Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011596.1 Corchorus olitorius cultivar O-4 contig11629, 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, 719

Length: 1199
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22


Found at i:281 original size:154 final size:154

Alignment explanation


    Indices: 1--1199  Score: 1930
    Period size: 154  Copynumber: 7.8  Consensus size: 154

                 *         *      **                 *                       
          1 AAATCAAAGACGATTTAAAACGGAACTAATGGGCCTCGATATGCCCAAAATAACAAGTGTTCCAA
          1 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAA

                                                   *                         
         66 ATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAAGGATTATAGTTAGGCCATAAACAATG
         66 ATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATG

                        *           
        131 GAAAGAAAAGCAATGAGGTTTGCC
        131 GAAAGAAAAGCATTGAGGTTTGCC

                                                                             
        155 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAA
          1 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAA

                                                    *          *             
        220 ATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATAATTATAGTTACGCCATAAACAATG
         66 ATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATG

                        *           
        285 GAAAGAAAAGCAATGAGGTTTGCC
        131 GAAAGAAAAGCATTGAGGTTTGCC

                                                                             
        309 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAA
          1 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAA

                                    *  *   *                              *  
        374 ATGAGCTAAAAACTTCAAAGTGGATTAGTCTAACCAAAATGATTATAGTTAGGCCATAAACATTG
         66 ATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATG

                 *            *   * 
        439 GAAAGGAAAGCATTGAGGGTTGTC
        131 GAAAGAAAAGCATTGAGGTTTGCC

                                  **           *  *         *   *            
        463 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGTTAGGCCCAATATATCAAGTGTTCCAA
          1 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAA

              *  *                                                           
        528 ATTAGATAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATG
         66 ATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATG

                              *     
        593 GAAAGAAAAGCATTGAGGGTTGCC
        131 GAAAGAAAAGCATTGAGGTTTGCC

                                         *            *                      
        617 AAATCGAAGACGATTCAAAACGTCACTAAAGGGCCTCGATAGACCCAAAATAACAAGTGTTCCAA
          1 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAA

                             * *           *                                 
        682 ATGAGCTAAAAACTTCACACTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
         66 ATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATG

                                    
        747 GAAAGAAAAGCATTGAGGTTTGCC
        131 GAAAGAAAAGCATTGAGGTTTGCC

                                  **           *  *         *                
        771 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGTTAGGCCCAATATAACAAGTGTTCCAA
          1 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAA

                 *            *                    *                         
        836 ATGAGATAAAAACTTCAACGTGGACTAATCTTACCAAAACGATTATAGTTAGGCCATAAACAATG
         66 ATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATG

               *              *     
        901 GAAGGAAAAGCATTGAGGGTTGCC
        131 GAAAGAAAAGCATTGAGGTTTGCC

                  **                                                         
        925 AAATCGTTGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAA
          1 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAA

                          *                        *          *              
        990 ATGAGCTAAAAACTACAAAGTGGACTAATCTTACCAAAACGATTATAGTTTGGCCATAAACAATG
         66 ATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATG

                        *           
       1055 GAAAGAAAAGCAATGAGGTTTGCC
        131 GAAAGAAAAGCATTGAGGTTTGCC

                *                                                         *  
       1079 AAATTGAAGAACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTACA
          1 AAATCGAAG-ACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCA

                              *             *                       
       1144 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
         65 AATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCC


Statistics
Matches: 960,  Mismatches: 84, Indels: 1
        0.92            0.08        0.00

Matches are distributed among these distances:
 154  855  0.89
 155  105  0.11

ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22


Consensus pattern (154 bp):   
AAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAA
ATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATG
GAAAGAAAAGCATTGAGGTTTGCC

Done.