Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1244

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: 2287
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36


Found at i:30 original size:7 final size:7

Alignment explanation


    Indices: 11--40  Score: 53
    Period size: 7  Copynumber: 4.4  Consensus size: 7

          1 AAATCAAATT

                   
         11 TAATAAA
          1 TAATAAA

                   
         18 -AATAAA
          1 TAATAAA

                   
         24 TAATAAA
          1 TAATAAA

                   
         31 TAATAAA
          1 TAATAAA

               
         38 TAA
          1 TAA

         41 AAAAAGACCA


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
   6    6  0.27
   7   16  0.73

ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27


Consensus pattern (7 bp):   
TAATAAA

Found at i:358 original size:19 final size:19

Alignment explanation


    Indices: 311--387  Score: 100
    Period size: 19  Copynumber: 3.8  Consensus size: 19

        301 AAATTAAATC

                         *      
        311 TCTAAGATTACAAAATCATA
          1 TCTAAGATTAC-ATATCATA

                        *         
        331 TCTTCTAAGATTGCATATCATA
          1 ---TCTAAGATTACATATCATA

                               
        353 TCTAAGATTACATATCATA
          1 TCTAAGATTACATATCATA

                            
        372 TCTAAGATTACATATC
          1 TCTAAGATTACATATC

        388 CTTGAAGATT


Statistics
Matches: 51,  Mismatches: 3, Indels: 4
        0.88            0.05        0.07

Matches are distributed among these distances:
  19   34  0.67
  22    7  0.14
  23   10  0.20

ACGTcount: A:0.40, C:0.17, G:0.06, T:0.36


Consensus pattern (19 bp):   
TCTAAGATTACATATCATA

Done.