Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g01571.F18

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: 5079
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29


Found at i:533 original size:4 final size:4

Alignment explanation


    Indices: 524--554  Score: 53
    Period size: 4  Copynumber: 7.8  Consensus size: 4

        514 TACATAATAT

                                   *              
        524 TATG TATG TATG TATG TATA TATG TATG TAT
          1 TATG TATG TATG TATG TATG TATG TATG TAT

        555 CCAACTCCAG


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   4   25  1.00

ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52


Consensus pattern (4 bp):   
TATG

Found at i:541 original size:12 final size:12

Alignment explanation


    Indices: 520--554  Score: 54
    Period size: 12  Copynumber: 3.0  Consensus size: 12

        510 TTTTTACATA

                        
        520 ATAT-TATGTAT
          1 ATATGTATGTAT

            *           
        531 GTATGTATGTAT
          1 ATATGTATGTAT

                        
        543 ATATGTATGTAT
          1 ATATGTATGTAT

        555 CCAACTCCAG


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  11    3  0.14
  12   18  0.86

ACGTcount: A:0.31, C:0.00, G:0.17, T:0.51


Consensus pattern (12 bp):   
ATATGTATGTAT

Found at i:3853 original size:57 final size:54

Alignment explanation


    Indices: 3792--3928  Score: 139
    Period size: 57  Copynumber: 2.4  Consensus size: 54

       3782 AGCAGCTTTT

                              *                          *      *    
       3792 ACAGCAACAGTATCAGCAACAGCCACAGCTGCTACAAGTGCAACAGCAATATCTTCA
          1 ACAGCAACAGTATCAGCAGCAGCCACAGCTGCTAC-A--GCAACAACAATATATTCA

                      *   *   *                 *             *      
       3849 ACAGCAACAATTACCCTATCAGCAGCCACAGCTGCTGCAGCAACAACAATTTATTCA
          1 ACAGCAAC-AGTA-TC-AGCAGCAGCCACAGCTGCTACAGCAACAACAATATATTCA

                          *        
       3906 ACAGCAACAGTATCTGCAGCAGC
          1 ACAGCAACAGTATCAGCAGCAGC

       3929 AGCAGCAACA


Statistics
Matches: 65,  Mismatches: 12, Indels: 9
        0.76            0.14        0.10

Matches are distributed among these distances:
  54    7  0.11
  55    1  0.02
  56    3  0.05
  57   31  0.48
  58    3  0.05
  59    2  0.03
  60   18  0.28

ACGTcount: A:0.37, C:0.31, G:0.15, T:0.17


Consensus pattern (54 bp):   
ACAGCAACAGTATCAGCAGCAGCCACAGCTGCTACAGCAACAACAATATATTCA

Found at i:4632 original size:70 final size:70

Alignment explanation


    Indices: 4545--4686  Score: 275
    Period size: 70  Copynumber: 2.0  Consensus size: 70

       4535 TTAATAATGA

                                                                             
       4545 AAGCTTAAAGTTTAAACTTGATCAACTTTGTCTGATAATGAGAAGAAAATGTCAATTGAAGAGCT
          1 AAGCTTAAAGTTTAAACTTGATCAACTTTGTCTGATAATGAGAAGAAAATGTCAATTGAAGAGCT

                 
       4610 CCTGG
         66 CCTGG

                                                       *                     
       4615 AAGCTTAAAGTTTAAACTTGATCAACTTTGTCTGATAATGAGAGGAAAATGTCAATTGAAGAGCT
          1 AAGCTTAAAGTTTAAACTTGATCAACTTTGTCTGATAATGAGAAGAAAATGTCAATTGAAGAGCT

                 
       4680 CCTGG
         66 CCTGG

              
       4685 AA
          1 AA

       4687 CATACTGCAT


Statistics
Matches: 71,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  70   71  1.00

ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30


Consensus pattern (70 bp):   
AAGCTTAAAGTTTAAACTTGATCAACTTTGTCTGATAATGAGAAGAAAATGTCAATTGAAGAGCT
CCTGG
Done.