Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g02775.F1

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: 3469
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32


Found at i:2127 original size:174 final size:174

Alignment explanation


    Indices: 1837--2162  Score: 438
    Period size: 174  Copynumber: 1.9  Consensus size: 174

       1827 CTGGGCCATA

                      *              *        *           *   *    ** *      
       1837 TCAGGCAGATTTCTGGAGCAAATTTGGTTATTCATGACCCAAAGCCGGGGGCCACTGATGGTTTA
          1 TCAGGCAGATATCTGGAGCAAATTTAGTTATTCAAGACCCAAAGCCAGGGACCACCAAGGGTTTA

                       *                    *  **      *              *      
       1902 GTTGTTGTCTCTGGAACATCGGATCAGTTACGTACTGCTCAAAGCCTTATTCAAGCTTTTATCCT
         66 GTTGTTGTCTCGGGAACATCGGATCAGTTACGGACAACTCAAACCCTTATTCAAGCTTATATCCT

                            *                           
       1967 ATGCGGACAAACTGCAGCTTGAGTATCTGTTAAATATTTGTCCT
        131 ATGCGGACAAACTGCAACTTGAGTATCTGTTAAATATTTGTCCT

                                                    *       *   *            
       2011 TCAGGCAGATATCTGGAGCAAATTTAGTTATTCAAGACCCGAAGCCAGTGACTACCAAGGGTTTA
          1 TCAGGCAGATATCTGGAGCAAATTTAGTTATTCAAGACCCAAAGCCAGGGACCACCAAGGGTTTA

                                  *       *           *                      
       2076 GTTGTTGTGCT-GGGAACATCGTATCAGTTGCGGACAACTCAGACCCTTATTCAAGCTTATATCC
         66 GTTGTTGT-CTCGGGAACATCGGATCAGTTACGGACAACTCAAACCCTTATTCAAGCTTATATCC

             *                     
       2140 TTTGCGGACAAACTGCAACTTGA
        130 TATGCGGACAAACTGCAACTTGA

       2163 AGATCTATTC


Statistics
Matches: 129,  Mismatches: 22, Indels: 2
        0.84            0.14        0.01

Matches are distributed among these distances:
 174  127  0.98
 175    2  0.02

ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30


Consensus pattern (174 bp):   
TCAGGCAGATATCTGGAGCAAATTTAGTTATTCAAGACCCAAAGCCAGGGACCACCAAGGGTTTA
GTTGTTGTCTCGGGAACATCGGATCAGTTACGGACAACTCAAACCCTTATTCAAGCTTATATCCT
ATGCGGACAAACTGCAACTTGAGTATCTGTTAAATATTTGTCCT

Found at i:3041 original size:78 final size:78

Alignment explanation


    Indices: 2874--3033  Score: 241
    Period size: 78  Copynumber: 2.1  Consensus size: 78

       2864 TTGTGTTATT

                *                                                          * 
       2874 TTTGCATATTTTCATGTTATAGTAGTGTTAAAGGTGTTTTACATTTGGTATAAAGCTCGATATTG
          1 TTTGTATATTTTCATGTTATAGTAGTGTTAAAGGTGTTTTACATTTGGTATAAAGCTCGATATCG

                         
       2939 GATAATTAGTACA
         66 GATAATTAGTACA

                                                    *        *     * *   *   
       2952 TTTGTATATTTTCATGTTATAGTAGTGTTAAAGGTGTTTTGCATTT-GTTTAAAGTTTGATGTCG
          1 TTTGTATATTTTCATGTTATAGTAGTGTTAAAGGTGTTTTACATTTGGTATAAAGCTCGATATCG

                *        
       3016 GATACTTAGTACA
         66 GATAATTAGTACA

                 
       3029 TTTGT
          1 TTTGT

       3034 GTTATTTTTG


Statistics
Matches: 74,  Mismatches: 8, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  77   30  0.41
  78   44  0.59

ACGTcount: A:0.26, C:0.07, G:0.20, T:0.47


Consensus pattern (78 bp):   
TTTGTATATTTTCATGTTATAGTAGTGTTAAAGGTGTTTTACATTTGGTATAAAGCTCGATATCG
GATAATTAGTACA
Done.