Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g00447.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, 607

Length: 1013
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.20


Found at i:226 original size:45 final size:45

Alignment explanation


    Indices: 158--629  Score: 484
    Period size: 45  Copynumber: 10.5  Consensus size: 45

        148 CCCCACCTTA

                 *         *  *        * *            *  
        158 TGAACATAAGCCACCTGTCTATGAACCTCTAAAGAAAGAAAAACC
          1 TGAACCTAAGCCACCAGTTTATGAACCACCAAAGAAAGAAAAGCC

               * *         *  *        *              *  
        203 TGAGCATAAGCCACCTGTCTATGAACCTCCAAAGAAAGAAAAACC
          1 TGAACCTAAGCCACCAGTTTATGAACCACCAAAGAAAGAAAAGCC

                  *            *                 *        
        248 TGAACCCAAGCCACC-GATGTATGAACCACCAAAGAAGGAAAAGCC
          1 TGAACCTAAGCCACCAG-TTTATGAACCACCAAAGAAAGAAAAGCC

            *     *                     *           *     
        293 CGAACCAAAGCCACCAGTTTAT-ACACCTCCAAAGAAAGAGAAGCC
          1 TGAACCTAAGCCACCAGTTTATGA-ACCACCAAAGAAAGAAAAGCC

                  *  *        *                 *        
        338 TGAACCCAAACCACCAGTATATGAACCACCAAAGAAGGAAAAGCC
          1 TGAACCTAAGCCACCAGTTTATGAACCACCAAAGAAAGAAAAGCC

               *                                    *     
        383 TGAGCCTAAGCCACCAGTTTAT-ACACCACCAAAGAAAGAGAAGCC
          1 TGAACCTAAGCCACCAGTTTATGA-ACCACCAAAGAAAGAAAAGCC

                  *           *                 *        
        428 TGAACCCAAGCCACCAGTGTATGAACCACCAAAGAAGGAAAAGCC
          1 TGAACCTAAGCCACCAGTTTATGAACCACCAAAGAAAGAAAAGCC

               *                                    *    *
        473 TGAGCCTAAGCCACCAGTTTAT-ACACCACCAAAGAAAGAGAAGCT
          1 TGAACCTAAGCCACCAGTTTATGA-ACCACCAAAGAAAGAAAAGCC

                              *        *        *        
        518 TGAACCTAAGCCACCAGTGTATGAACCGCCAAAGAAGGAAAAGCC
          1 TGAACCTAAGCCACCAGTTTATGAACCACCAAAGAAAGAAAAGCC

            *  *  *   *            *   *              *  
        563 CGAGCCAAAGTCACCAGTTTATGCACCTCCAAAGAAAGAAAAACC
          1 TGAACCTAAGCCACCAGTTTATGAACCACCAAAGAAAGAAAAGCC

            *     *  *            
        608 AGAACCCAAACCACCAGTTTAT
          1 TGAACCTAAGCCACCAGTTTAT

        630 CAGCCTCCGA


Statistics
Matches: 360,  Mismatches: 59, Indels: 16
        0.83            0.14        0.04

Matches are distributed among these distances:
  44    4  0.01
  45  352  0.98
  46    4  0.01

ACGTcount: A:0.42, C:0.28, G:0.17, T:0.13


Consensus pattern (45 bp):   
TGAACCTAAGCCACCAGTTTATGAACCACCAAAGAAAGAAAAGCC

Found at i:644 original size:90 final size:90

Alignment explanation


    Indices: 165--625  Score: 613
    Period size: 90  Copynumber: 5.1  Consensus size: 90

        155 TTATGAACAT

                    *  *        * *      *     *  *               *  *       
        165 AAGCCACCTGTCTATGAACCTCTAAAGAAAGAAAAACCTGAG-CATAAGCCACCTGTCTATGA-A
          1 AAGCCACCAGTGTATGAACCACCAAAGAAGGAAAAGCCCGAGCCA-AAGCCACCAGTTTAT-ACA

