Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g02160.N4

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: 9287
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34


Found at i:2191 original size:14 final size:15

Alignment explanation


    Indices: 2172--2211  Score: 55
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       2162 GAAGATGGAT

                           
       2172 AAATAAA-AAAAAAG
          1 AAATAAATAAAAAAG

                        *  
       2186 AAATAAATAAAATAG
          1 AAATAAATAAAAAAG

                       
       2201 AATATAAATAA
          1 AA-ATAAATAA

       2212 GATAAAGATA


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  14    7  0.30
  15    8  0.35
  16    8  0.35

ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17


Consensus pattern (15 bp):   
AAATAAATAAAAAAG

Found at i:2891 original size:11 final size:11

Alignment explanation


    Indices: 2875--2899  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

       2865 GCGATTATTG

                       
       2875 TATTTATTGTA
          1 TATTTATTGTA

                       
       2886 TATTTATTGTA
          1 TATTTATTGTA

               
       2897 TAT
          1 TAT

       2900 AAATATAAAG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64


Consensus pattern (11 bp):   
TATTTATTGTA

Found at i:3522 original size:21 final size:21

Alignment explanation


    Indices: 3483--3522  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       3473 TTTATTTAAA

                       *         
       3483 AATATAAATGATATAGAATAT
          1 AATATAAATGAAATAGAATAT

                          *    
       3504 AATATAAATGAAATGGAAT
          1 AATATAAATGAAATAGAAT

       3523 TACTGATAAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.57, C:0.00, G:0.12, T:0.30


Consensus pattern (21 bp):   
AATATAAATGAAATAGAATAT

Found at i:3666 original size:14 final size:14

Alignment explanation


    Indices: 3647--3675  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       3637 TAGATAAATA

                          
       3647 ATAATCTATATAAC
          1 ATAATCTATATAAC

                          
       3661 ATAATCTATATAAC
          1 ATAATCTATATAAC

             
       3675 A
          1 A

       3676 AAGTAAAAAG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34


Consensus pattern (14 bp):   
ATAATCTATATAAC

Found at i:5386 original size:19 final size:19

Alignment explanation


    Indices: 5362--5401  Score: 62
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       5352 ATTTTTTTTT

                    *       *  
       5362 ATTAGAATCGAAAAGTTTA
          1 ATTAGAATAGAAAAGTATA

                               
       5381 ATTAGAATAGAAAAGTATA
          1 ATTAGAATAGAAAAGTATA

              
       5400 AT
          1 AT

       5402 AAAAGTTTAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.53, C:0.03, G:0.15, T:0.30


Consensus pattern (19 bp):   
ATTAGAATAGAAAAGTATA

Found at i:6052 original size:16 final size:16

Alignment explanation


    Indices: 6031--6063  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       6021 TCTTATTCCT

                       *    
       6031 TTGCTACTATAGAATA
          1 TTGCTACTATAAAATA

                            
       6047 TTGCTACTATAAAATA
          1 TTGCTACTATAAAATA

             
       6063 T
          1 T

       6064 AGAATACCGT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39


Consensus pattern (16 bp):   
TTGCTACTATAAAATA
Done.