Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014207.1 Corchorus olitorius cultivar O-4 contig14240, 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: 3119
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34


Found at i:2857 original size:35 final size:36

Alignment explanation


    Indices: 2824--3119  Score: 273
    Period size: 35  Copynumber: 8.3  Consensus size: 36

       2814 ATCAGTCTTA

                                               *
       2824 CTTCAGTTTATTTCAGTTGACCCAGGGTGGTC-TTC
          1 CTTCAGTTTATTTCAGTTGACCCAGGGTGGTCGTTT

               *                  *      * *   *  
       2859 CTTGAGTTGT-TTTCAAGTTGATCCAGGGCGATC-ATT
          1 CTTCAGTT-TATTTC-AGTTGACCCAGGGTGGTCGTTT

                             *         *        
       2895 CTTCAGTTTATTTCAGTAGACCCAGGGCGGTC-TTT
          1 CTTCAGTTTATTTCAGTTGACCCAGGGTGGTCGTTT

                                            *   
       2930 CTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTT
          1 CTTCAGTTTATTTCAGTTGACCCAGGGTGGTCGTTT

                       *     **  * *             
       2966 CTTCAGTTTATGTCAGAACGATCGAGGGTGGTCGTTT
          1 CTTCAGTTTATTTCAG-TTGACCCAGGGTGGTCGTTT

                              *   *    *    *   
       3003 -TTCAGTTTATTTCAGTTTACCTAGGGCGGT-TTTT
          1 CTTCAGTTTATTTCAGTTGACCCAGGGTGGTCGTTT

               *                       *    *   
       3037 CTTGAGTTTATTTCAGTTGACCCAGGGAGGTCTTTT
          1 CTTCAGTTTATTTCAGTTGACCCAGGGTGGTCGTTT

                       *  *  *   *               
       3073 CTTCAGTTTATGTCCGAATGATCCAGGGTGGTCG-TT
          1 CTTCAGTTTATTTCAG-TTGACCCAGGGTGGTCGTTT

               *       
       3109 CTTTAGTTTAT
          1 CTTCAGTTTAT


Statistics
Matches: 214,  Mismatches: 39, Indels: 15
        0.80            0.15        0.06

Matches are distributed among these distances:
  34    3  0.01
  35   94  0.44
  36   89  0.42
  37   28  0.13

ACGTcount: A:0.17, C:0.18, G:0.24, T:0.41


Consensus pattern (36 bp):   
CTTCAGTTTATTTCAGTTGACCCAGGGTGGTCGTTT

Found at i:2944 original size:71 final size:70

Alignment explanation


    Indices: 2818--3119  Score: 279
    Period size: 71  Copynumber: 4.2  Consensus size: 70

       2808 CGACCGATCA

                 *                 *                 *   *                   
       2818 GTCTTACTTCAGTTTATTTCAGTTGACCCAGGGTGGTC-TTCCTTGAGTTGT-TTTCAAGTTGAT
          1 GTCTTTCTTCAGTTTATTTCAGTAGACCCAGGGTGGTCGTTTCTTCAGTT-TATTTC-AGTTGA-

                    
       2881 CCAGGGCG
         63 CCAGGGCG

            *  *                             *                               
       2889 ATCATTCTTCAGTTTATTTCAGTAGACCCAGGGCGGTC-TTTCTTCAGTTTATTTCAGTTGACCC
          1 GTCTTTCTTCAGTTTATTTCAGTAGACCCAGGGTGGTCGTTTCTTCAGTTTATTTCAGTTGA-CC

                * 
       2953 AGGGTG
         65 AGGGCG

                              *    *    * *                               *  
       2959 GTCTTTTCTTCAGTTTATGTCAGAACGATCGAGGGTGGTCGTTT-TTCAGTTTATTTCAGTTTAC
          1 GTC-TTTCTTCAGTTTATTTCAGTA-GACCCAGGGTGGTCGTTTCTTCAGTTTATTTCAGTTGAC

                    
       3023 CTAGGGCG
         64 C-AGGGCG

              *      *             *         *    *              *  *  *     
       3031 GTTTTTCTTGAGTTTATTTCAGTTGACCCAGGGAGGTCTTTTCTTCAGTTTATGTCCGAATGATC
          1 GTCTTTCTTCAGTTTATTTCAGTAGACCCAGGGTGGTCGTTTCTTCAGTTTATTTCAG-TTGA-C

                 * 
       3096 CAGGGTG
         64 CAGGGCG

               *     *       
       3103 GTCGTTCTTTAGTTTAT
          1 GTCTTTCTTCAGTTTAT


Statistics
Matches: 188,  Mismatches: 35, Indels: 15
        0.79            0.15        0.06

Matches are distributed among these distances:
  70   30  0.16
  71   96  0.51
  72   57  0.30
  73    5  0.03

ACGTcount: A:0.17, C:0.18, G:0.24, T:0.41


Consensus pattern (70 bp):   
GTCTTTCTTCAGTTTATTTCAGTAGACCCAGGGTGGTCGTTTCTTCAGTTTATTTCAGTTGACCA
GGGCG

Found at i:3045 original size:107 final size:107

Alignment explanation


    Indices: 2818--3119  Score: 387
    Period size: 107  Copynumber: 2.8  Consensus size: 107

       2808 CGACCGATCA

                 *                                   *   *        *      *   
       2818 GTCTTACTTCAGTTTATTTCAGTTGACCCAGGGTGGTC-TTCCTTGAGTTGT-TTTCA-AGTTGA
          1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTT-TATGTCAGA-ATGA

                   * *  *  *                            
       2880 TCCAGGGCGATCATTCTTCAGTTTATTTCAGTAGACCCAGGGCG
         64 TCCAGGGTGGTCGTTTTTCAGTTTATTTCAGTAGACCCAGGGCG

                                                                        *    
       2924 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAACGATC
          1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATC

            *                             **   *      
       2989 GAGGGTGGTCGTTTTTCAGTTTATTTCAGTTTACCTAGGGCG
         66 CAGGGTGGTCGTTTTTCAGTTTATTTCAGTAGACCCAGGGCG

              *      *                       *                      *        
       3031 GTTTTTCTTGAGTTTATTTCAGTTGACCCAGGGAGGTCTTTTCTTCAGTTTATGTCCGAATGATC
          1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATC

                                     
       3096 CAGGGTGGTCGTTCTTT-AGTTTAT
         66 CAGGGTGGTCGTT-TTTCAGTTTAT


Statistics
Matches: 172,  Mismatches: 20, Indels: 7
        0.86            0.10        0.04

Matches are distributed among these distances:
 106   38  0.22
 107  130  0.76
 108    4  0.02

ACGTcount: A:0.17, C:0.18, G:0.24, T:0.41


Consensus pattern (107 bp):   
GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATC
CAGGGTGGTCGTTTTTCAGTTTATTTCAGTAGACCCAGGGCG
Done.