Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold4133

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, 347

Length: 579
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30


Found at i:450 original size:44 final size:43

Alignment explanation


    Indices: 399--579  Score: 109
    Period size: 44  Copynumber: 4.2  Consensus size: 43

        389 ATGCGATCTA

                                                  *      
        399 CTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTGTTTTAATCCG
          1 CTCTACTGTAATC-TCAGAGAGATAAGATCC-TTGTTTCAATCCG

                             *      *    *  * *       * 
        443 CTCTACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
          1 CTCTACTGTAATCTCAGAGAGATAAGA-TCCTTGTTTCAATCCG

               **            *               * * *   **
        487 CTCCGCTGTAATCTCAGTGAGATAAGA-CC-TGATACGATCTT
          1 CTCTACTGTAATCTCAGAGAGATAAGATCCTTGTTTCAATCCG

                       *                   *  *   *      
        528 CTCTACTGT-AGCTTCAGAGAGATAAGATCATTTATTTTAATCCG
          1 CTCTACTGTAATC-TCAGAGAGATAAGATC-CTTGTTTCAATCCG

               *    
        572 CTCCACTG
          1 CTCTACTG


Statistics
Matches: 101,  Mismatches: 30, Indels: 12
        0.71            0.21        0.08

Matches are distributed among these distances:
  40    2  0.02
  41   27  0.27
  42    2  0.02
  44   67  0.66
  45    3  0.03

ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33


Consensus pattern (43 bp):   
CTCTACTGTAATCTCAGAGAGATAAGATCCTTGTTTCAATCCG

Found at i:517 original size:129 final size:129

Alignment explanation


    Indices: 327--579  Score: 353
    Period size: 129  Copynumber: 2.0  Consensus size: 129

        317 CCCCACAACG

                               *        *                 *     *           *
        327 TCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGGGGAGGTAAAACCTGATG
          1 TCAGGGAGATAGAATTACTAGCTTCAATCTACTCCACTGTAACCACAGGGAGATAAAACCTGATA

                                                *   *             *         
        392 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCGCTCTACTGTAATC
         66 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATC

                        *                 *    *      * *   *       *        
        456 TCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGTGAGATAAGACCTGATA
          1 TCAGGGAGATAGAATTACTAGCTTCAATCTACTCCACTGTAACCACAGGGAGATAAAACCTGATA

                  *          *                                         
        521 CGATCTTCTCTACTGTAGCTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTG
         66 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTG


Statistics
Matches: 107,  Mismatches: 17, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
 129  107  1.00

ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30


Consensus pattern (129 bp):   
TCAGGGAGATAGAATTACTAGCTTCAATCTACTCCACTGTAACCACAGGGAGATAAAACCTGATA
CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATC
Done.