Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g01305.P1

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: 5525
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35


Found at i:3924 original size:15 final size:15

Alignment explanation


    Indices: 3840--3932  Score: 71
    Period size: 15  Copynumber: 5.9  Consensus size: 15

       3830 ATATTTTAAA

                   *        
       3840 TAAAAAATTAGAAA-T
          1 TAAAAAAATA-AAATT

                      * *  
       3855 TAAAAAAATATATTT
          1 TAAAAAAATAAAATT

                            
       3870 TAAAAAAATTAAAATT
          1 TAAAAAAA-TAAAATT

             *                
       3886 AGAAAAAAATAAAACTCT
          1 -TAAAAAAATAAAA-T-T

             *    *        
       3904 TTAAAATATAAAATT
          1 TAAAAAAATAAAATT

                          
       3919 TAAAAAATATAAAA
          1 TAAAAAA-ATAAAA

       3933 GATAAAATAT


Statistics
Matches: 61,  Mismatches: 11, Indels: 11
        0.73            0.13        0.13

Matches are distributed among these distances:
  14    1  0.02
  15   24  0.39
  16   17  0.28
  17   18  0.30
  18    1  0.02

ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29


Consensus pattern (15 bp):   
TAAAAAAATAAAATT

Found at i:3925 original size:16 final size:16

Alignment explanation


    Indices: 3840--3932  Score: 63
    Period size: 16  Copynumber: 5.9  Consensus size: 16

       3830 ATATTTTAAA

                             
       3840 TAAAAAAT-TAGAAA-T
          1 TAAAAAATATA-AAATT

                       * *  
       3855 TAAAAAA-ATATATTT
          1 TAAAAAATATAAAATT

                             
       3870 TAAAAAA-ATTAAAA-T
          1 TAAAAAATA-TAAAATT

                    *          
       3885 TAGAAAAAAATAAAACTCT
          1 TA-AAAAATATAAAA-T-T

              *             
       3904 T-TAAAATATAAAATT
          1 TAAAAAATATAAAATT

                          
       3919 TAAAAAATATAAAA
          1 TAAAAAATATAAAA

       3933 GATAAAATAT


Statistics
Matches: 62,  Mismatches: 7, Indels: 17
        0.72            0.08        0.20

Matches are distributed among these distances:
  14    1  0.02
  15   23  0.37
  16   25  0.40
  17   11  0.18
  19    2  0.03

ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29


Consensus pattern (16 bp):   
TAAAAAATATAAAATT

Found at i:3938 original size:16 final size:16

Alignment explanation


    Indices: 3906--3939  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       3896 AAAACTCTTT

                       **   
       3906 AAAATATAAAATTTAA
          1 AAAATATAAAAGATAA

                            
       3922 AAAATATAAAAGATAA
          1 AAAATATAAAAGATAA

              
       3938 AA
          1 AA

       3940 TATTTTAAAA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24


Consensus pattern (16 bp):   
AAAATATAAAAGATAA

Found at i:3954 original size:24 final size:23

Alignment explanation


    Indices: 3905--3956  Score: 68
    Period size: 24  Copynumber: 2.2  Consensus size: 23

       3895 TAAAACTCTT

                 *                 
       3905 TAAAATATAAAATTTAAAAAATA
          1 TAAAAGATAAAATTTAAAAAATA

                            **      
       3928 TAAAAGATAAAATATTTTAAAATA
          1 TAAAAGATAAAAT-TTAAAAAATA

                 
       3952 TAAAA
          1 TAAAA

       3957 TTTCCAAAAA


Statistics
Matches: 25,  Mismatches: 3, Indels: 1
        0.86            0.10        0.03

Matches are distributed among these distances:
  23   12  0.48
  24   13  0.52

ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31


Consensus pattern (23 bp):   
TAAAAGATAAAATTTAAAAAATA
Done.