Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold4090

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, 353

Length: 589
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30


Found at i:205 original size:16 final size:16

Alignment explanation


    Indices: 184--214  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

        174 TGAATTATTT

                            
        184 ATTACAGCTCTATTCA
          1 ATTACAGCTCTATTCA

                           
        200 ATTACAGCTCTATTC
          1 ATTACAGCTCTATTC

        215 CATTCACTAC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.29, C:0.26, G:0.06, T:0.39


Consensus pattern (16 bp):   
ATTACAGCTCTATTCA

Found at i:348 original size:43 final size:43

Alignment explanation


    Indices: 299--526  Score: 314
    Period size: 43  Copynumber: 5.3  Consensus size: 43

        289 TTTTAGAAAT

                                     *                 
        299 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
          1 AAACGCCGCTAAAGACCAAGACCTTCAGCGGCGCTTTTCCCAC

                              *                        
        342 AAACGCCGCTAAAGACCATGACCTTCAGCGGCGCTTTTCCCAC
          1 AAACGCCGCTAAAGACCAAGACCTTCAGCGGCGCTTTTCCCAC

                              *                    *   
        385 AAACGCCGCTAAAGACCATGACCTTCAGCGGCGCTTTTCTCAC
          1 AAACGCCGCTAAAGACCAAGACCTTCAGCGGCGCTTTTCCCAC

              *          *                  *       * *
        428 AAGCGCCGCTAAAAACCAAGACCTTCAGCGGCACTTTTCCTAA
          1 AAACGCCGCTAAAGACCAAGACCTTCAGCGGCGCTTTTCCCAC

                   * *               *    *        *    
        471 AAACGCCACGAAAGACCAAGACCTTTAGCGACGCTTTTAACC-C
          1 AAACGCCGCTAAAGACCAAGACCTTCAGCGGCGCTTTT-CCCAC

                         
        514 AAACGCCGCTAAA
          1 AAACGCCGCTAAA

        527 AATATATCTT


Statistics
Matches: 162,  Mismatches: 22, Indels: 2
        0.87            0.12        0.01

Matches are distributed among these distances:
  43  161  0.99
  44    1  0.01

ACGTcount: A:0.30, C:0.34, G:0.18, T:0.18


Consensus pattern (43 bp):   
AAACGCCGCTAAAGACCAAGACCTTCAGCGGCGCTTTTCCCAC

Done.