Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024052.1 Corchorus olitorius cultivar O-4 contig24085, 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: 8209
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29


Found at i:78 original size:9 final size:9

Alignment explanation


    Indices: 64--194  Score: 54
    Period size: 9  Copynumber: 13.7  Consensus size: 9

         54 GAAAATTATT

                     
         64 TATAATATA
          1 TATAATATA

                        
         73 TATAATAAATTA
          1 TATAAT--A-TA

                     
         85 TATAATA-A
          1 TATAATATA

                *       
         93 TTCAGAATATGA
          1 -T-ATAATAT-A

                *    *
        105 TATATTACTT
          1 TATAATA-TA

                       
        115 TATAATAAATA
          1 TATAAT--ATA

                      
        126 ATATAATATA
          1 -TATAATATA

                     
        136 TATAATATA
          1 TATAATATA

                  *  
        145 TATAATTTA
          1 TATAATATA

            *      * 
        154 AATAA-AAA
          1 TATAATATA

                 *   
        162 TA-AAAATA
          1 TATAATATA

                *      
        170 CT-TCATAATA
          1 -TATAAT-ATA

                     
        180 TATAATATA
          1 TATAATATA

                  
        189 TATAAT
          1 TATAAT

        195 TTAAATAAAA


Statistics
Matches: 91,  Mismatches: 15, Indels: 32
        0.66            0.11        0.23

Matches are distributed among these distances:
   7    2  0.02
   8    5  0.05
   9   40  0.44
  10   24  0.26
  11    4  0.04
  12   16  0.18

ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40


Consensus pattern (9 bp):   
TATAATATA

Found at i:3156 original size:22 final size:22

Alignment explanation


    Indices: 3128--3176  Score: 64
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       3118 GAATAAAAGC

                     *   *         
       3128 ATCATGTCAGGCTGACT-ATCAT
          1 ATCATGTCAAGCTCA-TAATCAT

                                  
       3150 ATCATGTCAAGCTCATAATCAT
          1 ATCATGTCAAGCTCATAATCAT

                 
       3172 ATCAT
          1 ATCAT

       3177 ATTAATTTTA


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  21    1  0.04
  22   23  0.96

ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33


Consensus pattern (22 bp):   
ATCATGTCAAGCTCATAATCAT
Done.