Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold904

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: 19333
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.37


Found at i:2485 original size:15 final size:15

Alignment explanation


    Indices: 2465--2496  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       2455 TTATGTTGTA

                           
       2465 AAGGTGATGACAAAT
          1 AAGGTGATGACAAAT

                           
       2480 AAGGTGATGACAAAT
          1 AAGGTGATGACAAAT

              
       2495 AA
          1 AA

       2497 AATTGGGTCT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.50, C:0.06, G:0.25, T:0.19


Consensus pattern (15 bp):   
AAGGTGATGACAAAT

Found at i:6111 original size:16 final size:16

Alignment explanation


    Indices: 6090--6121  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       6080 TCCAACGAGA

                            
       6090 ATTTTTTATTTTTTTT
          1 ATTTTTTATTTTTTTT

                            
       6106 ATTTTTTATTTTTTTT
          1 ATTTTTTATTTTTTTT

       6122 GGGGAATAAG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88


Consensus pattern (16 bp):   
ATTTTTTATTTTTTTT

Found at i:13110 original size:29 final size:28

Alignment explanation


    Indices: 13054--13119  Score: 82
    Period size: 28  Copynumber: 2.4  Consensus size: 28

      13044 AAATTTACAG

                                        
      13054 TTAAAAATTTATGAATATAAATTAAAAA
          1 TTAAAAATTTATGAATATAAATTAAAAA

                        *                 
      13082 TTAAAAATTTATTAA-ATAAA-TAATTAAA
          1 TTAAAAATTTATGAATATAAATTAA--AAA

            *         
      13110 ATAAAAATTT
          1 TTAAAAATTT

      13120 GTTCATTTAG


Statistics
Matches: 34,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
  26    3  0.09
  27    5  0.15
  28   26  0.76

ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38


Consensus pattern (28 bp):   
TTAAAAATTTATGAATATAAATTAAAAA
Done.