Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016221.1 Corchorus olitorius cultivar O-4 contig16254, 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: 5955
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36


Found at i:3774 original size:22 final size:22

Alignment explanation


    Indices: 3749--4157  Score: 143
    Period size: 22  Copynumber: 18.5  Consensus size: 22

       3739 AAAATCAAAC

                   *   *          
       3749 CAAAATTACATGAGAAGGTTAT
          1 CAAAATTTCATAAGAAGGTTAT

                                  *
       3771 CAAAATTTCATACAGAA-GTTAC
          1 CAAAATTTCATA-AGAAGGTTAT

                         *        
       3793 CAAAATTTCATAAAAAGGTTAT
          1 CAAAATTTCATAAGAAGGTTAT

                       *        *  
       3815 CAAAATTTC-TTAG--GGATAAT
          1 CAAAATTTCATAAGAAGG-TTAT

                  *                
       3835 -AAAATATCATACA-AAGGTTAT
          1 CAAAATTTCATA-AGAAGGTTAT

             *      *    * *       
       3856 CGAAATTTTATAGTGTA-GTTAT
          1 CAAAATTTCATA-AGAAGGTTAT

                    *            *
       3878 CAAAATTTAATAAGAAGGTTAA
          1 CAAAATTTCATAAGAAGGTTAT

                                      
       3900 CAAAATTTCATAGGGAGGAAGGTTAT
          1 CAAAATTTCATA---A-GAAGGTTAT

                           * *    
       3926 CAAAA-TT--T--G-TGCTTAT
          1 CAAAATTTCATAAGAAGGTTAT

            *        *   *       *
       3942 TAAAATTTCCTAAAAAGGTTAA
          1 CAAAATTTCATAAGAAGGTTAT

                        * *       
       3964 CAAAATTTCATAGGGAGGTTAT
          1 CAAAATTTCATAAGAAGGTTAT

            *       *   *          
       3986 GAAAATTTTAT-GGAGAGGTTAT
          1 CAAAATTTCATAAGA-AGGTTAT

                                *   
       4008 CAAAATTAT-ATAGAGAA-GATAT
          1 CAAAATT-TCATA-AGAAGGTTAT

                   **         * *       
       4030 CACGGTTTCATTCTCATAGGGAGGTTAT
          1 CA-----AAATT-TCATAAGAAGGTTAT

             *          *  **      
       4058 CTAAATTTCAT-GGTGTGGTTAT
          1 CAAAATTTCATAAG-AAGGTTAT

                    *  *  *  *    
       4080 CAAAATTTTATGAGGAGCTTAT
          1 CAAAATTTCATAAGAAGGTTAT

                    *   * *  *    
       4102 CAAAATTTTATAGGGAGATTAT
          1 CAAAATTTCATAAGAAGGTTAT

                      *            
       4124 CAAAATTTCACAATGAA-GTTAT
          1 CAAAATTTCATAA-GAAGGTTAT

                        
       4146 CAAAATTTCATA
          1 CAAAATTTCATA

       4158 GTGTGGTTAT


Statistics
Matches: 286,  Mismatches: 67, Indels: 68
        0.68            0.16        0.16

Matches are distributed among these distances:
  16    9  0.03
  17    3  0.01
  19   10  0.03
  20    4  0.01
  21   15  0.05
  22  199  0.70
  23   14  0.05
  24    2  0.01
  25    3  0.01
  26   13  0.05
  27    6  0.02
  28    8  0.03

ACGTcount: A:0.41, C:0.09, G:0.16, T:0.33


Consensus pattern (22 bp):   
CAAAATTTCATAAGAAGGTTAT

Found at i:4133 original size:94 final size:94

Alignment explanation


    Indices: 3957--4133  Score: 216
    Period size: 94  Copynumber: 1.9  Consensus size: 94

       3947 TTTCCTAAAA

                                         *                *                  
       3957 AGGTTAACAAAATTTCATAGGGAGGTTATGAAAATTTTATGGAGAGGTTATCAAAATTATATAGA
          1 AGGTTAACAAAATTTCATAGGGAGGTTATCAAAATTTTATGGAGAGCTTATCAAAATTATATAGA

                      ***                
       4022 GAAGATATCACGGTTTCATTCTCATAGGG
         66 GAAGATATCAAAATTTCATTCTCATAGGG

                  * *              *                                    *    
       4051 AGGTTATCTAAATTTCAT-GGTGTGGTTATCAAAATTTTAT-GAGGAGCTTATCAAAATTTTATA
          1 AGGTTAACAAAATTTCATAGG-GAGGTTATCAAAATTTTATGGA-GAGCTTATCAAAATTATATA

               *                 
       4114 G-GGAGATTATCAAAATTTCA
         64 GAGAAGA-TATCAAAATTTCA

       4134 CAATGAAGTT


Statistics
Matches: 70,  Mismatches: 10, Indels: 6
        0.81            0.12        0.07

Matches are distributed among these distances:
  93    8  0.11
  94   62  0.89

ACGTcount: A:0.36, C:0.08, G:0.20, T:0.35


Consensus pattern (94 bp):   
AGGTTAACAAAATTTCATAGGGAGGTTATCAAAATTTTATGGAGAGCTTATCAAAATTATATAGA
GAAGATATCAAAATTTCATTCTCATAGGG

Found at i:4166 original size:22 final size:22

Alignment explanation


    Indices: 4043--4238  Score: 142
    Period size: 22  Copynumber: 8.9  Consensus size: 22

       4033 GGTTTCATTC

                  *         *     
       4043 TCATAGGGAGGTTATCTAAATT
          1 TCATAGTGAGGTTATCAAAATT

                *   *             
       4065 TCATGGTGTGGTTATCAAAATT
          1 TCATAGTGAGGTTATCAAAATT

             *         *           
       4087 TTATGAG-GAGCTTATCAAAATT
          1 TCAT-AGTGAGGTTATCAAAATT

             *    *   *           
       4109 TTATAGGGAGATTATCAAAATT
          1 TCATAGTGAGGTTATCAAAATT

               * *   *            
       4131 TCACAATGAAGTTATCAAAATT
          1 TCATAGTGAGGTTATCAAAATT

                    *      *  *   
       4153 TCATAGTGTGGTTATTAAGATT
          1 TCATAGTGAGGTTATCAAAATT

               **   *          *  
       4175 TCACCGTGTGGTTATCAAATTT
          1 TCATAGTGAGGTTATCAAAATT

               *  *           **   
       4197 TCACAGGGAGGTTATCGACCATT
          1 TCATAGTGAGGTTATC-AAAATT

                 * *           
       4220 TCATAATAAGGTTATCAAA
          1 TCATAGTGAGGTTATCAAA

       4239 TGGTCACAGT


Statistics
Matches: 133,  Mismatches: 38, Indels: 6
        0.75            0.21        0.03

Matches are distributed among these distances:
  21    2  0.02
  22  115  0.86
  23   16  0.12

ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36


Consensus pattern (22 bp):   
TCATAGTGAGGTTATCAAAATT

Done.