Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g01056.F2

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: 5282
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:1081 original size:45 final size:45

Alignment explanation


    Indices: 1017--1108  Score: 184
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       1007 CAGGTAAGCG

                                                         
       1017 AAGGTAAATTTCCTAACCGAGCATTATAGAAATCCAAATTAGGAT
          1 AAGGTAAATTTCCTAACCGAGCATTATAGAAATCCAAATTAGGAT

                                                         
       1062 AAGGTAAATTTCCTAACCGAGCATTATAGAAATCCAAATTAGGAT
          1 AAGGTAAATTTCCTAACCGAGCATTATAGAAATCCAAATTAGGAT

              
       1107 AA
          1 AA

       1109 TATTTTACCT


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  45   47  1.00

ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26


Consensus pattern (45 bp):   
AAGGTAAATTTCCTAACCGAGCATTATAGAAATCCAAATTAGGAT

Found at i:4390 original size:48 final size:48

Alignment explanation


    Indices: 4325--4702  Score: 373
    Period size: 48  Copynumber: 7.9  Consensus size: 48

       4315 ATACTAGGGT

                *                          *   *            
       4325 TATGTGAGCCAGTGTAAGACCATGTTTGGAATATGACATCGGCATTGA
          1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA

                     *               *               *  * *  
       4373 TATGAGAGCTAGTGTAAGACCATGTAT-GAGACATGGCATCAGCCTCGA
          1 TATGAGAGCCAGTGTAAGACCATGTTTGGA-ACATGGCATCGGCATTGA

                *            *                       *  *   
       4421 TATGTGAGCCAGTGTAAAACCATGTTTGGAACATGGCATCGACAATGA
          1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA

                     *               *   *             * ** 
       4469 TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAA
          1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA

                *              *                     *      
       4517 TATGTGAGCCAGTGTAAGATCATGTTTGGAACATGGCATCGACATTGA
          1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA

                     *         **    *   *         *   * *  
       4565 TATGAGAGCTAGTGTAAGATAATGTCTGGGACATGGCATTGGCCTCGA
          1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA

            *   * * **                               *        
       4613 CATGTGGGTTAGTGTAAGACCATGTTTGGAACATGGCAT-GACATTGATA
          1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTG--A

                                     *   *     *     
       4662 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGACATCG
          1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCG

       4703 ACATCTTACC


Statistics
Matches: 261,  Mismatches: 64, Indels: 8
        0.78            0.19        0.02

Matches are distributed among these distances:
  47    6  0.02
  48  220  0.84
  49   34  0.13
  50    1  0.00

ACGTcount: A:0.29, C:0.16, G:0.28, T:0.26


Consensus pattern (48 bp):   
TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA

Found at i:4489 original size:96 final size:96

Alignment explanation


    Indices: 4325--4702  Score: 560
    Period size: 96  Copynumber: 3.9  Consensus size: 96

       4315 ATACTAGGGT

                                           *   *     *                       
       4325 TATGTGAGCCAGTGTAAGACCATGTTTGGAATATGACATCGGCATTGATATGAGAGCTAGTGTAA
          1 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGATATGAGAGCTAGTGTAA

                    *  *           *       
       4390 GACCATGTATGAGACATGGCATCAGCCTCGA
         66 GACCATGTCTGGGACATGGCATCGGCCTCGA

                             *                          *                    
       4421 TATGTGAGCCAGTGTAAAACCATGTTTGGAACATGGCATCGACAATGATATGAGAGCTAGTGTAA
          1 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGATATGAGAGCTAGTGTAA

                                         * 
       4486 GACCATGTCTGGGACATGGCATCGGCCTCAA
         66 GACCATGTCTGGGACATGGCATCGGCCTCGA

                               *                                             
       4517 TATGTGAGCCAGTGTAAGATCATGTTTGGAACATGGCATCGACATTGATATGAGAGCTAGTGTAA
          1 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGATATGAGAGCTAGTGTAA

              **                  *        
       4582 GATAATGTCTGGGACATGGCATTGGCCTCGA
         66 GACCATGTCTGGGACATGGCATCGGCCTCGA

            *     * **                                                 *     
       4613 CATGTGGGTTAGTGTAAGACCATGTTTGGAACATGGCAT-GACATTGATATATGAGAGCCAGTGT
          1 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTG--ATATGAGAGCTAGTGT

                                *     
       4677 AAGACCATGTCTGGGACATGACATCG
         64 AAGACCATGTCTGGGACATGGCATCG

       4703 ACATCTTACC


Statistics
Matches: 254,  Mismatches: 26, Indels: 3
        0.90            0.09        0.01

Matches are distributed among these distances:
  95    7  0.03
  96  210  0.83
  97   37  0.15

ACGTcount: A:0.29, C:0.16, G:0.28, T:0.26


Consensus pattern (96 bp):   
TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGATATGAGAGCTAGTGTAA
GACCATGTCTGGGACATGGCATCGGCCTCGA

Done.