Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013019.1 Corchorus olitorius cultivar O-4 contig13052, 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: 10083
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32


Found at i:4777 original size:22 final size:22

Alignment explanation


    Indices: 4759--5348  Score: 208
    Period size: 22  Copynumber: 26.7  Consensus size: 22

       4749 ATACATAGGA

                   *  *           
       4759 AGGTTATTAATATTTCATAGTG
          1 AGGTTATCAAAATTTCATAGTG

            *     *                
       4781 TGGTTACCAAAATTTCATA-TGG
          1 AGGTTATCAAAATTTCATAGT-G

                        *         
       4803 AGGTTATCAAAACTTCATAGTG
          1 AGGTTATCAAAATTTCATAGTG

                    *  *    *       
       4825 TA-GTTATTAATATTTTAT-GTAG
          1 -AGGTTATCAAAATTTCATAGT-G

             **          *      ***
       4847 AAATTA-CAAAAAATTCATAAAA
          1 AGGTTATC-AAAATTTCATAGTG

                            *   * 
       4869 AGGTTATCAAAATTTCTTAGAG
          1 AGGTTATCAAAATTTCATAGTG

             *    *        *      *
       4891 ATGTTAACAAAATTTTATACG-A
          1 AGGTTATCAAAATTTCATA-GTG

                    * *    *      
       4913 AGGTTATCGATATTTTATAGTG
          1 AGGTTATCAAAATTTCATAGTG

            *              *      
       4935 CGGTTATCAAAATTTTATAG-G
          1 AGGTTATCAAAATTTCATAGTG

             *    *             * 
       4956 ATGTTAACAAAATTTCATAGGG
          1 AGGTTATCAAAATTTCATAGTG

                      *               
       4978 AGGGATGTTACCAAAA-TT--T-GT-
          1 A--G--GTTATCAAAATTTCATAGTG

              *             *   * 
       4999 -GCTTATCAAAATTTCCTAGAG
          1 AGGTTATCAAAATTTCATAGTG

                  *      *      * 
       5020 AGGTTAACAAAATGTCATAGGG
          1 AGGTTATCAAAATTTCATAGTG

              *    *       * ** * 
       5042 AGATTATGAAAATTTTACGGAG
          1 AGGTTATCAAAATTTCATAGTG

             *            *     **
       5064 ATGTTATCAAAATTACATAGAA
          1 AGGTTATCAAAATTTCATAGTG

               *                         
       5086 AGGATATCACAATTTCATTCTCATA-TGG
          1 AGGTTATCA-AA----ATT-TCATAGT-G

                        *          
       5114 AGGTTATCAAATTTTTCATAGTG
          1 AGGTTATCAAA-ATTTCATAGTG

            *        *     *      
       5137 TGGTTA-C-CAATTTTATAGTG
          1 AGGTTATCAAAATTTCATAGTG

            * *  *         *       
       5157 TGATTTTCAAAATTTAATACG-G
          1 AGGTTATCAAAATTTCATA-GTG

              *      *       * *  
       5179 AGATTATCACAATTTCACACT-
          1 AGGTTATCAAAATTTCATAGTG

                                   
       5200 ATGGTTATCAAAATTTCATAGTG
          1 A-GGTTATCAAAATTTCATAGTG

            *                     
       5223 TGGTTATCAAAATTTCATAGTG
          1 AGGTTATCAAAATTTCATAGTG

            *                *    
       5245 GGGTTATCAAAATTTCACAGTG
          1 AGGTTATCAAAATTTCATAGTG

            *          *           
       5267 TGGTTATCAAATTTTCATAAG-G
          1 AGGTTATCAAAATTTCAT-AGTG

            *       * *    *   ** 
       5289 TGGTTATCCAGATTTTATAACG
          1 AGGTTATCAAAATTTCATAGTG

                       *     *    
       5311 AGGTTATCAAATTTTCACAGTG
          1 AGGTTATCAAAATTTCATAGTG

            * *       *     
       5333 TGATTATCAATATTTC
          1 AGGTTATCAAAATTTC

       5349 TATGTTGGAG


Statistics
Matches: 413,  Mismatches: 118, Indels: 74
        0.68            0.20        0.12

Matches are distributed among these distances:
  16    8  0.02
  17    2  0.00
  18    1  0.00
  19    1  0.00
  20   14  0.03
  21   26  0.06
  22  309  0.75
  23   21  0.05
  24    3  0.01
  25    2  0.00
  26    9  0.02
  27    5  0.01
  28   12  0.03

ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37


Consensus pattern (22 bp):   
AGGTTATCAAAATTTCATAGTG

Found at i:6642 original size:19 final size:18

Alignment explanation


    Indices: 6618--6663  Score: 56
    Period size: 19  Copynumber: 2.4  Consensus size: 18

       6608 AAAAATCCCG

                               
       6618 AAAAAAAAACATAAAAAAT
          1 AAAAAAAAA-ATAAAAAAT

                           *   
       6637 AAAAAAGAAAATAAATAAT
          1 AAAAAA-AAAATAAAAAAT

                    
       6656 AAATAAAA
          1 AAA-AAAA

       6664 GTAATATCAG


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  19   18  0.75
  20    6  0.25

ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13


Consensus pattern (18 bp):   
AAAAAAAAAATAAAAAAT
Done.