Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00005.F1

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, 513

Length: 855
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29


Found at i:212 original size:19 final size:19

Alignment explanation


    Indices: 190--247  Score: 52
    Period size: 19  Copynumber: 3.2  Consensus size: 19

        180 AATCGGTAGT

                               
        190 CAGTCGCGCAACTCGCAAG
          1 CAGTCGCGCAACTCGCAAG

                           **  
        209 CAGT---GCAA-TCGGTAG
          1 CAGTCGCGCAACTCGCAAG

                       *        
        224 TCAGTCGCGCAGCTCGCAAG
          1 -CAGTCGCGCAACTCGCAAG

                
        244 CAGT
          1 CAGT

        248 GCGATCGGTA


Statistics
Matches: 29,  Mismatches: 5, Indels: 10
        0.66            0.11        0.23

Matches are distributed among these distances:
  15    5  0.17
  16    8  0.28
  19   11  0.38
  20    5  0.17

ACGTcount: A:0.24, C:0.31, G:0.29, T:0.16


Consensus pattern (19 bp):   
CAGTCGCGCAACTCGCAAG

Found at i:222 original size:35 final size:35

Alignment explanation


    Indices: 177--281  Score: 174
    Period size: 35  Copynumber: 3.0  Consensus size: 35

        167 ACTCAGCCCT

                                   *           
        177 TGCAATCGGTAGTCAGTCGCGCAACTCGCAAGCAG
          1 TGCAATCGGTAGTCAGTCGCGCAGCTCGCAAGCAG

                                               
        212 TGCAATCGGTAGTCAGTCGCGCAGCTCGCAAGCAG
          1 TGCAATCGGTAGTCAGTCGCGCAGCTCGCAAGCAG

               *           * *                 
        247 TGCGATCGGTAGTCAATTGCGCAGCTCGCAAGCAG
          1 TGCAATCGGTAGTCAGTCGCGCAGCTCGCAAGCAG

        282 CAAGCTCGTC


Statistics
Matches: 66,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  35   66  1.00

ACGTcount: A:0.24, C:0.28, G:0.30, T:0.18


Consensus pattern (35 bp):   
TGCAATCGGTAGTCAGTCGCGCAGCTCGCAAGCAG
Done.