Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1484

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, 996

Length: 1661
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.19

Warning! 279 characters in sequence are not A, C, G, or T


Found at i:269 original size:57 final size:58

Alignment explanation


    Indices: 178--478  Score: 383
    Period size: 58  Copynumber: 5.2  Consensus size: 58

        168 TCCAGCGCCC

                 *         *                           *              
        178 AACGCTGTCGACTTCACAGTCCAGCTTCCTACGCTGTCGACTTTTCAGTCCGGCTTCT
          1 AACGCCGTCGACTTCTCAGTCCAGCTTCCTACGCTGTCGACTTCTCAGTCCGGCTTCT

                                                                   *  
        236 AACGCCGTCGACTT-TCAGTCCAGCTTCCTACGCTGTCGACTTCTCAGTCCGGCTCCT
          1 AACGCCGTCGACTTCTCAGTCCAGCTTCCTACGCTGTCGACTTCTCAGTCCGGCTTCT

                           *         *  *                             
        293 AACGCCGTCGACTTCCCAGTCCAGCCTCTTACGCTGTCGAC-TCTCAGTCCGGCTTCT
          1 AACGCCGTCGACTTCTCAGTCCAGCTTCCTACGCTGTCGACTTCTCAGTCCGGCTTCT

                                  *            *         *      *      
        350 AACGCCGTCGACTTCTCAGTCCGGCTT-CTAACGCCGTCGACTTCCCAGTCCAGCTTCT
          1 AACGCCGTCGACTTCTCAGTCCAGCTTCCT-ACGCTGTCGACTTCTCAGTCCGGCTTCT

            *    *                *   *  *       *             *   * *
        408 TACGCTGTCGACTTCTCAGTCCGGCTCCCAACGCTGTTGACTTCTCAGTCCAGCTCCC
          1 AACGCCGTCGACTTCTCAGTCCAGCTTCCTACGCTGTCGACTTCTCAGTCCGGCTTCT

                    *    
        466 AACGCCGTTGACT
          1 AACGCCGTCGACT

        479 CCACAGTGGC


Statistics
Matches: 212,  Mismatches: 27, Indels: 8
        0.86            0.11        0.03

Matches are distributed among these distances:
  56    1  0.00
  57  103  0.49
  58  107  0.50
  59    1  0.00

ACGTcount: A:0.15, C:0.38, G:0.19, T:0.28


Consensus pattern (58 bp):   
AACGCCGTCGACTTCTCAGTCCAGCTTCCTACGCTGTCGACTTCTCAGTCCGGCTTCT

Found at i:313 original size:86 final size:86

Alignment explanation


    Indices: 165--478  Score: 396
    Period size: 86  Copynumber: 3.6  Consensus size: 86

        155 AAGAAGCATC

                     *                  *                   *        **      
        165 CAGTCCAGCGCCCAACGCTGTCGACTTCACAGTCCAGCTTCCT-ACGCTGTCGACTTTTCAGTCC
          1 CAGTCCAGCTCCCAACGCTGTCGACTTCTCAGTCCAGC-TCCTAACGCCGTCGACTTCCCAGTCC

            *      *    *         
        229 GGCTTCTAACGCCGTCGACTTT
         65 AGCTTCTTACGCTGTCGACTTT

                      *  *                     *                             
        251 CAGTCCAGCTTCCTACGCTGTCGACTTCTCAGTCCGGCTCCTAACGCCGTCGACTTCCCAGTCCA
          1 CAGTCCAGCTCCCAACGCTGTCGACTTCTCAGTCCAGCTCCTAACGCCGTCGACTTCCCAGTCCA

              *                * 
        316 GCCTCTTACGCTGTCGACTCT
         66 GCTTCTTACGCTGTCGACTTT

                  *   * *     *                *   *                         
        337 CAGTCCGGCTTCTAACGCCGTCGACTTCTCAGTCCGGCTTCTAACGCCGTCGACTTCCCAGTCCA
          1 CAGTCCAGCTCCCAACGCTGTCGACTTCTCAGTCCAGCTCCTAACGCCGTCGACTTCCCAGTCCA

                                  
        402 GCTTCTTACGCTGTCGACTTCT
         66 GCTTCTTACGCTGTCGACTT-T

                  *              *                   *        *    
        424 CAGTCCGGCTCCCAACGCTGTTGACTTCTCAGTCCAGCTCCCAACGCCGTTGACT
          1 CAGTCCAGCTCCCAACGCTGTCGACTTCTCAGTCCAGCTCCTAACGCCGTCGACT

        479 CCACAGTGGC


Statistics
Matches: 198,  Mismatches: 28, Indels: 3
        0.86            0.12        0.01

Matches are distributed among these distances:
  85    4  0.02
  86  146  0.74
  87   48  0.24

ACGTcount: A:0.15, C:0.39, G:0.19, T:0.27


Consensus pattern (86 bp):   
CAGTCCAGCTCCCAACGCTGTCGACTTCTCAGTCCAGCTCCTAACGCCGTCGACTTCCCAGTCCA
GCTTCTTACGCTGTCGACTTT

Found at i:485 original size:29 final size:29

Alignment explanation


    Indices: 178--462  Score: 344
    Period size: 29  Copynumber: 9.9  Consensus size: 29

        168 TCCAGCGCCC

                           *              
        178 AACGCTGTCGACTTCACAGTCCAGCTTCCT
          1 AACGCTGTCGACTTCTCAGTCCAGCTT-CT

                          *       *      
        208 -ACGCTGTCGACTTTTCAGTCCGGCTTCT
          1 AACGCTGTCGACTTCTCAGTCCAGCTTCT

                 *                        
        236 AACGCCGTCGACTT-TCAGTCCAGCTTCCT
          1 AACGCTGTCGACTTCTCAGTCCAGCTT-CT

                                  *   *  
        265 -ACGCTGTCGACTTCTCAGTCCGGCTCCT
          1 AACGCTGTCGACTTCTCAGTCCAGCTTCT

                 *         *         *   
        293 AACGCCGTCGACTTCCCAGTCCAGCCTCT
          1 AACGCTGTCGACTTCTCAGTCCAGCTTCT

            *                     *      
        322 TACGCTGTCGAC-TCTCAGTCCGGCTTCT
          1 AACGCTGTCGACTTCTCAGTCCAGCTTCT

                 *                *      
        350 AACGCCGTCGACTTCTCAGTCCGGCTTCT
          1 AACGCTGTCGACTTCTCAGTCCAGCTTCT

                 *         *             
        379 AACGCCGTCGACTTCCCAGTCCAGCTTCT
          1 AACGCTGTCGACTTCTCAGTCCAGCTTCT

            *                     *   * *
        408 TACGCTGTCGACTTCTCAGTCCGGCTCCC
          1 AACGCTGTCGACTTCTCAGTCCAGCTTCT

                    *                 
        437 AACGCTGTTGACTTCTCAGTCCAGCT
          1 AACGCTGTCGACTTCTCAGTCCAGCT

        463 CCCAACGCCG


Statistics
Matches: 219,  Mismatches: 31, Indels: 11
        0.84            0.12        0.04

Matches are distributed among these distances:
  28   50  0.23
  29  169  0.77

ACGTcount: A:0.15, C:0.38, G:0.19, T:0.28


Consensus pattern (29 bp):   
AACGCTGTCGACTTCTCAGTCCAGCTTCT
Done.