Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3666

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, 415

Length: 693
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.24


Found at i:538 original size:43 final size:43

Alignment explanation


    Indices: 475--659  Score: 185
    Period size: 43  Copynumber: 4.3  Consensus size: 43

        465 TTTTAAAAAT

                          **                           
        475 AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTCTTCCAC
          1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTCTTCCAC

                   *                            *     *
        518 AAACGCCACTAAAGACCATGACCTTTAGCGGCGCTTTTTCCAT
          1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTCTTCCAC

                         *  *     *             *   *   
        561 AAACGCCGCTAAAAACTATGACATTTAGCGGCGCTTTTTATCAC
          1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTCTT-CCAC

                  *    *   *   *          *            *
        605 AAACGCTGCTATAGAACA-AACCTTTAGCGACGCTTC-TCTCAA
          1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTCTTC-CAC

                 *       
        647 AAACGACGCTAAA
          1 AAACGCCGCTAAA

        660 AACATATCAT


Statistics
Matches: 115,  Mismatches: 25, Indels: 5
        0.79            0.17        0.03

Matches are distributed among these distances:
  42   13  0.11
  43   87  0.76
  44   15  0.13

ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24


Consensus pattern (43 bp):   
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTCTTCCAC

Found at i:628 original size:86 final size:87

Alignment explanation


    Indices: 473--662  Score: 208
    Period size: 86  Copynumber: 2.2  Consensus size: 87

        463 TTTTTTAAAA

                            **       *                                   *   
        473 ATAAACGCCGCT-AAAGGTCATGACCTTTAGCGGCGCTTCTTCCACAAACGCCACTAAAGACCAT
          1 ATAAACGCCGCTAAAAACTCATGACATTTAGCGGCGCTTCTTCCACAAACGCCACTAAAGAACAT

            *          *       *   
        537 GACCTTTAGCGGCGCTT-TTTCC
         66 AACCTTTAGCGACGCTTCTCT-C

                                                   *   *         **   *      
        559 ATAAACGCCGCTAAAAACT-ATGACATTTAGCGGCGCTTTTTATCACAAACGCTGCTATAGAACA
          1 ATAAACGCCGCTAAAAACTCATGACATTTAGCGGCGCTTCTT-CCACAAACGCCACTAAAGAACA

                                   
        623 -AACCTTTAGCGACGCTTCTCTC
         65 TAACCTTTAGCGACGCTTCTCTC

             *     *          
        645 AAAAACGACGCTAAAAAC
          1 ATAAACGCCGCTAAAAAC

        663 ATATCATGCA


Statistics
Matches: 87,  Mismatches: 14, Indels: 6
        0.81            0.13        0.06

Matches are distributed among these distances:
  86   64  0.74
  87   23  0.26

ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24


Consensus pattern (87 bp):   
ATAAACGCCGCTAAAAACTCATGACATTTAGCGGCGCTTCTTCCACAAACGCCACTAAAGAACAT
AACCTTTAGCGACGCTTCTCTC
Done.