Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000946.1 Corchorus olitorius cultivar O-4 contig00946, 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, 822

Length: 1370
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36


Found at i:758 original size:22 final size:22

Alignment explanation


    Indices: 740--1370  Score: 262
    Period size: 22  Copynumber: 28.7  Consensus size: 22

        730 ATACATAGGA

                      *           
        740 AGGTTATCAATATTTCATAGTG
          1 AGGTTATCAAAATTTCATAGTG

            *     *                
        762 TGGTTACCAAAATTTCATA-TGG
          1 AGGTTATCAAAATTTCATAGT-G

                        *         
        784 AGGTTATCAAAACTTCATAGTG
          1 AGGTTATCAAAATTTCATAGTG

                            *       
        806 TA-GTTATCAAAATTTTATA-TAG
          1 -AGGTTATCAAAATTTCATAGT-G

             **                 ***
        828 AAATTA-CAAAAATTTCATAAAA
          1 AGGTTATC-AAAATTTCATAGTG

              *            **   * 
        850 AGATTATCAAAATTTTTTAGAG
          1 AGGTTATCAAAATTTCATAGTG

             **   *  *            *
        872 ATATTAACATAATTTCATACG-A
          1 AGGTTATCAAAATTTCATA-GTG

                    * *    *      
        894 AGGTTATCGATATTTTATAGTG
          1 AGGTTATCAAAATTTCATAGTG

            *              *       
        916 TGGTTATCAAAATTTTATAAGT-
          1 AGGTTATCAAAATTTCAT-AGTG

             *    *             * 
        938 ATGTTAACAAAATTTCATAGGG
          1 AGGTTATCAAAATTTCATAGTG

                                      
        960 AGGGATGTTATCAAAA-TT--T-GT-
          1 A--G--GTTATCAAAATTTCATAGTG

              *             *   * 
        981 -GCTTATCAAAATTTCCTAGAG
          1 AGGTTATCAAAATTTCATAGTG

                     *   *      * 
       1002 AGGTTA--ACAATGTCATAGGG
          1 AGGTTATCAAAATTTCATAGTG

              *    *       * ** * 
       1022 AGATTATGAAAATTTTACGGAG
          1 AGGTTATCAAAATTTCATAGTG

             *            *     **
       1044 ATGTTATCAAAATTACATAGAA
          1 AGGTTATCAAAATTTCATAGTG

               *                         
       1066 AGGATATCACAATTTCATTCTCATA-TAG
          1 AGGTTATCA-AA----ATT-TCATAGT-G

                    *         *   
       1094 AGGTTATCGAAATTTCATGGTG
          1 AGGTTATCAAAATTTCATAGTG

               *            *       
       1116 TA-ATTA-CAAAATTTTATGAG-G
          1 -AGGTTATCAAAATTTCAT-AGTG

                                   
       1137 AGGTTATCAAAATTTTCATAGTG
          1 AGGTTATCAAAA-TTTCATAGTG

            *        *     *      
       1160 TGGTTA-C-CAATTTTATAGTG
          1 AGGTTATCAAAATTTCATAGTG

            ***                    
       1180 TCATTATCAAAATTTCATGAG-G
          1 AGGTTATCAAAATTTCAT-AGTG

              *    * *       * *  
       1202 AGATTATTACAATTTCACACTG
          1 AGGTTATCAAAATTTCATAGTG

                                  
       1224 AGGTTATCAAAATTTCATAGTG
          1 AGGTTATCAAAATTTCATAGTG

            *                     
       1246 TGGTTATCAAAATTTCATAGTG
          1 AGGTTATCAAAATTTCATAGTG

                             *    
       1268 AGGTTATCAAAATTTCACAGTG
          1 AGGTTATCAAAATTTCATAGTG

            *          *           
       1290 TGGTTATCAAATTTTCATAAG-G
          1 AGGTTATCAAAATTTCAT-AGTG

            *       * *        *  
       1312 TGGTTATCCAGATTTCATAATG
          1 AGGTTATCAAAATTTCATAGTG

                       *     *    
       1334 AGGTTATCAAATTTTCACAGTG
          1 AGGTTATCAAAATTTCATAGTG

            * *       *    
       1356 TGATTATCAATATTT
          1 AGGTTATCAAAATTT


Statistics
Matches: 449,  Mismatches: 116, Indels: 88
        0.69            0.18        0.13

Matches are distributed among these distances:
  16    9  0.02
  17    2  0.00
  18    1  0.00
  19    1  0.00
  20   30  0.07
  21   25  0.06
  22  324  0.72
  23   30  0.07
  25    2  0.00
  26    9  0.02
  27    5  0.01
  28   11  0.02

ACGTcount: A:0.36, C:0.10, G:0.16, T:0.37


Consensus pattern (22 bp):   
AGGTTATCAAAATTTCATAGTG

Done.