Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g00446.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, 617

Length: 1029
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.20


Found at i:232 original size:45 final size:45

Alignment explanation


    Indices: 155--551  Score: 360
    Period size: 45  Copynumber: 8.8  Consensus size: 45

        145 CACCACCATA

                  *  *        *        *                 
        155 TGAACCTAAGCCACCAGTGTATGAACCACCAAAAAAGGAGAAGCC
          1 TGAACCAAAACCACCAGTTTATGAACCTCCAAAAAAGGAGAAGCC

                  *  *     *       *                      
        200 TGAACCTAAGCCACCGGTTTATGCACCTCCAAAGAAA-GAGAAGCC
          1 TGAACCAAAACCACCAGTTTATGAACCTCCAAA-AAAGGAGAAGCC

              *   *           *              *           
        245 TGGACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCC
          1 TGAACCAAAACCACCAGTTTATGAACCTCCAAAAAAGGAGAAGCC

               *     *                                *    
        290 TGAGCCAAAGCCACCAGTTTAT-ACACCTCCAAAGAAA-GAGGAGCC
          1 TGAACCAAAACCACCAGTTTATGA-ACCTCCAAA-AAAGGAGAAGCC

             *    *           *              *        *  
        335 TAAACCTAAACCACCAGTATATGAACCTCCAAAGAAGGAGAAACC
          1 TGAACCAAAACCACCAGTTTATGAACCTCCAAAAAAGGAGAAGCC

               *                                         *  
        380 TGAGCCAAAACCACC-GATTTAT-ACACCTCCAAAGAAA-GAGAAACC
          1 TGAACCAAAACCACCAG-TTTATGA-ACCTCCAAA-AAAGGAGAAGCC

                  *        *  *              *           
        425 TGAACCCAAACCACCCGTATATGAACCTCCAAAGAAGGAGAAGCC
          1 TGAACCAAAACCACCAGTTTATGAACCTCCAAAAAAGGAGAAGCC

            *  *     *     *                            *  
        470 CGAGCCAAAGCCACCGGTTTAT-ACACCTCCAAAGAAA-GAGAAACC
          1 TGAACCAAAACCACCAGTTTATGA-ACCTCCAAA-AAAGGAGAAGCC

                  *         * *                  
        515 TGAACCCAAACCACCAATGTATGAACCTCCAAAAAAG
          1 TGAACCAAAACCACCAGTTTATGAACCTCCAAAAAAG

        552 CCTCCAATGT


Statistics
Matches: 285,  Mismatches: 51, Indels: 32
        0.77            0.14        0.09

Matches are distributed among these distances:
  44   13  0.05
  45  259  0.91
  46   13  0.05

ACGTcount: A:0.41, C:0.29, G:0.17, T:0.13


Consensus pattern (45 bp):   
TGAACCAAAACCACCAGTTTATGAACCTCCAAAAAAGGAGAAGCC

Found at i:318 original size:90 final size:90

Alignment explanation


    Indices: 155--646  Score: 599
    Period size: 90  Copynumber: 5.3  Consensus size: 90

        145 CACCACCATA

                  *  *                 *     *              *  *             
        155 TGAACCTAAGCCACCAGTGTATGAACCACCAAAAAAGGAGAAGCCTGAACCTAAGCCACCGGTTT
          1 TGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCCTGAGCCAAAGCCACCGGTTT

              *                   *  
        220 ATGCACCTCCAAAGAAAGAGAAGCC
         66 ATACACCTCCAAAGAAAGAGAAACC

              *                                                         *    
        245 TGGACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCCTGAGCCAAAGCCACCAGTTT
          1 TGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCCTGAGCCAAAGCCACCGGTTT

                                * *  
        310 ATACACCTCCAAAGAAAGAGGAGCC
         66 ATACACCTCCAAAGAAAGAGAAACC

             *    *           *                       *           *      *   
        335 TAAACCTAAACCACCAGTATATGAACCTCCAAAGAAGGAGAAACCTGAGCCAAAACCACCGATTT
          1 TGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCCTGAGCCAAAGCCACCGGTTT

                                     
        400 ATACACCTCCAAAGAAAGAGAAACC
         66 ATACACCTCCAAAGAAAGAGAAACC

                           *  *                          *                   
        425 TGAACCCAAACCACCCGTATATGAACCTCCAAAGAAGGAGAAGCCCGAGCCAAAGCCACCGGTTT
          1 TGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCCTGAGCCAAAGCCACCGGTTT

                                     
        490 ATACACCTCCAAAGAAAGAGAAACC
         66 ATACACCTCCAAAGAAAGAGAAACC

                            *                             *         *        
        515 TGAACCCAAACCACCAATGTATGAACCTCCAAAAAAGCCTCCAATGTATGAA-CCTAAGCCACCA
          1 TGAACCCAAACCACCAGTGTATGAACCTCC---AAAG-----AA-GGA-GAAGCCTGAG---CCA

                                            *     
        579 AAGCCACCGGTTTATACACCTCCAAAGAAAGAAAAACC
         53 AAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACC

            *        *      *     *       
        617 AGAACCCAAGCCACCAATGTATCAACCTCC
          1 TGAACCCAAACCACCAGTGTATGAACCTCC

        647 CAACAACCCA


Statistics
Matches: 352,  Mismatches: 37, Indels: 14
        0.87            0.09        0.03

Matches are distributed among these distances:
  90  270  0.77
  93    4  0.01
  98    2  0.01
  99    6  0.02
 100    3  0.01
 102   67  0.19

ACGTcount: A:0.41, C:0.30, G:0.16, T:0.13


Consensus pattern (90 bp):   
TGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCCTGAGCCAAAGCCACCGGTTT
ATACACCTCCAAAGAAAGAGAAACC

Found at i:596 original size:102 final size:102

Alignment explanation


    Indices: 474--731  Score: 336
    Period size: 102  Copynumber: 2.5  Consensus size: 102

        464 GAAGCCCGAG

                                               *     *                     * 
        474 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAATGTATGA
          1 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAAAAACCAGAACCCAAACCACCAATGTATCA

                        *  *     *        *  *   
        539 ACCTCCAAAAAAGCCTCCAATGTATGAACCTAAGCCA
         66 ACCTCCAAAAAACCCACCAATATATGAACCAAAACCA

                                                              *              
        576 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAAAAACCAGAACCCAAGCCACCAATGTATCA
          1 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAAAAACCAGAACCCAAACCACCAATGTATCA

                  *  *                 *         
        641 ACCTCCCAACAACCCACCAATATATGAGCCAAAACCA
         66 ACCTCCAAAAAACCCACCAATATATGAACCAAAACCA

              *        *      *    *      *       *   *    *      
        678 CCTAAGCCACCAGTTTATGCACCACCAAAGGAAGAAAAGCCAAAACCTAAACCA
          1 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAAAAACCAGAACCCAAACCA

        732 TCAGTTTATG


Statistics
Matches: 135,  Mismatches: 21, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
 102  135  1.00

ACGTcount: A:0.43, C:0.33, G:0.12, T:0.13


Consensus pattern (102 bp):   
CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAAAAACCAGAACCCAAACCACCAATGTATCA
ACCTCCAAAAAACCCACCAATATATGAACCAAAACCA

Done.