Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2906

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, 496

Length: 827
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41


Found at i:724 original size:10 final size:9

Alignment explanation


    Indices: 709--779  Score: 56
    Period size: 10  Copynumber: 7.8  Consensus size: 9

        699 TTCATCTTGA

                     
        709 TTTTTTTCT
          1 TTTTTTTCT

                      
        718 CTTTTTTT-T
          1 -TTTTTTTCT

             *       
        727 TGTTTTT-T
          1 TTTTTTTCT

            *    *   
        735 GTTTTGTCT
          1 TTTTTTTCT

                      
        744 GTTTTTTTCT
          1 -TTTTTTTCT

            *      * 
        754 GTTTTTTGT
          1 TTTTTTTCT

                     
        763 TTTTTTTCT
          1 TTTTTTTCT

                    
        772 ATTTTTTT
          1 -TTTTTTT

        780 TGTTTGTTTT


Statistics
Matches: 48,  Mismatches: 10, Indels: 6
        0.75            0.16        0.09

Matches are distributed among these distances:
   8   11  0.23
   9   16  0.33
  10   21  0.44

ACGTcount: A:0.01, C:0.07, G:0.08, T:0.83


Consensus pattern (9 bp):   
TTTTTTTCT

Found at i:739 original size:26 final size:26

Alignment explanation


    Indices: 710--794  Score: 109
    Period size: 26  Copynumber: 3.2  Consensus size: 26

        700 TCATCTTGAT

                                      
        710 TTTTTTCTCTTTTTTTTTGTTTTTTG
          1 TTTTTTCTCTTTTTTTTTGTTTTTTG

                *   *       *         
        736 TTTTGTCTGTTTTTTTCTGTTTTTTG
          1 TTTTTTCTCTTTTTTTTTGTTTTTTG

                  *                     
        762 TTTTTTTTCTATTTTTTTTGTTTGTTT-
          1 TTTTTTCTCT-TTTTTTTTGTTT-TTTG

                  
        789 TTTTTT
          1 TTTTTT

        795 AAGCATAATA


Statistics
Matches: 50,  Mismatches: 7, Indels: 3
        0.83            0.12        0.05

Matches are distributed among these distances:
  26   30  0.60
  27   17  0.34
  28    3  0.06

ACGTcount: A:0.01, C:0.06, G:0.09, T:0.84


Consensus pattern (26 bp):   
TTTTTTCTCTTTTTTTTTGTTTTTTG

Found at i:789 original size:9 final size:8

Alignment explanation


    Indices: 721--792  Score: 60
    Period size: 8  Copynumber: 8.9  Consensus size: 8

        711 TTTTTCTCTT

                    
        721 TTTTTTTG
          1 TTTTTTTG

                    
        729 -TTTTTTG
          1 TTTTTTTG

                  *  
        736 TTTTGTCTG
          1 TTTT-TTTG

                   *
        745 TTTTTTTC
          1 TTTTTTTG

                     
        753 TGTTTTTTG
          1 T-TTTTTTG

                    
        762 TTTTTTT-
          1 TTTTTTTG

                      
        769 TCTATTTTT-
          1 T-T-TTTTTG

               *    
        778 TTTGTTTG
          1 TTTTTTTG

                   
        786 TTTTTTT
          1 TTTTTTT

        793 TTAAGCATAA


Statistics
Matches: 52,  Mismatches: 6, Indels: 12
        0.74            0.09        0.17

Matches are distributed among these distances:
   7   12  0.23
   8   20  0.38
   9   20  0.38

ACGTcount: A:0.01, C:0.04, G:0.11, T:0.83


Consensus pattern (8 bp):   
TTTTTTTG
Done.