Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2434

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: 5783
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30


Found at i:829 original size:39 final size:40

Alignment explanation


    Indices: 785--985  Score: 276
    Period size: 39  Copynumber: 5.2  Consensus size: 40

        775 CCTTCGGAGT

                                 *  *                
        785 TTAG-CCGGATATAGCT-ACTAGCTCAAATGCCTTCGGGAC
          1 TTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGAC

                     *                              
        824 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTC-GGAC
          1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC

                                                    
        863 TTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGGAC
          1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC

                                                    
        902 TTAGCCCGGA-ATAGTAACTCGCACAAATGCCTTCGGG-C
          1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC

                          * *   *                   
        940 TTAGCCC-GA-AT-TTCACTAGCACAAATGCCTTCGGGAC
          1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC

                     
        977 TTAGCCCGG
          1 TTAGCCCGG

        986 TATCAATCCG


Statistics
Matches: 150,  Mismatches: 6, Indels: 13
        0.89            0.04        0.08

Matches are distributed among these distances:
  36   21  0.14
  37   12  0.08
  38   34  0.23
  39   58  0.39
  40   25  0.17

ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24


Consensus pattern (40 bp):   
TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC

Found at i:885 original size:38 final size:39

Alignment explanation


    Indices: 808--988  Score: 280
    Period size: 39  Copynumber: 4.7  Consensus size: 39

        798 GCTACTAGCT

                                                    
        808 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA

                                                   
        848 CAAATGCCTTC-GGACTTAGCCCGGTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA

                                     *             
        886 CAAATGCCTTCGGGACTTAGCCCGGAATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA

                                     *   * *   *   
        925 CAAATGCCTTCGGG-CTTAGCCC-GAAT-TTCACTAGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA

                                        
        961 CAAATGCCTTCGGGACTTAGCCCGGTAT
          1 CAAATGCCTTCGGGACTTAGCCCGGTAT

        989 CAATCCGAAT


Statistics
Matches: 133,  Mismatches: 5, Indels: 8
        0.91            0.03        0.05

Matches are distributed among these distances:
  36   21  0.16
  37   12  0.09
  38   36  0.27
  39   53  0.40
  40   11  0.08

ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24


Consensus pattern (39 bp):   
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA

Found at i:946 original size:77 final size:76

Alignment explanation


    Indices: 801--987  Score: 286
    Period size: 77  Copynumber: 2.4  Consensus size: 76

        791 GGATATAGCT

                  *                          *                               
        801 ACTAGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGACTTA
          1 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGTAATAGTAACTCGCACAAATGCCTTCGGACTTA

                  *      
        866 GCCCGGTATAGTA
         66 GCCC-GAAT-GTA

               *                                                        *    
        879 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-AATAGTAACTCGCACAAATGCCTTCGGGCTTA
          1 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGTAATAGTAACTCGCACAAATGCCTTCGGACTTA

                    * *
        943 GCCCGAATTTC
         66 GCCCGAATGTA

                                              
        954 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGTA
          1 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGTA

        988 TCAATCCGAA


Statistics
Matches: 100,  Mismatches: 8, Indels: 4
        0.89            0.07        0.04

Matches are distributed among these distances:
  75   32  0.32
  76    4  0.04
  77   34  0.34
  78   30  0.30

ACGTcount: A:0.26, C:0.29, G:0.22, T:0.24


Consensus pattern (76 bp):   
ACTAGCACAAATGCCTTCGGGACTTAGCCCGGTAATAGTAACTCGCACAAATGCCTTCGGACTTA
GCCCGAATGTA
Done.