Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g02260.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: 2959
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.26


Found at i:1302 original size:90 final size:90

Alignment explanation


    Indices: 833--1290  Score: 772
    Period size: 90  Copynumber: 5.1  Consensus size: 90

        823 AATGTTTGAA

                                                              *        *     
        833 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCTGATTGGACTTCCTT
          1 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT

                                     
        898 TTTAGAACGAAACAAGGAATGGAAT
         66 TTTAGAACGAAACAAGGAATGGAAT

                          *                                      *           
        923 CGTCGCCGTCTTCTTCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGACTGGACATCCTT
          1 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT

                                     
        988 TTTAGAACGAAACAAGGAATGGAAT
         66 TTTAGAACGAAACAAGGAATGGAAT

                 *        *            *                                     
       1013 CGTCGTCGTCTTCTTCAAGACGAAGATAGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT
          1 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT

                                     
       1078 TTTAGAACGAAACAAGGAATGGAAT
         66 TTTAGAACGAAACAAGGAATGGAAT

                                                   * *                       
       1103 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTGTCGGCCATTCCGATTGGACATCCTT
          1 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT

                           *         
       1168 TTTAGAACGAAACAAAGAATGGAAT
         66 TTTAGAACGAAACAAGGAATGGAAT

                 *                     *                                  *  
       1193 CGTCGTCGTCTTCTCCAAGACGAAGATAGACTTCCGGTTATTGGCCATTCCGATTGGACATCATT
          1 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT

                     *              *
       1258 TTTAGAACGGAACAAGGAATGGAAC
         66 TTTAGAACGAAACAAGGAATGGAAT

              *     
       1283 CGCCGCCG
          1 CGTCGCCG

       1291 GATGCTCCAA


Statistics
Matches: 345,  Mismatches: 23, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  90  345  1.00

ACGTcount: A:0.26, C:0.23, G:0.23, T:0.27


Consensus pattern (90 bp):   
CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT
TTTAGAACGAAACAAGGAATGGAAT

Found at i:2415 original size:51 final size:51

Alignment explanation


    Indices: 2355--2755  Score: 516
    Period size: 51  Copynumber: 7.9  Consensus size: 51

       2345 AAAACTGAAG

                *     *        *    *                   *      
       2355 ACAAAGGGTTGATCCCTACGTCCCTAGATGTTCCCGCTAGTAAATCCGAAA
          1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA

                                                          *    
       2406 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCTGAAA
          1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA

                                                               
       2457 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA
          1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA

               *    *             *                            
       2508 ACAGTGGGCTCATCCCTACCTCTCCAGATGTTCCCGCTAGTAAACCCGAAA
          1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA

               *       *               *         *              
       2559 ACAGTGAGG-TGATCCCTACCTCCCCAAATGTTCCCGTTAGTAAACCCGAAA
          1 ACAATG-GGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA

                                            *   *              
       2610 ACAATGGGTTCATCCCTACCTCCCCAGATGTTTCCGTTAGTAAACCCGAAA
          1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA

               *      *       *   *      *  *             *    
       2661 ACAGTGGGTTGATCCCTATCTCTCCAGATCTTTCCGCTAGTAAACCTGAAA
          1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA

                    * **  *   *       *  *  *           
       2712 ACAATGGGGTGGTCTCTATCTCCCCAAATCTTTCCGCTAGTAAA
          1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAA

       2756 GCCGCACACA


Statistics
Matches: 317,  Mismatches: 31, Indels: 4
        0.90            0.09        0.01

Matches are distributed among these distances:
  50    2  0.01
  51  313  0.99
  52    2  0.01

ACGTcount: A:0.27, C:0.31, G:0.17, T:0.24


Consensus pattern (51 bp):   
ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA

Found at i:2828 original size:21 final size:21

Alignment explanation


    Indices: 2804--2843  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       2794 ACACAAGAAA

                          *      
       2804 AAGAAGCACCATGGGAAAGGG
          1 AAGAAGCACCATGGAAAAGGG

                               
       2825 AAGAAGCACCATGGAAAAG
          1 AAGAAGCACCATGGAAAAG

       2844 TTGAGGCGAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.47, C:0.15, G:0.33, T:0.05


Consensus pattern (21 bp):   
AAGAAGCACCATGGAAAAGGG
Done.