Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g00501.N40

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, 471

Length: 785
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.35


Found at i:168 original size:40 final size:40

Alignment explanation


    Indices: 119--194  Score: 143
    Period size: 40  Copynumber: 1.9  Consensus size: 40

        109 TCTTTCTGCA

                                                    
        119 AATCTCATTCCTCCCTTTCTCTCTTTCTCAGGCAAAGGCC
          1 AATCTCATTCCTCCCTTTCTCTCTTTCTCAGGCAAAGGCC

                         *                      
        159 AATCTCATTCCTCTCTTTCTCTCTTTCTCAGGCAAA
          1 AATCTCATTCCTCCCTTTCTCTCTTTCTCAGGCAAA

        195 TCTCATTCCT


Statistics
Matches: 35,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  40   35  1.00

ACGTcount: A:0.18, C:0.36, G:0.08, T:0.38


Consensus pattern (40 bp):   
AATCTCATTCCTCCCTTTCTCTCTTTCTCAGGCAAAGGCC

Found at i:197 original size:34 final size:34

Alignment explanation


    Indices: 99--206  Score: 123
    Period size: 40  Copynumber: 3.1  Consensus size: 34

         89 TCATCTTCTT

                 *                            
         99 TCTCTCTCTCTCTTTCT---GCAAATCTCATTCC
          1 TCTCTTTCTCTCTTTCTCAGGCAAATCTCATTCC

              *                                     
        130 TCCCTTTCTCTCTTTCTCAGGCAAAGGCCAATCTCATTCC
          1 TCTCTTTCTCTCTTTCTCAGGC--A----AATCTCATTCC

                                              
        170 TCTCTTTCTCTCTTTCTCAGGCAAATCTCATTCC
          1 TCTCTTTCTCTCTTTCTCAGGCAAATCTCATTCC

               
        204 TCT
          1 TCT

        207 TCGCAAGGTC


Statistics
Matches: 65,  Mismatches: 3, Indels: 15
        0.78            0.04        0.18

Matches are distributed among these distances:
  31   15  0.23
  34   16  0.25
  36    1  0.02
  38    1  0.02
  40   32  0.49

ACGTcount: A:0.15, C:0.37, G:0.06, T:0.42


Consensus pattern (34 bp):   
TCTCTTTCTCTCTTTCTCAGGCAAATCTCATTCC
Done.