Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: CotAD_28673

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: 1998
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25


Found at i:1855 original size:3 final size:3

Alignment explanation


    Indices: 1847--1950  Score: 94
    Period size: 3  Copynumber: 35.3  Consensus size: 3

       1837 TCCATTTCGG

                                                                  *     
       1847 GAA GAA GAA -AA GAA -AA G-A GAA GAA GAA -AA GGAA GAA GGA GAA
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA

                          *                *                              
       1889 GAA GGAA GAA GGA GAA GAA GGAA GGA GAA GAA GAA -AA GAAA GAA G-A
          1 GAA -GAA GAA GAA GAA GAA -GAA GAA GAA GAA GAA GAA G-AA GAA GAA

                         *       
       1935 GAA GAA GAA GGA GAA G
          1 GAA GAA GAA GAA GAA G

       1951 GAGTCGGCAG


Statistics
Matches: 83,  Mismatches: 8, Indels: 20
        0.75            0.07        0.18

Matches are distributed among these distances:
   2   12  0.14
   3   60  0.72
   4   11  0.13

ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00


Consensus pattern (3 bp):   
GAA

Found at i:1895 original size:16 final size:16

Alignment explanation


    Indices: 1864--1950  Score: 94
    Period size: 16  Copynumber: 5.7  Consensus size: 16

       1854 AAAAGAAAAG

                 *          
       1864 AGAAGAAGAA-AAGGA
          1 AGAAGGAGAAGAAGGA

                            
       1879 AGAAGGAGAAGAAGGA
          1 AGAAGGAGAAGAAGGA

                            
       1895 AGAAGGAGAAGAAGGA
          1 AGAAGGAGAAGAAGGA

              *  *          
       1911 AGGAGAAGAAGAA--A
          1 AGAAGGAGAAGAAGGA

                          *  
       1925 AGAA--AGAAGAGAAGA
          1 AGAAGGAGAAGA-AGGA

                       
       1940 AGAAGGAGAAG
          1 AGAAGGAGAAG

       1951 GAGTCGGCAG


Statistics
Matches: 62,  Mismatches: 4, Indels: 10
        0.82            0.05        0.13

Matches are distributed among these distances:
  12    6  0.10
  13    1  0.02
  14    4  0.06
  15   14  0.23
  16   32  0.52
  17    5  0.08

ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00


Consensus pattern (16 bp):   
AGAAGGAGAAGAAGGA

Found at i:1919 original size:29 final size:31

Alignment explanation


    Indices: 1847--1950  Score: 108
    Period size: 33  Copynumber: 3.3  Consensus size: 31

       1837 TCCATTTCGG

                *                      *      
       1847 GAAGAAGAA-AAGAAAAGAGAAGAAGAAAAGGAA
          1 GAAGGAGAAGAAGAAAAGA-AAG-AGAGAA-GAA

                          *                
       1880 GAAGGAGAAGAAG-GAAG-AAG-GAGAAGAA
          1 GAAGGAGAAGAAGAAAAGAAAGAGAGAAGAA

                                             
       1908 GGAAGGAGAAGAAGAAAAGAAAGAAGAGAAGAA
          1 -GAAGGAGAAGAAGAAAAGAAAG-AGAGAAGAA

                      
       1941 GAAGGAGAAG
          1 GAAGGAGAAG

       1951 GAGTCGGCAG


Statistics
Matches: 61,  Mismatches: 4, Indels: 13
        0.78            0.05        0.17

Matches are distributed among these distances:
  28    3  0.05
  29   17  0.28
  30    3  0.05
  31    6  0.10
  32   10  0.16
  33   19  0.31
  34    3  0.05

ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00


Consensus pattern (31 bp):   
GAAGGAGAAGAAGAAAAGAAAGAGAGAAGAA

Done.