Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g00377.F1

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: 3545
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25


Found at i:2593 original size:78 final size:78

Alignment explanation


    Indices: 2502--2888  Score: 693
    Period size: 78  Copynumber: 5.0  Consensus size: 78

       2492 GTTGATGGCG

                                                       *                     
       2502 CTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGATACACCCAAGTCTACCAAATCC
          1 CTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTACCAAATCC

                 *      *
       2567 AAGGATGATGTCG
         66 AAGGAGGATGTCA

                    *                                                        
       2580 CTTCAAAAATAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTACCAAATCC
          1 CTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTACCAAATCC

                         
       2645 AAGGAGGATGTCA
         66 AAGGAGGATGTCA

                  *                                                          
       2658 CTTCAAGAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTACCAAATCC
          1 CTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTACCAAATCC

                         
       2723 AAGGAGGATGTCA
         66 AAGGAGGATGTCA

                                                                             
       2736 CTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTACCAAATCC
          1 CTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTACCAAATCC

                         
       2801 AAGGAGGATGTCA
         66 AAGGAGGATGTCA

                               *                           *                *
       2814 CTTCAAAAGTAGGCAACAAGTCCAAAAATGAGGACACTGGTGACACAGCCAAGTCTACCAAATCT
          1 CTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTACCAAATCC

                 *    
       2879 AAGGATGATG
         66 AAGGAGGATG

       2889 ACAATGTTAC


Statistics
Matches: 298,  Mismatches: 11, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  78  298  1.00

ACGTcount: A:0.41, C:0.24, G:0.20, T:0.16


Consensus pattern (78 bp):   
CTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTACCAAATCC
AAGGAGGATGTCA

Found at i:2643 original size:42 final size:42

Alignment explanation


    Indices: 2518--2802  Score: 140
    Period size: 42  Copynumber: 7.2  Consensus size: 42

       2508 AAGTAGGCAA

                                       *              
       2518 CAAATCCAAAAATGAGGACACTGGTGATACACCCAAGTCTAC
          1 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC

                     **    * * *            **    *   *
       2560 CAAATCCAAGGATGATGTCGCT--T--CA-A-AAATAGGC-AA
          1 CAAATCCAAAAATGAGGACACTGGTGACACACCCA-AGTCTAC

                                                      
       2596 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC
          1 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC

                     ** *  * *             ****  *   *
       2638 CAAATCCAAGGAGGATGTCACT--T--CA-AGAGTAGGC-AA
          1 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC

                                                      
       2674 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC
          1 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC

                     ** *  * *             ****  *   *
       2716 CAAATCCAAGGAGGATGTCACT--T--CA-AAAGTAGGC-AA
          1 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC

                                                      
       2752 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC
          1 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC

                     
       2794 CAAATCCAA
          1 CAAATCCAA

       2803 GGAGGATGTC


Statistics
Matches: 160,  Mismatches: 63, Indels: 40
        0.61            0.24        0.15

Matches are distributed among these distances:
  36   55  0.34
  37   12  0.08
  38    8  0.05
  40    9  0.06
  41   12  0.08
  42   64  0.40

ACGTcount: A:0.41, C:0.25, G:0.18, T:0.16


Consensus pattern (42 bp):   
CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC

Done.