Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold44

Parameters: 2 7 7 80 10 50 500

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500

Length: 1648
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.22


Found at i:240 original size:129 final size:128

Alignment explanation


    Indices: 1--1648  Score: 1760
    Period size: 129  Copynumber: 12.8  Consensus size: 128

                 *            *              *        *  *        *  *       
          1 GAATGGCTGTCTCGAGTGTACTCAGTACACCACTACTTGGACGACCACCGCAGGTGACGGTAAAG
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACTACGA-CGCAGGAGATGGTAAAG

            *                  *                          *     *     *  *  
         66 TGAGCACTGGTACGGGTATTGTTGATGTGACCACCGACTCTAACGGTTCGTTATACACGACGAC
         65 CGAGCACTGGTACGGGTATCGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC

            *                                                     *  *       
        130 TAATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACTACGACTGCAGGCGACGGTAAAG
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACTACGAC-GCAGGAGATGGTAAAG

            *               *           *           *                       
        195 TGAGCACTGGTACGGGCATCGTTGATGTTACCACCGACTCCAACGGGTCGTTGTACACAACTAC
         65 CGAGCACTGGTACGGGTATCGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC

                        *     *                 *      *     * *        **   
        259 GAATGACTGTCTTGAGTGTACTCAGTACACCACCACCTGGACTTCGACGGATGAGAATGGCCAAG
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACTACGACGCAGGAG-ATGGTAAAG

                            *       **                                      
        324 CGAGCACTGGTACGGGCATCGTTGCCGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC
         65 CGAGCACTGGTACGGGTATCGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC

            *     *     *     *                 *             * *            
        388 AAATGATTGTCTTGAGTGTACTCAGTACACCACCACCTGGACCT-CGACGGATGAGAATGGTAAA
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGA-CTACGACGCAGGAG-ATGGTAAA

                 *           *       *                       *               
        452 GCGAGAACTGGTACGGGGATCGTTGCTGTGACCACCGACTCTAACGGGTTGTTGTACACAACTAC
         64 GCGAGCACTGGTACGGGTATCGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC

                  *  *  *     *           *           *  *     *  *  *       
        517 GAATGATTGCCTTGAGTGTACTCAGTACACTACCACTTGGACGACCACCGCTGGCGACGGTAAAG
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACTACGA-CGCAGGAGATGGTAAAG

            *                  *                                            
        582 TGAGCACTGGTACGGGTATTGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC
         65 CGAGCACTGGTACGGGTATCGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC

                        *           *        *  *     *         **       ** *
        646 GAATGACTGTCTTGAGTGCACTCAATACACCACTACGTGGACCACGACTG-ATAAGAATGGCCAG
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACTACGAC-GCAGGAG-ATGGTAAA

              *           *  *       **                                 * *  
        710 GCCAGCACTGGTACCGGCATCGTTGCCGTGACCACCGACTCTAACGGGTCGTTGTACACATCGAC
         64 GCGAGCACTGGTACGGGTATCGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC

            *                                   *             * *            
        775 CAATGACTGTCTCGAGTGCACTCAGTACACCACCACCTGGACCT-CGACGGATGAGAATGGTAAA
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGA-CTACGACGCAGGAG-ATGGTAAA

                 *           *       *                       *            *  
        839 GCGAGAACTGGTACGGGGATCGTTGCTGTGACCACCGACTCTAACGGGTTGTTGTACACAACAAC
         64 GCGAGCACTGGTACGGGTATCGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC

                                    *        *  *     *      * *        ** * 
        904 GAATGACTGTCTCGAGTGCACTCAATACACCACTACGTGGACCACGACGGATGAGAATGGCCAGG
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACTACGACGCAGGAG-ATGGTAAAG

             *              *       **              *                  *    
        969 CCAGCACTGGTACGGGGATCGTTGCCGTGACCACCGACTCCAACGGGTCGTTGTACACATCTAC
         65 CGAGCACTGGTACGGGTATCGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC

                           *                    *             * *            
       1033 GAATGACTGTCTCGATTGCACTCAGTACACCACCACCTGGACCT-CGACGGATGAGAATGGTAAA
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGA-CTACGACGCAGGAG-ATGGTAAA

                                *                                      *  *  
       1097 GCGAGCACTGGTACGGGTATTGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACGACGAC
         64 GCGAGCACTGGTACGGGTATCGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC

            *                 *              *        *         **       **  
       1162 TAATGACTGTCTCGAGTGTACTCAGTACACCACTACTTGGACCACGACTG-ATAAGAATGGCCAA
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACTACGAC-GCAGGAG-ATGGTAAA

              *              *       *               *                 *  *  
       1226 GCCAGCACTGGTACGGGCATCGTTGCTGTGACCACCGACTCCAACGGGTCGTTGTACACGACGAC
         64 GCGAGCACTGGTACGGGTATCGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC

