Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_888 ID=scaffold_888-JGI_221_v2.0

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: 2901
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.25

Warning! 171 characters in sequence are not A, C, G, or T


Found at i:154 original size:88 final size:88

Alignment explanation


    Indices: 1--2901  Score: 2981
    Period size: 88  Copynumber: 33.0  Consensus size: 88

                                                 *  *                        
          1 GCAAGGTTTGTGTCTTCAGACCTGCTTCGCTGTCAATACAAGAAGGCAAGATCTGCTT-TCTTCA
          1 GCAAGGTTTGTGTCTTC-GACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTG-TTGTCTTCA

                                     
         65 ACCAGCTCCATCACAACCGAGAGAG
         64 ACCAGCTCCATCACAACCGAGAGAG

                                             *          *  *           *     
         90 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCTATGCAGGAAGCCATGATCTGTTGTCCTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

              *                    
        155 CACCTCCATCACAACCGAGAGAG
         66 CAGCTCCATCACAACCGAGAGAG

                 *          *                   *          *                 
        178 GCAAGATTTGTGTCTTTGACCTGCTTCGCTGTCAATACAGGAAGGCAGGATCTGTTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                               *   
        243 CAGCTCCATCACAACCGAGGGAG
         66 CAGCTCCATCACAACCGAGAGAG

                *                 *                    *         *           
        266 GCAAAGTTTGTGTCTTCGACCTACTTCGCTGTCAATGCAGGAACGCAAGATCTTTTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                              *    
        331 CAGCTCCATCACAACCGAAAGAG
         66 CAGCTCCATCACAACCGAGAGAG

                                                                 *           
        354 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                                  *
        419 CAGCTCCATCACAACCGAGAGAA
         66 CAGCTCCATCACAACCGAGAGAG

            *            *  *          **                         *          
        442 ACAAGGTTTGTGTTTTTGACCTGCTTCATTGTCAATGCAGGAAGGCAAGATCTGCTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                                   
        507 CAGCTCCATCACAACCGAGAGAG
         66 CAGCTCCATCACAACCGAGAGAG

                               *   *               *   *         *           
        530 GCAAGGTTTGTGTCTTCGATCTGATTCGCTGTCAATGCATGAACGCAAGATCTTTTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                                   
        595 CAGCTCCATCACAACCGAGAGAG
         66 CAGCTCCATCACAACCGAGAGAG

                                    *  *                 *          *        
        618 G-AAGGTTTGTGTCTTCGACCTGCCTCCCTGTCAATGCAGGAAGGAAAGATCTGTTATCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                                   
        682 CAGCTCCATCACAACCGAGAGAG
         66 CAGCTCCATCACAACCGAGAGAG

                             *                                               
        705 GCAAGGTTTGTGTCTTCAACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

            *     *      *         
        770 AAGCTCAATCACACCCGAGAGAG
         66 CAGCTCCATCACAACCGAGAGAG

                                                 *                           
        793 GCAAGGTTTGTGTCTGT-GACCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGTTGTCTTCAA
          1 GCAAGGTTTGTGTCT-TCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAA

                  *             *   
        857 CCAGCTTCATCACAACCGAGGGAG
         65 CCAGCTCCATCACAACCGAGAGAG

               *  *            *   *             *       *     * *           
        881 GCAGGGCTTGTGTCTTCGATCTGATTCGCTGTCAATGAAGGAAGGTAAGATTTTTTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                               *   
        946 CAGCTCCATCACAACCGAGGGAG
         66 CAGCTCCATCACAACCGAGAGAG

                                                *  *    * *                 *
        969 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAAGAAGCCTAGATCTGCTT-TCTTCAT
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTG-TTGTCTTCAA

                                    
       1033 CCAGCTCCATCACAACCGAGAGAG
         65 CCAGCTCCATCACAACCGAGAGAG

                                      *               *                      
       1057 GCAAGGTTTGTGTCTTCGACCTGCTTTGCTGTCAATGCAGGATGGCAAGATCTGTTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                  * *  *       *   
       1122 CAGCTCTACCATAACCGAGGGAG
         66 CAGCTCCATCACAACCGAGAGAG

                               *            *********************************
       1145 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

            ***********************
       1210 NNNNNNNNNNNNNNNNNNNNNNN
         66 CAGCTCCATCACAACCGAGAGAG

            *****************************************************************
       1233 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

            ***********************
       1298 NNNNNNNNNNNNNNNNNNNNNNN
         66 CAGCTCCATCACAACCGAGAGAG

            ***************************                                      
       1321 NNNNNNNNNNNNNNNNNNNNNNNNNNNGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                 *                 
       1386 CAGCTTCATCACAACCGAGAGAG
         66 CAGCTCCATCACAACCGAGAGAG

