Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_297 ID=scaffold_297-JGI_221_v2.0

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, 1000

Length: 10817
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.24

Warning! 2359 characters in sequence are not A, C, G, or T


Found at i:667 original size:57 final size:57

Alignment explanation


    Indices: 606--905  Score: 291
    Period size: 57  Copynumber: 5.3  Consensus size: 57

        596 TAAAATAACT

                    *  *    * *        *                        *    
        606 TTCCACATATAAGATAATATTGACGGATTTCCTACATATAAGATAGTCCTGGTGGAC
          1 TTCCACATTTACGATAGTCTTGACGGACTTCCTACATATAAGATAGTCCTGGCGGAC

                    *             *           *    *         *     *  
        663 TTCCACATATACGATAGTCTTGGCGGACTT-CTCGCATAAAAGATAGTCTTGGCGAAC
          1 TTCCACATTTACGATAGTCTTGACGGACTTCCT-ACATATAAGATAGTCCTGGCGGAC

                               *   *                           *  *   
        720 TTCCACATTTACGATAGTCCTGATGGACTT-CTAACATATAAGATAGTCCTCGCAGAC
          1 TTCCACATTTACGATAGTCTTGACGGACTTCCT-ACATATAAGATAGTCCTGGCGGAC

                              *     **        *               * *    
        777 TTCCACATTTACGATAGTGTTGACAAACTTCCTATATATAAGATAGTCCTAGTGGAC
          1 TTCCACATTTACGATAGTCTTGACGGACTTCCTACATATAAGATAGTCCTGGCGGAC

                       *     * *      **    *               *     *  
        834 TTCCACATTTATGATAGCCCTGACGGGTTTCCCACATAT-AGATAGTCTTGGCGAAC
          1 TTCCACATTTACGATAGTCTTGACGGACTTCCTACATATAAGATAGTCCTGGCGGAC

                            
        890 TTCCACATTTACGATA
          1 TTCCACATTTACGATA

        906 ATGCCATGAC


Statistics
Matches: 196,  Mismatches: 45, Indels: 5
        0.80            0.18        0.02

Matches are distributed among these distances:
  56   30  0.15
  57  164  0.84
  58    2  0.01

ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31


Consensus pattern (57 bp):   
TTCCACATTTACGATAGTCTTGACGGACTTCCTACATATAAGATAGTCCTGGCGGAC

Found at i:679 original size:28 final size:28

Alignment explanation


    Indices: 606--897  Score: 199
    Period size: 28  Copynumber: 10.3  Consensus size: 28

        596 TAAAATAACT

                            * **  *    *
        606 TTCCACATATAAGATAATATTGACGGAT
          1 TTCCACATATAAGATAGTCCTGGCGGAC

                                    *    
        634 TTCCTACATATAAGATAGTCCTGGTGGAC
          1 TTCC-ACATATAAGATAGTCCTGGCGGAC

                       *       *        
        663 TTCCACATATACGATAGTCTTGGCGGAC
          1 TTCCACATATAAGATAGTCCTGGCGGAC

                 *    *         *     *  
        691 TTCTCGCATAAAAGATAGTCTTGGCGAAC
          1 TTC-CACATATAAGATAGTCCTGGCGGAC

                    *  *          **    
        720 TTCCACATTTACGATAGTCCTGATGGAC
          1 TTCCACATATAAGATAGTCCTGGCGGAC

                *                 *  *   
        748 TTCTAACATATAAGATAGTCCTCGCAGAC
          1 TTC-CACATATAAGATAGTCCTGGCGGAC

                    *  *      **  * **  
        777 TTCCACATTTACGATAGTGTTGACAAAC
          1 TTCCACATATAAGATAGTCCTGGCGGAC

                  *               * *    
        805 TTCCTATATATAAGATAGTCCTAGTGGAC
          1 TTCC-ACATATAAGATAGTCCTGGCGGAC

                    *  *     *    *   **
        834 TTCCACATTTATGATAGCCCTGACGGGT
          1 TTCCACATATAAGATAGTCCTGGCGGAC

                                *     *  
        862 TTCCCACATAT-AGATAGTCTTGGCGAAC
          1 TT-CCACATATAAGATAGTCCTGGCGGAC

                    
        890 TTCCACAT
          1 TTCCACAT

        898 TTACGATAAT


Statistics
Matches: 196,  Mismatches: 63, Indels: 11
        0.73            0.23        0.04

Matches are distributed among these distances:
  27    6  0.03
  28   98  0.50
  29   92  0.47

ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31


Consensus pattern (28 bp):   
TTCCACATATAAGATAGTCCTGGCGGAC

Done.