            *                       * *      *  *     *         **       ** *
       1291 TAATGACTGTCTCGAGTGCACTCAATGCACCACTACATGGACCACGACTG-ATAAGAATGGCCAG
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACTACGAC-GCAGGAG-ATGGTAAA

              *                 *                            *               
       1355 GCCAGCACTGGTACGGGTATTGTTGATGTGACCACCGACTCTAACGGGTTGTTGTACACAACTAC
         64 GCGAGCACTGGTACGGGTATCGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC

                  *  *  *     *           *           *  *        *  *       
       1420 GAATGATTGCCTTGAGTGTACTCAGTACACTACCACTTGGACGACCACCGCAGGTGACGGTAAAG
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACTACGA-CGCAGGAGATGGTAAAG

                               *                                            
       1485 CGAGCACTGGTACGGGTATTGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC
         65 CGAGCACTGGTACGGGTATCGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC

                                             *        *  *     *  *  *       
       1549 GAATGACTGTCTCGAGTGCACTCAGTACACCACTACTTGGACGACCACCGCTGGCGACGGTAAAG
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACTACGA-CGCAGGAGATGGTAAAG

                               *               
       1614 CGAGCACTGGTACGGGTATTGTTGATGTGACCACC
         65 CGAGCACTGGTACGGGTATCGTTGATGTGACCACC


Statistics
Matches: 1317,  Mismatches: 187, Indels: 30
        0.86            0.12        0.02

Matches are distributed among these distances:
 128   11  0.01
 129  1294  0.98
 130   12  0.01

ACGTcount: A:0.26, C:0.27, G:0.26, T:0.22


Consensus pattern (128 bp):   
GAATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACTACGACGCAGGAGATGGTAAAGC
GAGCACTGGTACGGGTATCGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC

Left flanking sequence: None

Right flanking sequence: None


Found at i:476 original size:258 final size:258

Alignment explanation


    Indices: 1--1648  Score: 1956
    Period size: 258  Copynumber: 6.4  Consensus size: 258

                 *            *              *  *     ** *    * * *   *      
          1 GAATGGCTGTCTCGAGTGTACTCAGTACACCACTACTTGGACGACCACCGCAGGTG-ACGGTAAA
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACCTGGACCTCGA-CGGATGAGAATGGTAAA

             *                                             *     *     *  *  
         65 GTGAGCACTGGTACGGGTATTGTTGATGTGACCACCGACTCTAACGGTTCGTTATACACGACGAC
         65 GCGAGCACTGGTACGGGTATTGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC

            *                                         *       * * *   *  *   
        130 TAATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACTACGACTGCAGGCG-ACGGTAAA
        130 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACCACGAC-GGATGAGAATGGCAAA

             **                      *   *                                   
        194 GTGAGCACTGGTACGGGCATCGTTGATGTTACCACCGACTCCAACGGGTCGTTGTACACAACTAC
        194 GCCAGCACTGGTACGGGCATCGTTGCTGTGACCACCGACTCCAACGGGTCGTTGTACACAACTAC

                        *     *                       *                 **   
        259 GAATGACTGTCTTGAGTGTACTCAGTACACCACCACCTGGACTTCGACGGATGAGAATGGCCAAG
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACCTGGACCTCGACGGATGAGAATGGTAAAG

                            *  *    **                                      *
        324 CGAGCACTGGTACGGGCATCGTTGCCGTGACCACCGACTCTAACGGGTCGTTGTACACAACTACA
         66 CGAGCACTGGTACGGGTATTGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTACG

                 *     *     *                 *      *                *     
        389 AATGATTGTCTTGAGTGTACTCAGTACACCACCACCTGGACCTCGACGGATGAGAATGGTAAAGC
        131 AATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACCACGACGGATGAGAATGGCAAAGC

            *  *           *                       *       *               
        454 GAGAACTGGTACGGGGATCGTTGCTGTGACCACCGACTCTAACGGGTTGTTGTACACAACTAC
        196 CAGCACTGGTACGGGCATCGTTGCTGTGACCACCGACTCCAACGGGTCGTTGTACACAACTAC

                  *  *  *     *           *     *     ** *  * *     * *      
        517 GAATGATTGCCTTGAGTGTACTCAGTACACTACCACTTGGACGACCACCGCTG-GCGACGGTAAA
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACCTGGACCTCGACGGATGAG-AATGGTAAA

             *                                                               
        581 GTGAGCACTGGTACGGGTATTGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC
         65 GCGAGCACTGGTACGGGTATTGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC

                        *           *        *  *           *   *        * * 
        646 GAATGACTGTCTTGAGTGCACTCAATACACCACTACGTGGACCACGACTGATAAGAATGGCCAGG
        130 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACCACGACGGATGAGAATGGCAAAG

