Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold4054

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, 358

Length: 597
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26


Found at i:286 original size:44 final size:44

Alignment explanation


    Indices: 223--414  Score: 124
    Period size: 44  Copynumber: 4.4  Consensus size: 44

        213 GCCACCAAGC

                       *             *                  
        223 CTTATCTCCCTGAGCAGTAGCAGAGTAGGTTCAAGATTGTAGAT
          1 CTTATCTCCCTAAGCAGTAGCAGAGCAGGTTCAAGATTGTAGAT

                                **       *        * * *  
        267 CTTATCTCCCTAAGCAGTAGTGGAGCA-GATCAAAGATGGCAAAT
          1 CTTATCTCCCTAAGCAGTAGCAGAGCAGGTTC-AAGATTGTAGAT

                    *       *     *       *  *        **   *
        311 CTTATCTTTCC-AAGATAGTAGGA-AGCAGATTTAAGCCA-TAAAG-C
          1 CTTATC-TCCCTAAG-CAGTAGCAGAGCAGGTTCAAG--ATTGTAGAT

                       *             *                  
        355 CTTATCTCCCTGAGCAGTAGCAGAGTAGGTTCAAGATTGTAGAT
          1 CTTATCTCCCTAAGCAGTAGCAGAGCAGGTTCAAGATTGTAGAT

                  **        
        399 CTTATCGACCTAAGCA
          1 CTTATCTCCCTAAGCA

        415 TATTGGAGCA


Statistics
Matches: 105,  Mismatches: 33, Indels: 20
        0.66            0.21        0.13

Matches are distributed among these distances:
  42    1  0.01
  43   15  0.14
  44   78  0.74
  45   10  0.10
  46    1  0.01

ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27


Consensus pattern (44 bp):   
CTTATCTCCCTAAGCAGTAGCAGAGCAGGTTCAAGATTGTAGAT

Found at i:485 original size:131 final size:132

Alignment explanation


    Indices: 1--597  Score: 842
    Period size: 132  Copynumber: 4.5  Consensus size: 132

                                  *                             *            
          1 ATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGATTGG-AAATCTTATATTTCCAAGATAG
          1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGA-TGGCAAATCTTATCTTTCCAAGATAG

                           *             *    **    *      *   *            *
         65 TGGGAAGCAAATTTACGCCACAAAGCCTTCTCTCTTTGAGTAGCAGCGGAGAAGGTTCAAGATTA
         65 TGGGAAGCAAATTTAAGCCACAAAGCCTTATCTCCCTGAGCAGCAGCAGAGTAGGTTCAAGATTG

               
        130 TAG
        130 TAG

                                                  * *      *                 
        133 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCCTATCTTTCCAAGATAGT
          1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGT

                                *                     *                      
        198 GGGAAGCAAATTTAAGCCACCAAGCCTTATCTCCCTGAGCAGTAGCAGAGTAGGTTCAAGATTGT
         66 GGGAAGCAAATTTAAGCCACAAAGCCTTATCTCCCTGAGCAGCAGCAGAGTAGGTTCAAGATTGT

              
        263 AG
        131 AG

                                                                             
        265 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGT
          1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGT

            *       *          *                      *                      
        330 AGGAAGCAGATTTAAGCCATAAAGCCTTATCTCCCTGAGCAGTAGCAGAGTAGGTTCAAGATTGT
         66 GGGAAGCAAATTTAAGCCACAAAGCCTTATCTCCCTGAGCAGCAGCAGAGTAGGTTCAAGATTGT

              
        395 AG
        131 AG

                    **           *                                  *        
        397 ATCTTATCGACCTAAGCA-TATTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCAAAGATAGT
          1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGT

                                        *    **    *     **                  
        461 GGGAAGCAAATTTAAGCCACAAAGCCTTGTCTCTATGAGTAGCAGTGGAG-ACGGTTCAAGATTG
         66 GGGAAGCAAATTTAAGCCACAAAGCCTTATCTCCCTGAGCAGCAGCAGAGTA-GGTTCAAGATTG

               
        525 TAG
        130 TAG

                    **                   *         *                *        
        528 ATCTTATCGACCTAAGCA-TAGTGGAGCAAATCAAAGATAGCAAATCTTATCTTTCAAAGATAGT
          1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGT

                  
        592 GGGAAG
         66 GGGAAG


Statistics
Matches: 424,  Mismatches: 39, Indels: 5
        0.91            0.08        0.01

Matches are distributed among these distances:
 130    1  0.00
 131  167  0.39
 132  256  0.60

ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26


Consensus pattern (132 bp):   
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGT
GGGAAGCAAATTTAAGCCACAAAGCCTTATCTCCCTGAGCAGCAGCAGAGTAGGTTCAAGATTGT
AG
Done.