Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1336

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: 1991
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34


Found at i:230 original size:45 final size:38

Alignment explanation


    Indices: 187--261  Score: 150
    Period size: 38  Copynumber: 2.0  Consensus size: 38

        177 ACAGAATATG

                                                  
        187 GAATATAATTTGTTTATTCTCAATTAATTGCTAATTGA
          1 GAATATAATTTGTTTATTCTCAATTAATTGCTAATTGA

                                                 
        225 GAATATAATTTGTTTATTCTCAATTAATTGCTAATTG
          1 GAATATAATTTGTTTATTCTCAATTAATTGCTAATTG

        262 TTATCTATTT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  38   37  1.00

ACGTcount: A:0.33, C:0.08, G:0.11, T:0.48


Consensus pattern (38 bp):   
GAATATAATTTGTTTATTCTCAATTAATTGCTAATTGA

Found at i:252 original size:19 final size:19

Alignment explanation


    Indices: 192--253  Score: 63
    Period size: 19  Copynumber: 3.3  Consensus size: 19

        182 ATATGGAATA

                               
        192 TAATTTGTTTATTCTCAAT
          1 TAATTTGTTTATTCTCAAT

                   * *   ***   
        211 TAA-TTGCTAATTGAGAAT
          1 TAATTTGTTTATTCTCAAT

                                
        229 ATAATTTGTTTATTCTCAAT
          1 -TAATTTGTTTATTCTCAAT

                 
        249 TAATT
          1 TAATT

        254 GCTAATTGTT


Statistics
Matches: 31,  Mismatches: 10, Indels: 4
        0.69            0.22        0.09

Matches are distributed among these distances:
  18   10  0.32
  19   11  0.35
  20   10  0.32

ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52


Consensus pattern (19 bp):   
TAATTTGTTTATTCTCAAT
Done.