Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2071

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: 1121
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23


Found at i:1003 original size:1 final size:1

Alignment explanation


    Indices: 999--1072  Score: 76
    Period size: 1  Copynumber: 74.0  Consensus size: 1

        989 AAAAGTAGAC

                    *        *        *         *       *          *      *  
        999 AAAAAAAACAAAAAAAACAAAAAAAACAAAAAAAAACAAAAAAATAAAAAAAAAACAAAAAAGAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

               *     
       1064 AAAGAAAAA
          1 AAAAAAAAA

       1073 TCAAGATCAA


Statistics
Matches: 57,  Mismatches: 16, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
   1   57  1.00

ACGTcount: A:0.89, C:0.07, G:0.03, T:0.01


Consensus pattern (1 bp):   
A

Found at i:1011 original size:9 final size:9

Alignment explanation


    Indices: 997--1060  Score: 101
    Period size: 9  Copynumber: 6.9  Consensus size: 9

        987 AAAAAAGTAG

                     
        997 ACAAAAAAA
          1 ACAAAAAAA

                     
       1006 ACAAAAAAA
          1 ACAAAAAAA

                     
       1015 ACAAAAAAA
          1 ACAAAAAAA

                      
       1024 ACAAAAAAAA
          1 AC-AAAAAAA

                     
       1034 ACAAAAAAA
          1 ACAAAAAAA

              *       
       1043 TAAAAAAAAA
          1 -ACAAAAAAA

                    
       1053 ACAAAAAA
          1 ACAAAAAA

       1061 GAAAAAGAAA


Statistics
Matches: 51,  Mismatches: 2, Indels: 4
        0.89            0.04        0.07

Matches are distributed among these distances:
   9   34  0.67
  10   17  0.33

ACGTcount: A:0.89, C:0.09, G:0.00, T:0.02


Consensus pattern (9 bp):   
ACAAAAAAA

Found at i:1065 original size:18 final size:17

Alignment explanation


    Indices: 999--1072  Score: 94
    Period size: 18  Copynumber: 4.2  Consensus size: 17

        989 AAAAGTAGAC

                             
        999 AAAAAAAACAAAAAAAA
          1 AAAAAAAACAAAAAAAA

                              
       1016 CAAAAAAAACAAAAAAAA
          1 -AAAAAAAACAAAAAAAA

                     *        
       1034 ACAAAAAAATAAAAAAAA
          1 A-AAAAAAACAAAAAAAA

                     *     *  
       1052 AACAAAAAAGAAAAAGAA
          1 AA-AAAAAACAAAAAAAA

               
       1070 AAA
          1 AAA

       1073 TCAAGATCAA


Statistics
Matches: 51,  Mismatches: 3, Indels: 5
        0.86            0.05        0.08

Matches are distributed among these distances:
  17    3  0.06
  18   48  0.94

ACGTcount: A:0.89, C:0.07, G:0.03, T:0.01


Consensus pattern (17 bp):   
AAAAAAAACAAAAAAAA

Found at i:1066 original size:19 final size:18

Alignment explanation


    Indices: 997--1072  Score: 107
    Period size: 19  Copynumber: 4.0  Consensus size: 18

        987 AAAAAAGTAG

                      *       
        997 ACAAAAAAAACAAAAAAA
          1 ACAAAAAAAAAAAAAAAA

                               
       1015 ACAAAAAAAACAAAAAAAA
          1 ACAAAAAAAA-AAAAAAAA

                               
       1034 ACAAAAAAATAAAAAAAAA
          1 ACAAAAAAA-AAAAAAAAA

                                
       1053 ACAAAAAAGAAAAAGAAAAA
          1 ACAAAAAA-AAAAA-AAAAA

       1073 TCAAGATCAA


Statistics
Matches: 53,  Mismatches: 1, Indels: 6
        0.88            0.02        0.10

Matches are distributed among these distances:
  18   10  0.19
  19   36  0.68
  20    7  0.13

ACGTcount: A:0.88, C:0.08, G:0.03, T:0.01


Consensus pattern (18 bp):   
ACAAAAAAAAAAAAAAAA
Done.