Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g00303.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: 4012
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33


Found at i:1729 original size:46 final size:45

Alignment explanation


    Indices: 1678--1844  Score: 203
    Period size: 46  Copynumber: 3.7  Consensus size: 45

       1668 GACGAGGGCT

                                                          
       1678 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGAGCC
          1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAG-ATGAGAGCC

                                        *   *        *    
       1724 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGATAGCC
          1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGATGAGAGCC

                 *                   *  *  *          *  *
       1770 AGTGTCAGACATGTCTGGGACATGCGTCGGCTAC-GA-GATGTGCT
          1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGATGA-GAGCC

                                     *     
       1814 AGTGTAAGACATGTCTGGGACATGCGTCAGC
          1 AGTGTAAGACATGTCTGGGACATGCATCAGC

       1845 ACGGTTACAT


Statistics
Matches: 107,  Mismatches: 12, Indels: 6
        0.86            0.10        0.05

Matches are distributed among these distances:
  43    2  0.02
  44   33  0.31
  46   70  0.65
  47    2  0.02

ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22


Consensus pattern (45 bp):   
AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGATGAGAGCC

Found at i:1774 original size:92 final size:90

Alignment explanation


    Indices: 1627--1838  Score: 246
    Period size: 92  Copynumber: 2.3  Consensus size: 90

       1617 AGATTTGTGT

                              *  *                *        *  *              
       1627 GCCAGTGTAAGACCATGTATGAGACATGGCATCGGCATTGAGACGAGGGCTAGTGTAAGACATGT
          1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGT

                                          
       1692 CTGGGACATGCATCAGCCAC-AGTATGAGA
         64 CTGGGACATGCATCAGCCACGAG-AT--GA

                                              *      *  *         *          
       1721 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGATAGCCAGTGTCAGACATGTCT
          1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGTCT

                     *  *  *        *
       1786 GGGACATGCGTCGGCTACGAGATGT
         66 GGGACATGCATCAGCCACGAGATGA

              *                         
       1811 GCTAGTGTAAGACATGTCTGGGACATGC
          1 GCCAGTGTAAGACATGTCTGGGACATGC

       1839 GTCAGCACGG


Statistics
Matches: 103,  Mismatches: 14, Indels: 6
        0.84            0.11        0.05

Matches are distributed among these distances:
  90   28  0.27
  92   49  0.48
  93   14  0.14
  94   12  0.12

ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22


Consensus pattern (90 bp):   
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGTCT
GGGACATGCATCAGCCACGAGATGA

Found at i:1875 original size:46 final size:43

Alignment explanation


    Indices: 1678--1881  Score: 171
    Period size: 46  Copynumber: 4.5  Consensus size: 43

       1668 GACGAGGGCT

                                     *     *     *     *   
       1678 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGTATGAGAGCC
          1 AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGA-CAT--GTG-C

                                     *  *        *         
       1724 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGATAGCC
          1 AGTGTAAGACATGTCTGGGACATGCGTCAG-CTACGACATG-T-G-C

                 *                      *       *      
       1770 AGTGTCAGACATGTCTGGGACATGCGTCGGCTACGAGATGTGC
          1 AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGACATGTGC

                                                            
       1813 TAGTGTAAGACATGTCTGGGACATGCGTCAGC-ACGGTTACATGTGTC
          1 -AGTGTAAGACATGTCTGGGACATGCGTCAGCTAC-G--ACATGTG-C

                      *           
       1860 AGTGTAAGACCTGTCTGGGACA
          1 AGTGTAAGACATGTCTGGGACA

       1882 CGGCATCGAC


Statistics
Matches: 138,  Mismatches: 10, Indels: 20
        0.82            0.06        0.12

Matches are distributed among these distances:
  43    3  0.02
  44   32  0.23
  45    3  0.02
  46   97  0.70
  47    3  0.02

ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23


Consensus pattern (43 bp):   
AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGACATGTGC

Found at i:1881 original size:90 final size:91

Alignment explanation


    Indices: 1678--1844  Score: 221
    Period size: 90  Copynumber: 1.8  Consensus size: 91

       1668 GACGAGGGCT

                                                                             
       1678 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGAGCCAGTGTAAGACATGTCTGGG
          1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTAT-AGAGCCAGTGTAAGACATGTCTGGG

                     *       *         
       1743 ACATGCATCGGCCTCGAGATGATAGCC
         65 ACATGCATCAGCCTCGACATGATAGCC

                 *                   *  *  *          *  *                   
       1770 AGTGTCAGACATGTCTGGGACATGCGTCGGCTACGAG-AT-GTGCTAGTGTAAGACATGTCTGGG
          1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGTATAGAGCCAGTGTAAGACATGTCTGGG

                  *     
       1833 ACATGCGTCAGC
         65 ACATGCATCAGC

       1845 ACGGTTACAT


Statistics
Matches: 66,  Mismatches: 8, Indels: 4
        0.85            0.10        0.05

Matches are distributed among these distances:
  90   32  0.48
  92   32  0.48
  93    2  0.03

ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22


Consensus pattern (91 bp):   
AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATAGAGCCAGTGTAAGACATGTCTGGGA
CATGCATCAGCCTCGACATGATAGCC
Done.