Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011387.1 Corchorus capsularis cultivar CVL-1 contig11408, 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: 9212
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:8939 original size:51 final size:50

Alignment explanation


    Indices: 8884--9168  Score: 238
    Period size: 51  Copynumber: 5.6  Consensus size: 50

       8874 AAAAATCAAA

                        *      *                               
       8884 TGAGTCTATAGGTTTTTAATAATAAAAATTAAATCTTTATGTAGTAAGGGT
          1 TGAGTCTATA-GATTTTAACAATAAAAATTAAATCTTTATGTAGTAAGGGT

                                       *                      * 
       8935 TGAGTTCTA-ATGATTTTAACAATAAAGATTAAATCTTTATGTAGTAAGGAT
          1 TGAG-TCTATA-GATTTTAACAATAAAAATTAAATCTTTATGTAGTAAGGGT

                   *           * *         *       * *        * 
       8986 TGAGTTCAAGTA-ATTTTAGCCATAAAAATTGAATCTTTGTATAGTAAGGAT
          1 TGAG-TCTA-TAGATTTTAACAATAAAAATTAAATCTTTATGTAGTAAGGGT

                               * *         * *              *   
       9037 TGAGTTCTAGTA-ATTTTAGCCATAAAAATTGAGTCTTTATGTAGTAAAGGT
          1 TGAG-TCTA-TAGATTTTAACAATAAAAATTAAATCTTTATGTAGTAAGGGT

             *                  *                            *  
       9088 TAAGTGCTAGTA-ATTTTAATAATAAAAATTAAATCTTTATGTAGTAAGAGT
          1 TGAGT-CTA-TAGATTTTAACAATAAAAATTAAATCTTTATGTAGTAAGGGT

              *    *        *              
       9139 TGGGT-TTTAGTAATTCTAACAATAAAAATT
          1 TGAGTCTATAG--ATTTTAACAATAAAAATT

       9169 GAGTCTTGAT


Statistics
Matches: 196,  Mismatches: 31, Indels: 14
        0.81            0.13        0.06

Matches are distributed among these distances:
  48    2  0.01
  49    1  0.01
  50    1  0.01
  51  187  0.95
  52    4  0.02
  53    1  0.01

ACGTcount: A:0.38, C:0.06, G:0.16, T:0.39


Consensus pattern (50 bp):   
TGAGTCTATAGATTTTAACAATAAAAATTAAATCTTTATGTAGTAAGGGT

Found at i:9169 original size:102 final size:101

Alignment explanation


    Indices: 8897--9175  Score: 344
    Period size: 102  Copynumber: 2.7  Consensus size: 101

       8887 GTCTATAGGT

                                                           * *              *
       8897 TTTTAATAATAAAAATTAAATCTTTATGTAGTAAGGGTTGAGTTCTAATGATTTTAACAATAAAG
          1 TTTTAATAATAAAAATTAAATCTTTATGTAGTAA-GGTTGAGTTCTAGTAATTTTAACAATAAAA

               * *                   *   *       
       8962 ATTAAATCTTTATGTAGTAAGGATTGAGTTCAAGTAA
         65 ATTGAGTCTTTATGTAGTAAGGATTAAGTGCAAGTAA

                 ***         *       * *                            * *      
       8999 TTTTAGCCATAAAAATTGAATCTTTGTATAGTAAGGATTGAGTTCTAGTAATTTTAGCCATAAAA
          1 TTTTAATAATAAAAATTAAATCTTTATGTAGTAAGG-TTGAGTTCTAGTAATTTTAACAATAAAA

                                            *     
       9064 ATTGAGTCTTTATGTAGTAAAGG-TTAAGTGCTAGTAA
         65 ATTGAGTCTTTATGTAGT-AAGGATTAAGTGCAAGTAA

                                                    *   *        *           
       9101 TTTTAATAATAAAAATTAAATCTTTATGTAGTAAGAGTTGGGTTTTAGTAATTCTAACAATAAAA
          1 TTTTAATAATAAAAATTAAATCTTTATGTAGTAAG-GTTGAGTTCTAGTAATTTTAACAATAAAA

                      
       9166 ATTGAGTCTT
         65 ATTGAGTCTT

       9176 GATGGTTTTA


Statistics
Matches: 147,  Mismatches: 27, Indels: 6
        0.82            0.15        0.03

Matches are distributed among these distances:
 101    2  0.01
 102  140  0.95
 103    5  0.03

ACGTcount: A:0.38, C:0.06, G:0.16, T:0.39


Consensus pattern (101 bp):   
TTTTAATAATAAAAATTAAATCTTTATGTAGTAAGGTTGAGTTCTAGTAATTTTAACAATAAAAA
TTGAGTCTTTATGTAGTAAGGATTAAGTGCAAGTAA
Done.