Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2631

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, 535

Length: 893
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34


Found at i:481 original size:41 final size:41

Alignment explanation


    Indices: 424--685  Score: 206
    Period size: 41  Copynumber: 6.4  Consensus size: 41

        414 ATTTTTAAAC

                     *        * *      *             
        424 CTTTAGCGGTGTTTTTATTTTAGCGCCGCTAATTCTCCGAT
          1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATTCTCCGAT

                  * **       * *                  * **
        465 CTTTAGTGATGTTTTTAACCGAGCGCCACTAATGT-TCTGGC
          1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAAT-TCTCCGAT

                     *      *   *      *     *        
        506 CTTTAGCGGTGTTTTTGTCTAAGCGCCGCTAATGCT-CGTAT
          1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATTCTCCG-AT

             *    *                              * * 
        547 CATTAGTGGCGTTTTTATCTGAGCGCCACTAATTCTCTGTT
          1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATTCTCCGAT

                            *   *      *     *        
        588 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCT-CGTAT
          1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATTCTCCG-AT

             *    *                              * * 
        629 CATTAGTGGCGTTTTTATCTGAGCGCCACTAATTCTCTGTT
          1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATTCTCCGAT

                      *     
        670 CTTTAGCGGCATTTTT
          1 CTTTAGCGGCGTTTTT

        686 TATATGTAAG


Statistics
Matches: 166,  Mismatches: 49, Indels: 12
        0.73            0.22        0.05

Matches are distributed among these distances:
  40    2  0.01
  41  161  0.97
  42    3  0.02

ACGTcount: A:0.16, C:0.22, G:0.21, T:0.40


Consensus pattern (41 bp):   
CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATTCTCCGAT

Found at i:561 original size:82 final size:82

Alignment explanation


    Indices: 423--705  Score: 363
    Period size: 82  Copynumber: 3.4  Consensus size: 82

        413 GATTTTTAAA

                               * *            *         *      **       * *  
        423 CCTTTAGCGGTGTTTTTATTTTAGCGCCGCTAATTCTCCG-ATCTTTAGTGATGTTTTTAACCGA
          1 CCTTTAGCGGTGTTTTTATCTAAGCGCCGCTAATGCT-CGTATCATTAGTGGCGTTTTTATCTGA

                              *
        487 GCGCCACTAATGT-TCTGG
         65 GCGCCACTAAT-TCTCTGT

                             *                                               
        505 CCTTTAGCGGTGTTTTTGTCTAAGCGCCGCTAATGCTCGTATCATTAGTGGCGTTTTTATCTGAG
          1 CCTTTAGCGGTGTTTTTATCTAAGCGCCGCTAATGCTCGTATCATTAGTGGCGTTTTTATCTGAG

                             
        570 CGCCACTAATTCTCTGT
         66 CGCCACTAATTCTCTGT

            *         *      *                                               
        587 TCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGTATCATTAGTGGCGTTTTTATCTGAG
          1 CCTTTAGCGGTGTTTTTATCTAAGCGCCGCTAATGCTCGTATCATTAGTGGCGTTTTTATCTGAG

                             
        652 CGCCACTAATTCTCTGT
         66 CGCCACTAATTCTCTGT

            *            *        *              
        669 TCTTTAGCGGCATTTTTTATATGTAAGCGCCGCTAAT
          1 CCTTTAGCGG--TGTTTT-TATCTAAGCGCCGCTAAT

        706 AGTAACAAAA


Statistics
Matches: 180,  Mismatches: 16, Indels: 7
        0.89            0.08        0.03

Matches are distributed among these distances:
  81    3  0.02
  82  157  0.87
  84    4  0.02
  85   16  0.09

ACGTcount: A:0.17, C:0.22, G:0.21, T:0.40


Consensus pattern (82 bp):   
CCTTTAGCGGTGTTTTTATCTAAGCGCCGCTAATGCTCGTATCATTAGTGGCGTTTTTATCTGAG
CGCCACTAATTCTCTGT
Done.