                         *           *              *                  * *  
        711 CCAGCACTGGTACCGGCATCGTTGCCGTGACCACCGACTCTAACGGGTCGTTGTACACATCGAC
        195 CCAGCACTGGTACGGGCATCGTTGCTGTGACCACCGACTCCAACGGGTCGTTGTACACAACTAC

            *                                                                
        775 CAATGACTGTCTCGAGTGCACTCAGTACACCACCACCTGGACCTCGACGGATGAGAATGGTAAAG
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACCTGGACCTCGACGGATGAGAATGGTAAAG

                *           *  *    *                       *            *   
        840 CGAGAACTGGTACGGGGATCGTTGCTGTGACCACCGACTCTAACGGGTTGTTGTACACAACAACG
         66 CGAGCACTGGTACGGGTATTGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTACG

                                   *        *  *                        * *  
        905 AATGACTGTCTCGAGTGCACTCAATACACCACTACGTGGACCACGACGGATGAGAATGGCCAGGC
        131 AATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACCACGACGGATGAGAATGGCAAAGC

                           *        *                                 *    
        970 CAGCACTGGTACGGGGATCGTTGCCGTGACCACCGACTCCAACGGGTCGTTGTACACATCTAC
        196 CAGCACTGGTACGGGCATCGTTGCTGTGACCACCGACTCCAACGGGTCGTTGTACACAACTAC

                           *                                                 
       1033 GAATGACTGTCTCGATTGCACTCAGTACACCACCACCTGGACCTCGACGGATGAGAATGGTAAAG
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACCTGGACCTCGACGGATGAGAATGGTAAAG

                                                                      *  *  *
       1098 CGAGCACTGGTACGGGTATTGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACGACGACT
         66 CGAGCACTGGTACGGGTATTGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTACG

                             *              *              *   *        *    
       1163 AATGACTGTCTCGAGTGTACTCAGTACACCACTACTTGGACCACGACTGATAAGAATGGCCAAGC
        131 AATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACCACGACGGATGAGAATGGCAAAGC

                                                                     *  *  
       1228 CAGCACTGGTACGGGCATCGTTGCTGTGACCACCGACTCCAACGGGTCGTTGTACACGACGAC
        196 CAGCACTGGTACGGGCATCGTTGCTGTGACCACCGACTCCAACGGGTCGTTGTACACAACTAC

            *                       * *      *  *      *    *   *       ** * 
       1291 TAATGACTGTCTCGAGTGCACTCAATGCACCACTACATGGACCACGACTGATAAGAATGGCCAGG
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACCTGGACCTCGACGGATGAGAATGGTAAAG

             *                                              *                
       1356 CCAGCACTGGTACGGGTATTGTTGATGTGACCACCGACTCTAACGGGTTGTTGTACACAACTACG
         66 CGAGCACTGGTACGGGTATTGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTACG

                 *  *  *     *           *           *  *    * * *   *  *    
       1421 AATGATTGCCTTGAGTGTACTCAGTACACTACCACTTGGACGACCACCGCAGGTG-ACGGTAAAG
        131 AATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACCACGA-CGGATGAGAATGGCAAAG

             *              *  *    *               *                       
       1485 CGAGCACTGGTACGGGTATTGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTAC
        195 CCAGCACTGGTACGGGCATCGTTGCTGTGACCACCGACTCCAACGGGTCGTTGTACACAACTAC

                                             *  *     ** *  * *     * *      
       1549 GAATGACTGTCTCGAGTGCACTCAGTACACCACTACTTGGACGACCACCGCTG-GCGACGGTAAA
          1 GAATGACTGTCTCGAGTGCACTCAGTACACCACCACCTGGACCTCGACGGATGAG-AATGGTAAA

                                                
       1613 GCGAGCACTGGTACGGGTATTGTTGATGTGACCACC
         65 GCGAGCACTGGTACGGGTATTGTTGATGTGACCACC


Statistics
Matches: 1203,  Mismatches: 181, Indels: 12
        0.86            0.13        0.01

Matches are distributed among these distances:
 257   11  0.01
 258  1188  0.99
 259    4  0.00

ACGTcount: A:0.26, C:0.27, G:0.26, T:0.22


Consensus pattern (258 bp):   
GAATGACTGTCTCGAGTGCACTCAGTACACCACCACCTGGACCTCGACGGATGAGAATGGTAAAG
CGAGCACTGGTACGGGTATTGTTGATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTACG
AATGACTGTCTCGAGTGCACTCAGTACACCACCACTTGGACCACGACGGATGAGAATGGCAAAGC
CAGCACTGGTACGGGCATCGTTGCTGTGACCACCGACTCCAACGGGTCGTTGTACACAACTAC

Left flanking sequence: None

Right flanking sequence: None


Done.