                                                                 *           
       1409 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                                   
       1474 CAGCTCCATCACAACCGAGAGAG
         66 CAGCTCCATCACAACCGAGAGAG

                                                *  *             **          
       1497 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAAGAAGGCAAGATCTACTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                                   
       1562 CAGCTCCATCACAACCGAGAGAG
         66 CAGCTCCATCACAACCGAGAGAG

                                                                 **          
       1585 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTACTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

            *  *                   
       1650 GAGGTCCATCACAACCGAGAGAG
         66 CAGCTCCATCACAACCGAGAGAG

                               *   *        *           *        *           
       1673 GCAAGGTTTGTGTCTTCGATCTGATTCGCTGTTAATGCAGGAAGACAAGATCTTTTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                                   
       1738 CAGCTCCATCACAACCGAGAGAG
         66 CAGCTCCATCACAACCGAGAGAG

                            *                   *          *                 
       1761 GCAAGGTTTGTGTCTTTGACCTGCTTCGCTGTCAATACAGGAAGGCAGGATCTGTTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                                    
       1826 CAGCTCCATCACAACCGAG-GAAG
         66 CAGCTCCATCACAACCGAGAG-AG

                *              *                                             
       1849 GCAAAGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

            *     *              * 
       1914 AAGCTCAATCACAACCGAGAGTG
         66 CAGCTCCATCACAACCGAGAGAG

             *              *                                                
       1937 GTAAGGTTTGTGTCTTTGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                                   
       2002 CAGCTCCATCACAACCGAGAGAG
         66 CAGCTCCATCACAACCGAGAGAG

                             *    *                                          
       2025 GCAAGGTTTGTGTCTTCAACCTCCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

            *     *  *             
       2090 AAGCTCAATAACAACCGAGAGAG
         66 CAGCTCCATCACAACCGAGAGAG

                               *                                 *           
       2113 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                                   
       2178 CAGCTCCATCACAACCGAGAGAG
         66 CAGCTCCATCACAACCGAGAGAG

                                                                  *      *   
       2201 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTGTCTTTAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                                   
       2266 CAGCTCCATCACAACCGAGAGAG
         66 CAGCTCCATCACAACCGAGAGAG

                               *   *   *                         *     *     
       2289 GCAAGGTTTGTGTCTTCGATCTGATTCACTGTCAATGCAGGAAGGCAAGATCTTTTGTCCTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                *                   
       2354 CAGCGCCATCACAACCGATG-GAG
         66 CAGCTCCATCACAACCGA-GAGAG

                *    *         *  **       *                            *    
       2377 GCAAAGTTTATGTCTTCGATCTAATTCGCTGCCAATGCAGGAAGGCAAGATCT-TCTGTCCTCAA
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGT-TGTCTTCAA

                       *            
       2441 CCAGCTCCATCGCAACCGAGAGAG
         65 CCAGCTCCATCACAACCGAGAGAG

                *                                                            
       2465 GCAAAGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

            *     *                
       2530 AAGCTCAATCACAACCGAGAGAG
         66 CAGCTCCATCACAACCGAGAGAG

                            *                    *                           
       2553 GCAAGGTTTGTGTCTTTGACCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTGTTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                                   
       2618 CAGCTCCATCACAACCGAGAGAG
         66 CAGCTCCATCACAACCGAGAGAG

               *  *            *   *      *              *     * *           
       2641 GCAGGGCTTGTGTCTTCGATCTGATTCGCTATCAATGCAGGAAGGTAAGATTTTTTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                               *   
       2706 CAGCTCCATCACAACCGAGGGAG
         66 CAGCTCCATCACAACCGAGAGAG

                                                *  *              *          
       2729 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAAGAAGGCAAGATCTGCTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

              *                    
       2794 CAACTCCATCACAACCGAGAGAG
         66 CAGCTCCATCACAACCGAGAGAG

                                                    *                        
       2817 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTGTTGTCTTCAAC
          1 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC

                                
       2882 CAGCCTCCATCACAACCGAG
         66 CAG-CTCCATCACAACCGAG


Statistics
Matches: 2395,  Mismatches: 404, Indels: 26
        0.85            0.14        0.01

Matches are distributed among these distances:
  87   86  0.04
  88  2270  0.95
  89   39  0.02

ACGTcount: A:0.24, C:0.24, G:0.22, T:0.25


Consensus pattern (88 bp):   
GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC
CAGCTCCATCACAACCGAGAGAG

Done.