATTATT
          1 TTTATTATTATT

                        
      17912 TTTATTATTATT
          1 TTTATTATTATT

             
      17924 T
          1 T

      17925 ATTAATGTAT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76


Consensus pattern (12 bp):   
TTTATTATTATT
Done.