Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g00566.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, 907

Length: 1512
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27


Found at i:241 original size:18 final size:18

Alignment explanation


    Indices: 215--261  Score: 58
    Period size: 18  Copynumber: 2.6  Consensus size: 18

        205 GGTTAATGGC

                *           * 
        215 GAAGTAGAAGAAGAAGCT
          1 GAAGAAGAAGAAGAAGAT

                *         *   
        233 GAAGGAGAAGAAGATGAT
          1 GAAGAAGAAGAAGAAGAT

                       
        251 GAAGAAGAAGA
          1 GAAGAAGAAGA

        262 GATTGGTGAT


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  18   25  1.00

ACGTcount: A:0.53, C:0.02, G:0.36, T:0.09


Consensus pattern (18 bp):   
GAAGAAGAAGAAGAAGAT

Found at i:243 original size:15 final size:15

Alignment explanation


    Indices: 220--261  Score: 57
    Period size: 15  Copynumber: 2.8  Consensus size: 15

        210 ATGGCGAAGT

                       *   
        220 AGAAGAAGAAGCTGA
          1 AGAAGAAGAAGATGA

              *            
        235 AGGAGAAGAAGATGA
          1 AGAAGAAGAAGATGA

            *           
        250 TGAAGAAGAAGA
          1 AGAAGAAGAAGA

        262 GATTGGTGAT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  15   23  1.00

ACGTcount: A:0.55, C:0.02, G:0.36, T:0.07


Consensus pattern (15 bp):   
AGAAGAAGAAGATGA

Found at i:254 original size:9 final size:9

Alignment explanation


    Indices: 242--354  Score: 54
    Period size: 9  Copynumber: 12.2  Consensus size: 9

        232 TGAAGGAGAA

                     
        242 GAAGATGAT
          1 GAAGATGAT

                 *  *
        251 GAAGAAGAA
          1 GAAGATGAT

                    * 
        260 G-AGATTGGT
          1 GAAGA-TGAT

              *      
        269 GATGATGAT
          1 GAAGATGAT

              *      
        278 GATGATGAT
          1 GAAGATGAT

              *      
        287 GATGATGAT
          1 GAAGATGAT

              *      
        296 GATGATGAT
          1 GAAGATGAT

                         
        305 GAATTAGA-GAAT
          1 G-A--AGATG-AT

                      
        317 -AATGATGAT
          1 GAA-GATGAT

              *      
        326 GACGATGAT
          1 GAAGATGAT

             *        
        335 GGAG-TAGAT
          1 GAAGAT-GAT

                     
        344 GAAGATGAT
          1 GAAGATGAT

              
        353 GA
          1 GA

        355 TGAAGAAGAA


Statistics
Matches: 81,  Mismatches: 12, Indels: 22
        0.70            0.10        0.19

Matches are distributed among these distances:
   8    5  0.06
   9   64  0.79
  10    7  0.09
  11    1  0.01
  12    4  0.05

ACGTcount: A:0.40, C:0.01, G:0.34, T:0.26


Consensus pattern (9 bp):   
GAAGATGAT

Found at i:274 original size:3 final size:3

Alignment explanation


    Indices: 268--357  Score: 85
    Period size: 3  Copynumber: 29.0  Consensus size: 3

        258 AAGAGATTGG

                                                                  *     
        268 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGAA TTA -GA
          1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG-A TGA TGA

                  *              *                      *              
        313 -GAA TAA TGA TGA TGA CGA TGA TGGA GTAGA TGA AGA TGA TGA TGA
          1 TG-A TGA TGA TGA TGA TGA TGA T-GA -T-GA TGA TGA TGA TGA TGA

        358 AGAAGAAGAG


Statistics
Matches: 73,  Mismatches: 9, Indels: 10
        0.79            0.10        0.11

Matches are distributed among these distances:
   2    2  0.03
   3   63  0.86
   4    5  0.07
   5    3  0.04

ACGTcount: A:0.38, C:0.01, G:0.32, T:0.29


Consensus pattern (3 bp):   
TGA

Found at i:365 original size:18 final size:18

Alignment explanation


    Indices: 232--366  Score: 64
    Period size: 18  Copynumber: 7.7  Consensus size: 18

        222 AAGAAGAAGC

                 *      *     
        232 TGAAGGAGAAGAAGATGA
          1 TGAAGAAGAAGATGATGA

                              *
        250 TGAAGAAGAAGA-GATTGG
          1 TGAAGAAGAAGATGA-TGA

               *  *  *        
        268 TGATGATGATGATGATGA
          1 TGAAGAAGAAGATGATGA

               *  *  *        
        286 TGATGATGATGATGATGA
          1 TGAAGAAGAAGATGATGA

                **          * 
        304 TGAATTAG-AGA--ATAA
          1 TGAAGAAGAAGATGATGA

               *  *  *         
        319 TGATGATGACGATGATGGA
          1 TGAAGAAGAAGATGAT-GA

              *   *           
        338 -GTAGATGAAGATGATGA
          1 TGAAGAAGAAGATGATGA

                        
        355 TGAAGAAGAAGA
          1 TGAAGAAGAAGA

        367 GGAGGAGGAT


Statistics
Matches: 87,  Mismatches: 23, Indels: 14
        0.70            0.19        0.11

Matches are distributed among these distances:
  15    7  0.08
  16    2  0.02
  17    6  0.07
  18   69  0.79
  19    3  0.03

ACGTcount: A:0.42, C:0.01, G:0.34, T:0.23


Consensus pattern (18 bp):   
TGAAGAAGAAGATGATGA
Done.