Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g02043.M2

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: 2392
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26


Found at i:54 original size:19 final size:17

Alignment explanation


    Indices: 30--69  Score: 53
    Period size: 19  Copynumber: 2.2  Consensus size: 17

         20 AGGCTATTGT

                               
         30 TTTTCTTCTTCCTCTCTCG
          1 TTTTCTTC-TCCTCTCT-G

                        *    
         49 TTTTCTTCTCCTTTCTG
          1 TTTTCTTCTCCTCTCTG

                
         66 TTTT
          1 TTTT

         70 TCTTTCCCTT


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  17    5  0.25
  18    7  0.35
  19    8  0.40

ACGTcount: A:0.00, C:0.30, G:0.05, T:0.65


Consensus pattern (17 bp):   
TTTTCTTCTCCTCTCTG

Found at i:70 original size:18 final size:19

Alignment explanation


    Indices: 27--73  Score: 62
    Period size: 18  Copynumber: 2.5  Consensus size: 19

         17 GTCAGGCTAT

                               
         27 TGTTTTTCTTCTTCCTCTC
          1 TGTTTTTCTTCTTCCTCTC

                             *  
         46 TCG-TTTTCTTC-TCCTTTC
          1 T-GTTTTTCTTCTTCCTCTC

                      
         64 TGTTTTTCTT
          1 TGTTTTTCTT

         74 TCCCTTTCAC


Statistics
Matches: 25,  Mismatches: 1, Indels: 5
        0.81            0.03        0.16

Matches are distributed among these distances:
  17    1  0.04
  18   14  0.56
  19    9  0.36
  20    1  0.04

ACGTcount: A:0.00, C:0.28, G:0.06, T:0.66


Consensus pattern (19 bp):   
TGTTTTTCTTCTTCCTCTC

Found at i:79 original size:18 final size:18

Alignment explanation


    Indices: 27--81  Score: 51
    Period size: 18  Copynumber: 3.0  Consensus size: 18

         17 GTCAGGCTAT

                        *   *  
         27 TGTTTTTCTTCTTCCTCTC
          1 TGTTTTTCTT-TCCCTTTC

                                
         46 TCG-TTTTC-TTCTCCTTTC
          1 T-GTTTTTCTTTC-CCTTTC

                              
         64 TGTTTTTCTTTCCCTTTC
          1 TGTTTTTCTTTCCCTTTC

         82 ACCGACTCTT


Statistics
Matches: 30,  Mismatches: 2, Indels: 9
        0.73            0.05        0.22

Matches are distributed among these distances:
  17    2  0.07
  18   18  0.60
  19    9  0.30
  20    1  0.03

ACGTcount: A:0.00, C:0.31, G:0.05, T:0.64


Consensus pattern (18 bp):   
TGTTTTTCTTTCCCTTTC
Done.