Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g00841.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, 413

Length: 689
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35


Found at i:268 original size:15 final size:15

Alignment explanation


    Indices: 246--436  Score: 184
    Period size: 15  Copynumber: 12.7  Consensus size: 15

        236 CTCTACCATT

                      *    
        246 GTACCAAATGTTGCG
          1 GTACCAAATGCTGCG

             *            *
        261 GCACCAAATGCTGCA
          1 GTACCAAATGCTGCG

                       *  *
        276 GTACCAAATGCAGCT
          1 GTACCAAATGCTGCG

                        *  
        291 GTACCAAATGCTACG
          1 GTACCAAATGCTGCG

            *        *    *
        306 ATACCAAATACTGCT
          1 GTACCAAATGCTGCG

              *       *  **
        321 GTTCCAAATGTTGTT
          1 GTACCAAATGCTGCG

                    * *    
        336 GTACCAAACGTTGCG
          1 GTACCAAATGCTGCG

                          *
        351 GTACCAAATGCTGCT
          1 GTACCAAATGCTGCG

                  *   *    
        366 GTACCAGATGTTGCG
          1 GTACCAAATGCTGCG

                      *   *
        381 GTACCAAATGTTGCT
          1 GTACCAAATGCTGCG

                      *    
        396 GTACCAAATGTTGCG
          1 GTACCAAATGCTGCG

            *              
        411 ATACCAAATGCTGCG
          1 GTACCAAATGCTGCG

                       
        426 GTACCAAATGC
          1 GTACCAAATGC

        437 GAACGAGAAA


Statistics
Matches: 142,  Mismatches: 34, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  15  142  1.00

ACGTcount: A:0.29, C:0.24, G:0.21, T:0.25


Consensus pattern (15 bp):   
GTACCAAATGCTGCG

Found at i:282 original size:30 final size:30

Alignment explanation


    Indices: 245--435  Score: 213
    Period size: 30  Copynumber: 6.4  Consensus size: 30

        235 CCTCTACCAT

                             *            
        245 TGTACCAAATGTTGCGGCACCAAATGCTGC
          1 TGTACCAAATGTTGCGGTACCAAATGCTGC

            *          **  *            * 
        275 AGTACCAAATGCAGCTGTACCAAATGCTAC
          1 TGTACCAAATGTTGCGGTACCAAATGCTGC

                       **   *  *       *  *
        305 -GATACCAAATACTGCTGTTCCAAATGTTGT
          1 TG-TACCAAATGTTGCGGTACCAAATGCTGC

                     *                    
        335 TGTACCAAACGTTGCGGTACCAAATGCTGC
          1 TGTACCAAATGTTGCGGTACCAAATGCTGC

                   *                  *   
        365 TGTACCAGATGTTGCGGTACCAAATGTTGC
          1 TGTACCAAATGTTGCGGTACCAAATGCTGC

                            *             
        395 TGTACCAAATGTTGCGATACCAAATGCTGC
          1 TGTACCAAATGTTGCGGTACCAAATGCTGC

            *          
        425 GGTACCAAATG
          1 TGTACCAAATG

        436 CGAACGAGAA


Statistics
Matches: 133,  Mismatches: 26, Indels: 4
        0.82            0.16        0.02

Matches are distributed among these distances:
  29    1  0.01
  30  131  0.98
  31    1  0.01

ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26


Consensus pattern (30 bp):   
TGTACCAAATGTTGCGGTACCAAATGCTGC

Found at i:312 original size:45 final size:45

Alignment explanation


    Indices: 245--435  Score: 213
    Period size: 45  Copynumber: 4.2  Consensus size: 45

        235 CCTCTACCAT

                             *            *           *  
        245 TGTACCAAATGTTGCGGCACCAAATGCTGCAGTACCAAATGCAGC
          1 TGTACCAAATGTTGCGGTACCAAATGCTGCTGTACCAAATGCTGC

                       * *  *        *       *       *  *
        290 TGTACCAAATGCTACGATACCAAATACTGCTGTTCCAAATGTTGT
          1 TGTACCAAATGTTGCGGTACCAAATGCTGCTGTACCAAATGCTGC

                     *                           *   *   
        335 TGTACCAAACGTTGCGGTACCAAATGCTGCTGTACCAGATGTTGC
          1 TGTACCAAATGTTGCGGTACCAAATGCTGCTGTACCAAATGCTGC

            *              *          *                   
        380 GGTACCAAATGTTGCTGTACCAAATGTTGC-GATACCAAATGCTGC
          1 TGTACCAAATGTTGCGGTACCAAATGCTGCTG-TACCAAATGCTGC

            *          
        425 GGTACCAAATG
          1 TGTACCAAATG

        436 CGAACGAGAA


Statistics
Matches: 121,  Mismatches: 24, Indels: 2
        0.82            0.16        0.01

Matches are distributed among these distances:
  44    1  0.01
  45  120  0.99

ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26


Consensus pattern (45 bp):   
TGTACCAAATGTTGCGGTACCAAATGCTGCTGTACCAAATGCTGC
Done.