Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g00685.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, 1000

Length: 2740
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31


Found at i:81 original size:26 final size:25

Alignment explanation


    Indices: 24--81  Score: 64
    Period size: 26  Copynumber: 2.2  Consensus size: 25

         14 ATCGCTCCAA

                                    * 
         24 GAAAGAGAAATTTCTTGAAAGAAATC
          1 GAAAGAGAAATTTCTTG-AAGAAAAC

             *                         
         50 GGAAGAGAAATATTCTCTG-AGAAAAC
          1 GAAAGAGAAAT-TTCT-TGAAGAAAAC

                  
         76 GAAAGA
          1 GAAAGA

         82 AGAAGAAAGA


Statistics
Matches: 27,  Mismatches: 3, Indels: 4
        0.79            0.09        0.12

Matches are distributed among these distances:
  26   21  0.78
  27    4  0.15
  28    2  0.07

ACGTcount: A:0.50, C:0.09, G:0.22, T:0.19


Consensus pattern (25 bp):   
GAAAGAGAAATTTCTTGAAGAAAAC

Found at i:1795 original size:18 final size:18

Alignment explanation


    Indices: 1772--1810  Score: 78
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       1762 TGTTAACATG

                              
       1772 TTATGCATAATATTAATT
          1 TTATGCATAATATTAATT

                              
       1790 TTATGCATAATATTAATT
          1 TTATGCATAATATTAATT

               
       1808 TTA
          1 TTA

       1811 ATTAAATTGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51


Consensus pattern (18 bp):   
TTATGCATAATATTAATT

Found at i:2412 original size:52 final size:50

Alignment explanation


    Indices: 2334--2435  Score: 177
    Period size: 52  Copynumber: 2.0  Consensus size: 50

       2324 CTAACAAAAG

                                                                
       2334 TCTGTAATTTCAATTTACAATAGGATAAATCAACCCCCATGAAAAGGATGGA
          1 TCTGTAATTTCAATTTACAATAGGAT-AATCAA-CCCCATGAAAAGGATGGA

                                         *                    
       2386 TCTGTAATTTCAATTTACAATAGGATAATGAACCCCATGAAAAGGATGGA
          1 TCTGTAATTTCAATTTACAATAGGATAATCAACCCCATGAAAAGGATGGA

       2436 ATTGGGGGAT


Statistics
Matches: 49,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  50   18  0.37
  51    5  0.10
  52   26  0.53

ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27


Consensus pattern (50 bp):   
TCTGTAATTTCAATTTACAATAGGATAATCAACCCCATGAAAAGGATGGA
Done.