Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g01212.N1

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: 2244
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35


Found at i:1756 original size:40 final size:40

Alignment explanation


    Indices: 1712--1967  Score: 279
    Period size: 40  Copynumber: 6.5  Consensus size: 40

       1702 TATTCGAGCC

                     *                               
       1712 TAAAGACCCACAGGCTAT-ATGCTGGAATTATATCCGGGCT
          1 TAAAGACCCGCAGGCT-TCATGCTGGAATTATATCCGGGCT

                                              * *    
       1752 TAAAGACCCGCAGGCTAT-ATGCTGGAATTATATTCAGGCT
          1 TAAAGACCCGCAGGCT-TCATGCTGGAATTATATCCGGGCT

                  *           *          *          
       1792 TAAAGATCCGCAGGCTTCGTGCTGGAATTGTATCCGGGCT
          1 TAAAGACCCGCAGGCTTCATGCTGGAATTATATCCGGGCT

                                          *          
       1832 TAAAGACCCGCAGGCTAT-ATGCTGGAATTGTATCCGGGCT
          1 TAAAGACCCGCAGGCT-TCATGCTGGAATTATATCCGGGCT

                              *          *       *  
       1872 TAAAGACCCGCAGGCTTCGTGCTGGAATTGTATCCGGACT
          1 TAAAGACCCGCAGGCTTCATGCTGGAATTATATCCGGGCT

                  * **        *      * *         *  
       1912 T-AAGATCAACAGGCTTCGTGCTGGTACTATATCCGGACT
          1 TAAAGACCCGCAGGCTTCATGCTGGAATTATATCCGGGCT

                 **           
       1951 T-AAGGTCCGCAGGCTTC
          1 TAAAGACCCGCAGGCTTC

       1968 GTACTGGTGC


Statistics
Matches: 192,  Mismatches: 21, Indels: 7
        0.87            0.10        0.03

Matches are distributed among these distances:
  39   48  0.25
  40  143  0.74
  41    1  0.01

ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26


Consensus pattern (40 bp):   
TAAAGACCCGCAGGCTTCATGCTGGAATTATATCCGGGCT

Found at i:1833 original size:80 final size:80

Alignment explanation


    Indices: 1712--1914  Score: 318
    Period size: 80  Copynumber: 2.5  Consensus size: 80

       1702 TATTCGAGCC

                     *         *          *                                  
       1712 TAAAGACCCACAGGCTAT-ATGCTGGAATTATATCCGGGCTTAAAGACCCGCAGGCTATATGCTG
          1 TAAAGACCCGCAGGCT-TCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGCTG

                     *      
       1776 GAATTATATTCAGGCT
         65 GAATTATATCCAGGCT

                  *                                                          
       1792 TAAAGATCCGCAGGCTTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGCTGG
          1 TAAAGACCCGCAGGCTTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGCTGG

                *     *    
       1857 AATTGTATCCGGGCT
         66 AATTATATCCAGGCT

                                                 *     
       1872 TAAAGACCCGCAGGCTTCGTGCTGGAATTGTATCCGGACTTAA
          1 TAAAGACCCGCAGGCTTCGTGCTGGAATTGTATCCGGGCTTAA

       1915 GATCAACAGG


Statistics
Matches: 113,  Mismatches: 9, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
  79    1  0.01
  80  112  0.99

ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26


Consensus pattern (80 bp):   
TAAAGACCCGCAGGCTTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGCTGG
AATTATATCCAGGCT

Found at i:1945 original size:39 final size:39

Alignment explanation


    Indices: 1882--1986  Score: 138
    Period size: 39  Copynumber: 2.7  Consensus size: 39

       1872 TAAAGACCCG

                           * * *                   
       1882 CAGGCTTCGTGCTGGAATTGTATCCGGACTTAAGATCAA
          1 CAGGCTTCGTGCTGGTACTATATCCGGACTTAAGATCAA

                                              *  **
       1921 CAGGCTTCGTGCTGGTACTATATCCGGACTTAAGGTCCG
          1 CAGGCTTCGTGCTGGTACTATATCCGGACTTAAGATCAA

                      *     *          
       1960 CAGGCTTCGTACTGGTGCTATATCCGG
          1 CAGGCTTCGTGCTGGTACTATATCCGG

       1987 GGTTAACGTC


Statistics
Matches: 58,  Mismatches: 8, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  39   58  1.00

ACGTcount: A:0.20, C:0.24, G:0.28, T:0.29


Consensus pattern (39 bp):   
CAGGCTTCGTGCTGGTACTATATCCGGACTTAAGATCAA

Found at i:2016 original size:40 final size:39

Alignment explanation


    Indices: 1879--2016  Score: 125
    Period size: 39  Copynumber: 3.5  Consensus size: 39

       1869 GCTTAAAGAC

                              *** *                 
       1879 CCGCAGGCTTCGTGCTGGAATTGTATCCGGACTTAA-GAT
          1 CCGCAGGCTTCGTGCTGGTGCTATATCCGGACTTAACG-T

             **                *                *  
       1918 CAACAGGCTTCGTGCTGGTACTATATCCGGACTTAAGGT
          1 CCGCAGGCTTCGTGCTGGTGCTATATCCGGACTTAACGT

                         *                **       
       1957 CCGCAGGCTTCGTACTGGTGCTATATCCGGGGTTAACGT
          1 CCGCAGGCTTCGTGCTGGTGCTATATCCGGACTTAACGT

                *      *   *     
       1996 CCCGTAGGCTTTGTGTTGGTG
          1 -CCGCAGGCTTCGTGCTGGTG

       2017 ATTGAATTCG


Statistics
Matches: 81,  Mismatches: 16, Indels: 3
        0.81            0.16        0.03

Matches are distributed among these distances:
  39   64  0.79
  40   17  0.21

ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30


Consensus pattern (39 bp):   
CCGCAGGCTTCGTGCTGGTGCTATATCCGGACTTAACGT
Done.