Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g01745.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: 3792
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.32


Found at i:3479 original size:46 final size:45

Alignment explanation


    Indices: 3428--3594  Score: 194
    Period size: 46  Copynumber: 3.7  Consensus size: 45

       3418 GACGAGGGCT

                                                          
       3428 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGAGCC
          1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAG-ATGAGAGCC

                                        *   *        *    
       3474 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGATAGCC
          1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGATGAGAGCC

                 *                   *  *  *          *  *
       3520 AGTGTCAGACATGTCTGGGACATGCGTCGGCTAC-GA-GATGTGCT
          1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGATGA-GAGCC

                          *          *     
       3564 AGTGTAAGACATGTATGGGACATGCGTCAGC
          1 AGTGTAAGACATGTCTGGGACATGCATCAGC

       3595 ACGGTTACAT


Statistics
Matches: 106,  Mismatches: 13, Indels: 6
        0.85            0.10        0.05

Matches are distributed among these distances:
  43    2  0.02
  44   32  0.30
  46   70  0.66
  47    2  0.02

ACGTcount: A:0.26, C:0.20, G:0.31, T:0.22


Consensus pattern (45 bp):   
AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGATGAGAGCC

Found at i:3524 original size:92 final size:90

Alignment explanation


    Indices: 3377--3588  Score: 246
    Period size: 92  Copynumber: 2.3  Consensus size: 90

       3367 AGATTTGTGT

                                 *                *        *  *              
       3377 GCCAGTGTAAGACCATGTATGAGACATGGCATCGGCATTGAGACGAGGGCTAGTGTAAGACATGT
          1 GCCAGTGTAAGA-CATGTATGGGACAT-GCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGT

                                          
       3442 CTGGGACATGCATCAGCCAC-AGTATGAGA
         64 CTGGGACATGCATCAGCCACGAG-AT--GA

                             *                *      *  *         *          
       3471 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGATAGCCAGTGTCAGACATGTCT
          1 GCCAGTGTAAGACATGTATGGGACATGCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGTCT

                     *  *  *        *
       3536 GGGACATGCGTCGGCTACGAGATGT
         66 GGGACATGCATCAGCCACGAGATGA

              *                         
       3561 GCTAGTGTAAGACATGTATGGGACATGC
          1 GCCAGTGTAAGACATGTATGGGACATGC

       3589 GTCAGCACGG


Statistics
Matches: 102,  Mismatches: 15, Indels: 6
        0.83            0.12        0.05

Matches are distributed among these distances:
  90   27  0.26
  92   49  0.48
  93   14  0.14
  94   12  0.12

ACGTcount: A:0.27, C:0.20, G:0.32, T:0.22


Consensus pattern (90 bp):   
GCCAGTGTAAGACATGTATGGGACATGCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGTCT
GGGACATGCATCAGCCACGAGATGA

Found at i:3629 original size:46 final size:43

Alignment explanation


    Indices: 3428--3631  Score: 162
    Period size: 46  Copynumber: 4.5  Consensus size: 43

       3418 GACGAGGGCT

                                     *     *     *     *   
       3428 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGTATGAGAGCC
          1 AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGA-CAT--GTG-C

                                     *  *        *         
       3474 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGATAGCC
          1 AGTGTAAGACATGTCTGGGACATGCGTCAG-CTACGACATG-T-G-C

                 *                      *       *      
       3520 AGTGTCAGACATGTCTGGGACATGCGTCGGCTACGAGATGTGC
          1 AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGACATGTGC

                           *                                
       3563 TAGTGTAAGACATGTATGGGACATGCGTCAGC-ACGGTTACATGTGTC
          1 -AGTGTAAGACATGTCTGGGACATGCGTCAGCTAC-G--ACATGTG-C

                      *           
       3610 AGTGTAAGACCTGTCTGGGACA
          1 AGTGTAAGACATGTCTGGGACA

       3632 CGGCATCGAC


Statistics
Matches: 136,  Mismatches: 12, Indels: 20
        0.81            0.07        0.12

Matches are distributed among these distances:
  43    3  0.02
  44   31  0.23
  45    3  0.02
  46   96  0.71
  47    3  0.02

ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23


Consensus pattern (43 bp):   
AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGACATGTGC
Done.