Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1653

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, 863

Length: 1439
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30


Found at i:111 original size:9 final size:9

Alignment explanation


    Indices: 93--145  Score: 65
    Period size: 9  Copynumber: 6.1  Consensus size: 9

         83 AACTTGTCGG

                *    
         93 ACTTGCATA
          1 ACTTACATA

                 *   
        102 ACTTATATA
          1 ACTTACATA

                  *  
        111 A--TACTTA
          1 ACTTACATA

                     
        118 ACTTACATA
          1 ACTTACATA

                     
        127 ACTTACATA
          1 ACTTACATA

                     
        136 ACTTACATA
          1 ACTTACATA

             
        145 A
          1 A

        146 TACTTGGGTT


Statistics
Matches: 37,  Mismatches: 5, Indels: 4
        0.80            0.11        0.09

Matches are distributed among these distances:
   7    5  0.14
   9   32  0.86

ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36


Consensus pattern (9 bp):   
ACTTACATA

Found at i:173 original size:16 final size:16

Alignment explanation


    Indices: 98--177  Score: 79
    Period size: 16  Copynumber: 4.9  Consensus size: 16

         88 GTCGGACTTG

                     *      
         98 CATAACTTATATAATA
          1 CATAACTTACATAATA

             *                
        114 CTTAACTTACATAACTTA
          1 CATAACTTACATAA--TA

                            
        132 CATAACTTACATAATA
          1 CATAACTTACATAATA

             * ***    *     
        148 CTTGGGTTACGTAATA
          1 CATAACTTACATAATA

                          
        164 CATAACTTACATAA
          1 CATAACTTACATAA

        178 CTCATATATA


Statistics
Matches: 49,  Mismatches: 13, Indels: 4
        0.74            0.20        0.06

Matches are distributed among these distances:
  16   34  0.69
  18   15  0.31

ACGTcount: A:0.42, C:0.17, G:0.05, T:0.35


Consensus pattern (16 bp):   
CATAACTTACATAATA
Done.