Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g00580.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, 586

Length: 978
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28


Found at i:291 original size:16 final size:16

Alignment explanation


    Indices: 270--309  Score: 57
    Period size: 15  Copynumber: 2.6  Consensus size: 16

        260 GTCCCACCAA

                            
        270 TACCAAACCCTCCCGT
          1 TACCAAACCCTCCCGT

                         *  
        286 TACC-AACCCTCCTGT
          1 TACCAAACCCTCCCGT

                      
        301 TA-CAAACCC
          1 TACCAAACCC

        310 ACCACCTTCT


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  14    1  0.05
  15   17  0.77
  16    4  0.18

ACGTcount: A:0.28, C:0.47, G:0.05, T:0.20


Consensus pattern (16 bp):   
TACCAAACCCTCCCGT

Found at i:371 original size:15 final size:15

Alignment explanation


    Indices: 347--393  Score: 58
    Period size: 15  Copynumber: 3.1  Consensus size: 15

        337 TGGTGGAGGG

                 *         
        347 GGAGGCGGCGGTGGA
          1 GGAGGTGGCGGTGGA

                          *
        362 GGAGGTGGCGGTGGC
          1 GGAGGTGGCGGTGGA

              *     *      
        377 GGTGGTGGAGGTGGA
          1 GGAGGTGGCGGTGGA

              
        392 GG
          1 GG

        394 TGGAGGTGGT


Statistics
Matches: 27,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  15   27  1.00

ACGTcount: A:0.11, C:0.09, G:0.68, T:0.13


Consensus pattern (15 bp):   
GGAGGTGGCGGTGGA

Found at i:377 original size:21 final size:21

Alignment explanation


    Indices: 337--417  Score: 99
    Period size: 21  Copynumber: 3.9  Consensus size: 21

        327 ACCCACCTTC

                     *     *     
        337 TGGTGGAGGGGGAGGCGGCGG
          1 TGGTGGAGGTGGAGGTGGCGG

               *        *        
        358 TGGAGGAGGTGGCGGTGGCGG
          1 TGGTGGAGGTGGAGGTGGCGG

                              *  
        379 TGGTGGAGGTGGAGGTGGAGG
          1 TGGTGGAGGTGGAGGTGGCGG

                  *     *     
        400 TGGTGGCGGTGGTGGTGG
          1 TGGTGGAGGTGGAGGTGG

        418 TGGGGGTAGC


Statistics
Matches: 51,  Mismatches: 9, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   51  1.00

ACGTcount: A:0.09, C:0.06, G:0.68, T:0.17


Consensus pattern (21 bp):   
TGGTGGAGGTGGAGGTGGCGG

Found at i:383 original size:9 final size:9

Alignment explanation


    Indices: 365--420  Score: 58
    Period size: 9  Copynumber: 6.2  Consensus size: 9

        355 CGGTGGAGGA

                 *   
        365 GGTGGCGGT
          1 GGTGGTGGT

              *      
        374 GGCGGTGGT
          1 GGTGGTGGT

              *     *
        383 GGAGGTGGA
          1 GGTGGTGGT

                 *   
        392 GGTGGAGGT
          1 GGTGGTGGT

                 *   
        401 GGTGGCGGT
          1 GGTGGTGGT

                     
        410 GGTGGTGGT
          1 GGTGGTGGT

              
        419 GG
          1 GG

        421 GGGTAGCACT


Statistics
Matches: 38,  Mismatches: 9, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
   9   38  1.00

ACGTcount: A:0.05, C:0.05, G:0.68, T:0.21


Consensus pattern (9 bp):   
GGTGGTGGT

Found at i:395 original size:15 final size:15

Alignment explanation


    Indices: 356--420  Score: 76
    Period size: 15  Copynumber: 4.3  Consensus size: 15

        346 GGGAGGCGGC

                    *     *
        356 GGTGGAGGAGGTGGC
          1 GGTGGAGGTGGTGGT

                 *        *
        371 GGTGGCGGTGGTGGA
          1 GGTGGAGGTGGTGGT

                       *   
        386 GGTGGAGGTGGAGGT
          1 GGTGGAGGTGGTGGT

                 *         
        401 GGTGGCGGTGGTGGT
          1 GGTGGAGGTGGTGGT

                 
        416 GGTGG
          1 GGTGG

        421 GGGTAGCACT


Statistics
Matches: 42,  Mismatches: 8, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  15   42  1.00

ACGTcount: A:0.08, C:0.05, G:0.68, T:0.20


Consensus pattern (15 bp):   
GGTGGAGGTGGTGGT

Found at i:413 original size:12 final size:12

Alignment explanation


    Indices: 359--417  Score: 55
    Period size: 12  Copynumber: 4.9  Consensus size: 12

        349 AGGCGGCGGT

                 *      
        359 GGAGGAGGTGGC
          1 GGAGGTGGTGGC

              *  *     *
        371 GGTGGCGGTGGT
          1 GGAGGTGGTGGC

                    *  *
        383 GGAGGTGGAGGT
          1 GGAGGTGGTGGC

                        
        395 GGAGGTGGTGGC
          1 GGAGGTGGTGGC

              *        
        407 GGTGGTGGTGG
          1 GGAGGTGGTGG

        418 TGGGGGTAGC


Statistics
Matches: 38,  Mismatches: 9, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  12   38  1.00

ACGTcount: A:0.08, C:0.05, G:0.68, T:0.19


Consensus pattern (12 bp):   
GGAGGTGGTGGC

Found at i:418 original size:6 final size:6

Alignment explanation


    Indices: 365--420  Score: 58
    Period size: 6  Copynumber: 9.3  Consensus size: 6

        355 CGGTGGAGGA

                 *      *          *      *      *         *       
        365 GGTGGC GGTGGC GGTGGT GGAGGT GGAGGT GGAGGT GGTGGC GGTGGT
          1 GGTGGT GGTGGT GGTGGT GGTGGT GGTGGT GGTGGT GGTGGT GGTGGT

                     
        413 GGTGGT GG
          1 GGTGGT GG

        421 GGGTAGCACT


Statistics
Matches: 45,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
   6   45  1.00

ACGTcount: A:0.05, C:0.05, G:0.68, T:0.21


Consensus pattern (6 bp):   
GGTGGT
Done.