Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2073

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, 672

Length: 1120
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36


Found at i:931 original size:69 final size:69

Alignment explanation


    Indices: 856--1120  Score: 442
    Period size: 69  Copynumber: 3.8  Consensus size: 69

        846 GGACAGCTCT

                    *     *                         *                        
        856 TATATACAACAAATGGGCAGCATATACATACCAAATTTAATAGCACTTTTACACCAAAATTTAAC
          1 TATATACAGCAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC

              * 
        921 AGTA
         66 AGCA

                     *                                                       
        925 TATATACAGTAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
          1 TATATACAGCAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC

                
        990 AGCA
         66 AGCA

                                                                             
        994 TATATACAGCAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
          1 TATATACAGCAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC

                
       1059 AGCA
         66 AGCA

                                                  * *     *            
       1063 TATATACAGCAAAT-GGACAGCATATACATACCAAATTGAGCAGCATTTTTACACCAAA
          1 TATATACAGCAAATAGG-CAGCATATACATACCAAATTTAACAGCACTTTTACACCAAA


Statistics
Matches: 186,  Mismatches: 9, Indels: 2
        0.94            0.05        0.01

Matches are distributed among these distances:
  68    2  0.01
  69  184  0.99

ACGTcount: A:0.45, C:0.20, G:0.09, T:0.26


Consensus pattern (69 bp):   
TATATACAGCAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
AGCA

Found at i:932 original size:24 final size:24

Alignment explanation


    Indices: 873--1075  Score: 124
    Period size: 24  Copynumber: 8.8  Consensus size: 24

        863 AACAAATGGG

                     * *            
        873 CAGCATATACATACC-AAATTTAA
          1 CAGCATATATACACCAAAATTTAA

            *        *               
        896 TAGCACT-TTTACACCAAAATTTAA
          1 CAGCA-TATATACACCAAAATTTAA

               *          **        *
        920 CAGTATATATACA-GTAAA--TAGG
          1 CAGCATATATACACCAAAATTTA-A

                     * *            
        942 CAGCATATACATACC-AAATTTAA
          1 CAGCATATATACACCAAAATTTAA

                     *               
        965 CAGCACT-TTTACACCAAAATTTAA
          1 CAGCA-TATATACACCAAAATTTAA

                         *          *
        989 CAGCATATATACAGC-AAA--TAGG
          1 CAGCATATATACACCAAAATTTA-A

                     * *            
       1011 CAGCATATACATACC-AAATTTAA
          1 CAGCATATATACACCAAAATTTAA

                     *               
       1034 CAGCACT-TTTACACCAAAATTTAA
          1 CAGCA-TATATACACCAAAATTTAA

                         *    
       1058 CAGCATATATACAGCAAA
          1 CAGCATATATACACCAAA

       1076 TGGACAGCAT


Statistics
Matches: 134,  Mismatches: 30, Indels: 31
        0.69            0.15        0.16

Matches are distributed among these distances:
  21    4  0.03
  22   28  0.21
  23   38  0.28
  24   64  0.48

ACGTcount: A:0.45, C:0.21, G:0.08, T:0.26


Consensus pattern (24 bp):   
CAGCATATATACACCAAAATTTAA

Found at i:1097 original size:22 final size:22

Alignment explanation


    Indices: 1057--1108  Score: 59
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       1047 CCAAAATTTA

                      *   *       
       1057 ACAGCATATATACAGCAAATGG
          1 ACAGCATATACACACCAAATGG

                        *       * 
       1079 ACAGCATATACATACCAAATTG
          1 ACAGCATATACACACCAAATGG

                    
       1101 AGCAGCAT
          1 A-CAGCAT

       1109 TTTTACACCA


Statistics
Matches: 25,  Mismatches: 4, Indels: 1
        0.83            0.13        0.03

Matches are distributed among these distances:
  22   19  0.76
  23    6  0.24

ACGTcount: A:0.44, C:0.21, G:0.15, T:0.19


Consensus pattern (22 bp):   
ACAGCATATACACACCAAATGG
Done.