Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g00070.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, 1000

Length: 1740
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29


Found at i:1198 original size:15 final size:15

Alignment explanation


    Indices: 1178--1222  Score: 51
    Period size: 15  Copynumber: 3.2  Consensus size: 15

       1168 AAAAGAAAAA

                           
       1178 GAAAAATGAAGAGTC
          1 GAAAAATGAAGAGTC

                         **
       1193 GAAAAA-GAA-A-AA
          1 GAAAAATGAAGAGTC

                           
       1205 GAAAAATGAAGAGTC
          1 GAAAAATGAAGAGTC

               
       1220 GAA
          1 GAA

       1223 GCAGTATATA


Statistics
Matches: 23,  Mismatches: 4, Indels: 6
        0.70            0.12        0.18

Matches are distributed among these distances:
  12    6  0.26
  13    4  0.17
  14    4  0.17
  15    9  0.39

ACGTcount: A:0.62, C:0.04, G:0.24, T:0.09


Consensus pattern (15 bp):   
GAAAAATGAAGAGTC

Found at i:1205 original size:27 final size:27

Alignment explanation


    Indices: 1167--1222  Score: 112
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       1157 CATAAATGTT

                                       
       1167 AAAAAGAAAAAGAAAAATGAAGAGTCG
          1 AAAAAGAAAAAGAAAAATGAAGAGTCG

                                       
       1194 AAAAAGAAAAAGAAAAATGAAGAGTCG
          1 AAAAAGAAAAAGAAAAATGAAGAGTCG

              
       1221 AA
          1 AA

       1223 GCAGTATATA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   29  1.00

ACGTcount: A:0.68, C:0.04, G:0.21, T:0.07


Consensus pattern (27 bp):   
AAAAAGAAAAAGAAAAATGAAGAGTCG
Done.