Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g00177.P2

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: 4126
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35


Found at i:1756 original size:9 final size:9

Alignment explanation


    Indices: 1717--1848  Score: 63
    Period size: 9  Copynumber: 13.8  Consensus size: 9

       1707 CTTTATAAAA

                     
       1717 TTTTATAAT
          1 TTTTATAAT

                *    
       1726 TTTTCT-AT
          1 TTTTATAAT

                      
       1734 TTTCTAT-AT
          1 TTT-TATAAT

                         
       1743 ATTTTATAATTTT
          1 -TTTTATAA---T

                     
       1756 TTTTATAAT
          1 TTTTATAAT

                     *
       1765 TTTTATAAAA
          1 TTTTAT-AAT

              *  *    
       1775 TTGTACAATT
          1 TTTTATAA-T

                     
       1785 TTTTATAAT
          1 TTTTATAAT

                      
       1794 TTTT-TAACT
          1 TTTTATAA-T

                *   *
       1803 TTTTCTAAC
          1 TTTTATAAT

                 *    
       1812 TTTTAAATAT
          1 TTTTATA-AT

                      *
       1822 TTTTATTAAAA
          1 TTTTA-T-AAT

               *     
       1833 TTTAATAAT
          1 TTTTATAAT

                   
       1842 TTTTATA
          1 TTTTATA

       1849 TCTTTAATTA


Statistics
Matches: 93,  Mismatches: 17, Indels: 26
        0.68            0.12        0.19

Matches are distributed among these distances:
   8    8  0.09
   9   44  0.47
  10   26  0.28
  11    5  0.05
  12    9  0.10
  13    1  0.01

ACGTcount: A:0.33, C:0.05, G:0.01, T:0.62


Consensus pattern (9 bp):   
TTTTATAAT

Found at i:1761 original size:12 final size:12

Alignment explanation


    Indices: 1744--1768  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       1734 TTTCTATATA

                        
       1744 TTTTATAATTTT
          1 TTTTATAATTTT

                        
       1756 TTTTATAATTTT
          1 TTTTATAATTTT

             
       1768 T
          1 T

       1769 ATAAAATTGT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76


Consensus pattern (12 bp):   
TTTTATAATTTT

Found at i:1762 original size:21 final size:21

Alignment explanation


    Indices: 1733--1772  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       1723 AATTTTTCTA

                                  
       1733 TTTTCTAT-ATATTTTATAATT
          1 TTTTCTATAAT-TTTTATAATT

                *              
       1754 TTTTTTATAATTTTTATAA
          1 TTTTCTATAATTTTTATAA

       1773 AATTGTACAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  21   15  0.88
  22    2  0.12

ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68


Consensus pattern (21 bp):   
TTTTCTATAATTTTTATAATT

Done.