Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g00387.P3

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: 6746
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31


Found at i:1152 original size:32 final size:32

Alignment explanation


    Indices: 1087--1158  Score: 103
    Period size: 32  Copynumber: 2.3  Consensus size: 32

       1077 TTGTTCCTTA

                       *               *    
       1087 TTGTTTGTTTGGAAAGAAAGAAACATTCATTG
          1 TTGTTTGTTTGAAAAGAAAGAAACATTAATTG

                                             
       1119 TTGTTTGTTTGAAAAGAAAGAAACA-TAAGTTG
          1 TTGTTTGTTTGAAAAGAAAGAAACATTAA-TTG

                     
       1151 TT-TTTGTT
          1 TTGTTTGTT

       1159 ACTATAAAAA


Statistics
Matches: 37,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  31    8  0.22
  32   29  0.78

ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42


Consensus pattern (32 bp):   
TTGTTTGTTTGAAAAGAAAGAAACATTAATTG

Found at i:6064 original size:16 final size:16

Alignment explanation


    Indices: 6034--6081  Score: 57
    Period size: 15  Copynumber: 3.1  Consensus size: 16

       6024 GAAAATTAAT

                             
       6034 ATAAAATCT-AAAAT-A
          1 ATAAAAT-TAAAAATAA

                             
       6049 ATAATAATTAAAAATAA
          1 ATAA-AATTAAAAATAA

                            
       6066 ATAAAATT-AAAATAA
          1 ATAAAATTAAAAATAA

             
       6081 A
          1 A

       6082 CTTAAAATAG


Statistics
Matches: 30,  Mismatches: 0, Indels: 6
        0.83            0.00        0.17

Matches are distributed among these distances:
  15   13  0.43
  16   12  0.40
  17    5  0.17

ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27


Consensus pattern (16 bp):   
ATAAAATTAAAAATAA

Found at i:6080 original size:11 final size:11

Alignment explanation


    Indices: 6025--6095  Score: 58
    Period size: 11  Copynumber: 6.5  Consensus size: 11

       6015 ATAGCTTAAG

                    *  
       6025 AAAATTAATAT
          1 AAAATTAAAAT

                        
       6036 AAAATCTAAAAT
          1 AAAAT-TAAAAT

                      * 
       6048 AATAA-T-AATT
          1 AA-AATTAAAAT

                *      
       6058 AAAAAT-AAAT
          1 AAAATTAAAAT

                       
       6068 AAAATTAAAAT
          1 AAAATTAAAAT

               *       
       6079 AAACTTAAAAT
          1 AAAATTAAAAT

             *    
       6090 AGAATT
          1 AAAATT

       6096 TCCTATTTTT


Statistics
Matches: 49,  Mismatches: 7, Indels: 8
        0.77            0.11        0.12

Matches are distributed among these distances:
   9    2  0.04
  10   14  0.29
  11   24  0.49
  12    7  0.14
  13    2  0.04

ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30


Consensus pattern (11 bp):   
AAAATTAAAAT
Done.