Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00674.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: 2032
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30


Found at i:155 original size:18 final size:18

Alignment explanation


    Indices: 134--194  Score: 59
    Period size: 18  Copynumber: 3.2  Consensus size: 18

        124 ACGATGCTAT

                     *        
        134 TGAAGAAGACGATGAAGA
          1 TGAAGAAGAAGATGAAGA

                  *           
        152 TGAAGATGAAGATGAAGA
          1 TGAAGAAGAAGATGAAGA

            *              *     
        170 CGAATACGAAGAAGACGAAGA
          1 TG-A-A-GAAGAAGATGAAGA

                
        191 TGAA
          1 TGAA

        195 AACGACGACG


Statistics
Matches: 34,  Mismatches: 6, Indels: 5
        0.76            0.13        0.11

Matches are distributed among these distances:
  18   17  0.50
  19    2  0.06
  20    2  0.06
  21   13  0.38

ACGTcount: A:0.51, C:0.07, G:0.31, T:0.11


Consensus pattern (18 bp):   
TGAAGAAGAAGATGAAGA

Found at i:168 original size:27 final size:26

Alignment explanation


    Indices: 138--199  Score: 70
    Period size: 27  Copynumber: 2.3  Consensus size: 26

        128 TGCTATTGAA

                          *     *      
        138 GAAGACGATGAAGATGAAGATGAAGAT
          1 GAAGACGAT-AAGAAGAAGACGAAGAT

                       *               
        165 GAAGACGAATACGAAGAAGACGAAGAT
          1 GAAGACG-ATAAGAAGAAGACGAAGAT

               *    
        192 GAAAACGA
          1 GAAGACGA

        200 CGACGTCTTG


Statistics
Matches: 30,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  26    1  0.03
  27   27  0.90
  28    2  0.07

ACGTcount: A:0.52, C:0.08, G:0.31, T:0.10


Consensus pattern (26 bp):   
GAAGACGATAAGAAGAAGACGAAGAT

Found at i:183 original size:21 final size:21

Alignment explanation


    Indices: 159--199  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        149 AGATGAAGAT

                 *         *     
        159 GAAGATGAAGACGAATACGAA
          1 GAAGACGAAGACGAAAACGAA

                       *        
        180 GAAGACGAAGATGAAAACGA
          1 GAAGACGAAGACGAAAACGA

        200 CGACGTCTTG


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.54, C:0.10, G:0.29, T:0.07


Consensus pattern (21 bp):   
GAAGACGAAGACGAAAACGAA

Found at i:189 original size:6 final size:6

Alignment explanation


    Indices: 134--169  Score: 54
    Period size: 6  Copynumber: 6.0  Consensus size: 6

        124 ACGATGCTAT

                   *  *                              
        134 TGAAGA AGACGA TGAAGA TGAAGA TGAAGA TGAAGA
          1 TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA

        170 CGAATACGAA


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
   6   26  1.00

ACGTcount: A:0.50, C:0.03, G:0.33, T:0.14


Consensus pattern (6 bp):   
TGAAGA

Found at i:199 original size:12 final size:12

Alignment explanation


    Indices: 147--199  Score: 52
    Period size: 12  Copynumber: 4.2  Consensus size: 12

        137 AGAAGACGAT

                       *
        147 GAAGATGAAGAT
          1 GAAGATGAAGAC

                        
        159 GAAGATGAAGAC
          1 GAAGATGAAGAC

                    *      
        171 GAATACGAAGAAGAC
          1 G-A-A-GATGAAGAC

                     *  
        186 GAAGATGAAAAC
          1 GAAGATGAAGAC

              
        198 GA
          1 GA

        200 CGACGTCTTG


Statistics
Matches: 34,  Mismatches: 4, Indels: 6
        0.77            0.09        0.14

Matches are distributed among these distances:
  12   21  0.62
  13    2  0.06
  14    2  0.06
  15    9  0.26

ACGTcount: A:0.53, C:0.08, G:0.30, T:0.09


Consensus pattern (12 bp):   
GAAGATGAAGAC
Done.