Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g01281.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: 4761
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33


Found at i:1001 original size:26 final size:26

Alignment explanation


    Indices: 965--1074  Score: 184
    Period size: 26  Copynumber: 4.2  Consensus size: 26

        955 TGATACAAAT

                                      
        965 TGATAATAGGTTAGGTAAATGTTCCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                                      
        991 TGATAATAGGTTAGGTAAATGTTCCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                   *               *  
       1017 TGATAATGGGTTAGGTAAATGTTTCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                   *               *  
       1043 TGATAATGGGTTAGGTAAATGTTTCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                  
       1069 TGATAA
          1 TGATAA

       1075 GAATTTCATG


Statistics
Matches: 82,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  26   82  1.00

ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36


Consensus pattern (26 bp):   
TGATAATAGGTTAGGTAAATGTTCCA

Found at i:2556 original size:28 final size:26

Alignment explanation


    Indices: 2514--2588  Score: 78
    Period size: 26  Copynumber: 2.8  Consensus size: 26

       2504 AAAAGTAGCT

                    * *     *         * 
       2514 AAATTACTATAATACCTCTATGTATGGA
          1 AAATTACTGTTATACCCCTA-G-ATGCA

                                 *    
       2542 AAATTACTGTTATACCCCTAGGTGCA
          1 AAATTACTGTTATACCCCTAGATGCA

                   *             
       2568 AAATTACCGTTATACCCCTAG
          1 AAATTACTGTTATACCCCTAG

       2589 GGTTAATTTT


Statistics
Matches: 41,  Mismatches: 6, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  26   23  0.56
  27    1  0.02
  28   17  0.41

ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32


Consensus pattern (26 bp):   
AAATTACTGTTATACCCCTAGATGCA

Found at i:2733 original size:27 final size:27

Alignment explanation


    Indices: 2692--2804  Score: 129
    Period size: 27  Copynumber: 4.2  Consensus size: 27

       2682 GAGGAAGCGT

                      *                
       2692 TCTGGTGGCTATGCCACAAATATCTGA
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                              *       *
       2719 TCTGGTGGCTCTGCCACATATATCTGT
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                             * *        
       2746 TCTGGTGGCTCTGCCACGATTATCTGTA
          1 TCTGGTGGCTCTGCCACAAATATCTG-A

                   *     *     *      *
       2774 TCTGGTGACTCTGTCAC-ATTATCTGT
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                 
       2800 TCTGG
          1 TCTGG

       2805 CAGCCATGCT


Statistics
Matches: 75,  Mismatches: 10, Indels: 3
        0.85            0.11        0.03

Matches are distributed among these distances:
  26    5  0.07
  27   55  0.73
  28   15  0.20

ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36


Consensus pattern (27 bp):   
TCTGGTGGCTCTGCCACAAATATCTGA

Found at i:2797 original size:54 final size:54

Alignment explanation


    Indices: 2690--2804  Score: 169
    Period size: 54  Copynumber: 2.1  Consensus size: 54

       2680 TGGAGGAAGC

                                                *                 
       2690 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
          1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT

                        *      * *                     *           
       2744 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
          1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT

                   
       2798 GTTCTGG
          1 GTTCTGG

       2805 CAGCCATGCT


Statistics
Matches: 55,  Mismatches: 5, Indels: 2
        0.89            0.08        0.03

Matches are distributed among these distances:
  54   37  0.67
  55   18  0.33

ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37


Consensus pattern (54 bp):   
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Done.