Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g00303.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: 5374
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33


Found at i:423 original size:47 final size:46

Alignment explanation


    Indices: 369--545  Score: 218
    Period size: 47  Copynumber: 3.8  Consensus size: 46

        359 TGGTTGAGCA

                                                           
        369 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGGAATG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGT-GAATG

                                          * *                
        416 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGT-AACTAGG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA-T--G

                                                      *   * 
        461 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
          1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG

            *    *                               
        509 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG

        546 GCGGGTTACA


Statistics
Matches: 113,  Mismatches: 8, Indels: 19
        0.81            0.06        0.14

Matches are distributed among these distances:
  42    2  0.02
  43    1  0.01
  44    5  0.04
  45    1  0.01
  46   37  0.33
  47   58  0.51
  48    3  0.03
  50    4  0.04
  51    2  0.02

ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29


Consensus pattern (46 bp):   
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG

Found at i:3091 original size:46 final size:45

Alignment explanation


    Indices: 3040--3206  Score: 203
    Period size: 46  Copynumber: 3.7  Consensus size: 45

       3030 GACGAGGGCT

                                                          
       3040 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGAGCC
          1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAG-ATGAGAGCC

                                        *   *        *    
       3086 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGATAGCC
          1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGATGAGAGCC

                 *                   *  *  *          *  *
       3132 AGTGTCAGACATGTCTGGGACATGCGTCGGCTAC-GA-GATGTGCT
          1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGATGA-GAGCC

                                     *     
       3176 AGTGTAAGACATGTCTGGGACATGCGTCAGC
          1 AGTGTAAGACATGTCTGGGACATGCATCAGC

       3207 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:3136 original size:92 final size:90

Alignment explanation


    Indices: 2989--3200  Score: 246
    Period size: 92  Copynumber: 2.3  Consensus size: 90

       2979 AGATTTGTGT

                              *  *                *        *  *              
       2989 GCCAGTGTAAGACCATGTATGAGACATGGCATCGGCATTGAGACGAGGGCTAGTGTAAGACATGT
          1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGT

                                          
       3054 CTGGGACATGCATCAGCCAC-AGTATGAGA
         64 CTGGGACATGCATCAGCCACGAG-AT--GA

                                              *      *  *         *          
       3083 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGATAGCCAGTGTCAGACATGTCT
          1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGTCT

                     *  *  *        *
       3148 GGGACATGCGTCGGCTACGAGATGT
         66 GGGACATGCATCAGCCACGAGATGA

              *                         
       3173 GCTAGTGTAAGACATGTCTGGGACATGC
          1 GCCAGTGTAAGACATGTCTGGGACATGC

       3201 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:3237 original size:46 final size:43

Alignment explanation


    Indices: 3040--3243  Score: 171
    Period size: 46  Copynumber: 4.5  Consensus size: 43

       3030 GACGAGGGCT

                                     *     *     *     *   
       3040 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGTATGAGAGCC
          1 AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGA-CAT--GTG-C

                                     *  *        *         
       3086 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGATAGCC
          1 AGTGTAAGACATGTCTGGGACATGCGTCAG-CTACGACATG-T-G-C

                 *                      *       *      
       3132 AGTGTCAGACATGTCTGGGACATGCGTCGGCTACGAGATGTGC
          1 AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGACATGTGC

                                                            
       3175 TAGTGTAAGACATGTCTGGGACATGCGTCAGC-ACGGTTACATGTGTC
          1 -AGTGTAAGACATGTCTGGGACATGCGTCAGCTAC-G--ACATGTG-C

                      *           
       3222 AGTGTAAGACCTGTCTGGGACA
          1 AGTGTAAGACATGTCTGGGACA

       3244 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:3243 original size:90 final size:91

Alignment explanation


    Indices: 3040--3206  Score: 221
    Period size: 90  Copynumber: 1.8  Consensus size: 91

       3030 GACGAGGGCT

                                                                             
       3040 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGAGCCAGTGTAAGACATGTCTGGG
          1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTAT-AGAGCCAGTGTAAGACATGTCTGGG

                     *       *         
       3105 ACATGCATCGGCCTCGAGATGATAGCC
         65 ACATGCATCAGCCTCGACATGATAGCC

                 *                   *  *  *          *  *                   
       3132 AGTGTCAGACATGTCTGGGACATGCGTCGGCTACGAG-AT-GTGCTAGTGTAAGACATGTCTGGG
          1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGTATAGAGCCAGTGTAAGACATGTCTGGG

                  *     
       3195 ACATGCGTCAGC
         65 ACATGCATCAGC

       3207 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.