Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011733.1 Corchorus olitorius cultivar O-4 contig11766, 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, 918

Length: 1530
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22


Found at i:665 original size:154 final size:154

Alignment explanation


    Indices: 1--1530  Score: 2278
    Period size: 154  Copynumber: 9.9  Consensus size: 154

                      *    *                                               * 
          1 GGAACTAATGAGCCCAGATAGGCCCAAAATAACAAGTGTTCCAAATCGAGCT-AAAACTTCACCG
          1 GGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAAT-GAGCTAAAAACTTCACAG

                                                                             
         65 TGGACTAATCTCACCAAAAGTGATTATAGTTAGGCCATAAACAATAGGAAAGAAAAGCATTGAGG
         65 TGGACTAATCTCACCAAAA-TGATTATAGTTAGGCCATAAACAAT-GGAAAGAAAAGCATTGAGG

                 *                  *  
        130 TTTGCTAAATCGAAGACGATTCAATAC
        128 TTTGCCAAATCGAAGACGATTCAAAAC

             **                                              *      *        
        157 GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGAT-AAAAGTTCACAGT
          1 GGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT

                                                *                            
        221 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATTAACAATGGAAAGAAAAGCATTGAGGTTT
         66 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT

              *                     
        286 GCTAAATCGAAGACGATTCAAAAC
        131 GCCAAATCGAAGACGATTCAAAAC

                      * *  *                                         *       
        310 GGAACTAATGAGTCCAGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACCTCACAGT
          1 GGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT

                         *                                         *         
        375 GGACTAATCTCACTAAAATGATTATAGTTAGG-C-TAAACAATGGAAAGAAAAGCTTTGAGGTTT
         66 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT

                                     
        438 GCCAAATCGAAGACGAGTTCAAAAC
        131 GCCAAATCGAAGACGA-TTCAAAAC

                          *                           *                      
        463 GGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCTAATGAGCTAAAAACTTCACAGT
          1 GGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT

                                                                             
        528 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT
         66 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT

                                    
        593 GCCAAATCGAAGACGATTCAAAAC
        131 GCCAAATCGAAGACGATTCAAAAC

                          *      **                  *                       
        617 GGAACTAATGGGCCTCGATAGAACCAAAATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAGT
          1 GGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT

                        *             *                *    *                
        682 GGACTAATCTCATCAAAATGATTATAATTAGGCCATAAACAATAGAAATAAAAGCATTGAGGTTT
         66 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT

                         *       *  
        747 GCCAAATCGAAGAAGATTCAATAC
        131 GCCAAATCGAAGACGATTCAAAAC

             **                   *              *        *         *      * 
        771 GTCACTAATGGGCCCCGATAGGGCCAAAATAACAAGTTTTCCAAATAAGCTAAAAAGTTCACAAT
          1 GGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT

                      *      *       *                      *                
        836 GGACTAATCTGACCAAATTGATTATGGTTAGGCCATAAACAATGGAAACAAAAGCATTGAGGTTT
         66 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT

                                   *
        901 GCCAAATCGAAGACGATTCAAAAT
        131 GCCAAATCGAAGACGATTCAAAAC

                          *     **                   *     *             *   
        925 GGAACTAATGGGCCTCGATAAACCCAAAATAACAAGTGTTCTAAATGCGCTAAAAACTTCATAGT
          1 GGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT

                                 *    **  *                 *                
        990 GGACTAATCTCACCAAAATGAATATAAATATGCCATAAACAATGGAAAAAAAAGCATTGAGGTTT
         66 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT

                         *       *  
       1055 GCCAAATCGAAGAAGATTCAATAC
        131 GCCAAATCGAAGACGATTCAAAAC

             **           *       *              *        *         *      * 
       1079 GTCACTAATGGGCCTCGATAGGTCCAAAATAACAAGTTTTCCAAATAAGCTAAAAAGTTCACAAT
          1 GGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT

                      * **   *       *                                   *   
       1144 GGACTAATCTGAATAAATTGATTATGGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGATTT
         66 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT

                                     
       1209 GCCAAATCGAAGACGATTCAAAAAC
        131 GCCAAATCGAAGACGATTC-AAAAC

              *        *                     *  *                            
       1234 GGGACTAATGGACCCCGATAGGCCCAAAATAACTAGGGTTCCAAATGAGCTAAAAACTTCACAGT
          1 GGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT

                         *                                                   
       1299 GGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCCATTGAGGTT
         66 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG-CATTGAGGTT

                       *             
       1364 TGCCAAATCGAGGACGATTCAAAAC
        130 TGCCAAATCGAAGACGATTCAAAAC

                                                         *                   
       1389 GGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAAAGAGCTAAAAACTTCACAGT
          1 GGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT

                                                                    *        
       1454 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT-GAAGAGAAAAGCTTTGAGGTT
         66 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA-AGAAAAGCATTGAGGTT

                         
       1518 TGCCAAATCGAAG
        130 TGCCAAATCGAAG


Statistics
Matches: 1234,  Mismatches: 133, Indels: 16
        0.89            0.10        0.01

Matches are distributed among these distances:
 152   43  0.03
 153  189  0.15
 154  632  0.51
 155  300  0.24
 156   70  0.06

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


Consensus pattern (154 bp):   
GGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT
GCCAAATCGAAGACGATTCAAAAC

Done.