                          *  *         
        228 CCTCCAAAGAAAGAAAAACCTGAACCC
         64 CCTCCAAAGAAAGAGAAGCCTGAACCC

                                                      *                      
        255 AAGCCACC-GATGTATGAACCACCAAAGAAGGAAAAGCCCGAACCAAAGCCACCAGTTTATACAC
          1 AAGCCACCAG-TGTATGAACCACCAAAGAAGGAAAAGCCCGAGCCAAAGCCACCAGTTTATACAC

                                      
        319 CTCCAAAGAAAGAGAAGCCTGAACCC
         65 CTCCAAAGAAAGAGAAGCCTGAACCC

              *        *                          *     *                    
        345 AAACCACCAGTATATGAACCACCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATACACC
          1 AAGCCACCAGTGTATGAACCACCAAAGAAGGAAAAGCCCGAGCCAAAGCCACCAGTTTATACACC

            *                        
        410 ACCAAAGAAAGAGAAGCCTGAACCC
         66 TCCAAAGAAAGAGAAGCCTGAACCC

                                                  *     *                    
        435 AAGCCACCAGTGTATGAACCACCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATACACC
          1 AAGCCACCAGTGTATGAACCACCAAAGAAGGAAAAGCCCGAGCCAAAGCCACCAGTTTATACACC

            *                *      *
        500 ACCAAAGAAAGAGAAGCTTGAACCT
         66 TCCAAAGAAAGAGAAGCCTGAACCC

                                *                           *           *    
        525 AAGCCACCAGTGTATGAACCGCCAAAGAAGGAAAAGCCCGAGCCAAAGTCACCAGTTTATGCACC
          1 AAGCCACCAGTGTATGAACCACCAAAGAAGGAAAAGCCCGAGCCAAAGCCACCAGTTTATACACC

                        *  *  *      
        590 TCCAAAGAAAGAAAAACCAGAACCC
         66 TCCAAAGAAAGAGAAGCCTGAACCC

              *        
        615 AAACCACCAGT
          1 AAGCCACCAGT

        626 TTATCAGCCT


Statistics
Matches: 334,  Mismatches: 33, Indels: 8
        0.89            0.09        0.02

Matches are distributed among these distances:
  89    2  0.01
  90  329  0.99
  91    3  0.01

ACGTcount: A:0.42, C:0.29, G:0.17, T:0.12


Consensus pattern (90 bp):   
AAGCCACCAGTGTATGAACCACCAAAGAAGGAAAAGCCCGAGCCAAAGCCACCAGTTTATACACC
TCCAAAGAAAGAGAAGCCTGAACCC

Found at i:745 original size:102 final size:102

Alignment explanation


    Indices: 567--752  Score: 228
    Period size: 102  Copynumber: 1.8  Consensus size: 102

        557 AAAGCCCGAG

                  *          **    *                  *                **    
        567 CCAAAGTCACCAGTTTATGCACCTCCAAAGAAAGAAAAACCAGAACCCAAACCACCAGTTTATCA
          1 CCAAAGCCACCAGTTTACACACCACCAAAGAAAGAAAAACCAAAACCCAAACCACCAGTACATCA

                  *     *                        
        632 GCCTCCGAAGAAGCCACCAGTTTATGAGCCTAAACCA
         66 GCCTCCCAAGAAACCACCAGTTTATGAGCCTAAACCA

                       *                       *  *      * *               * 
        669 CCAAAGCCACCGGTTTACACACCACCAAAGAAAGAGAAGCCAAAATCTAAACCACCAGTACATGA
          1 CCAAAGCCACCAGTTTACACACCACCAAAGAAAGAAAAACCAAAACCCAAACCACCAGTACATCA

             *                 
        734 GTCTCCCAAGAAACCACCA
         66 GCCTCCCAAGAAACCACCA

        753 TACAGTCACT


Statistics
Matches: 68,  Mismatches: 16, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
 102   68  1.00

ACGTcount: A:0.41, C:0.32, G:0.13, T:0.13


Consensus pattern (102 bp):   
CCAAAGCCACCAGTTTACACACCACCAAAGAAAGAAAAACCAAAACCCAAACCACCAGTACATCA
GCCTCCCAAGAAACCACCAGTTTATGAGCCTAAACCA
Done.