Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g02160.N1

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: 9334
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34


Found at i:2238 original size:14 final size:15

Alignment explanation


    Indices: 2219--2258  Score: 55
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       2209 GAAGATGGAT

                           
       2219 AAATAAA-AAAAAAG
          1 AAATAAATAAAAAAG

                        *  
       2233 AAATAAATAAAATAG
          1 AAATAAATAAAAAAG

                       
       2248 AATATAAATAA
          1 AA-ATAAATAA

       2259 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:2938 original size:11 final size:11

Alignment explanation


    Indices: 2922--2946  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

       2912 GCGATTATTG

                       
       2922 TATTTATTGTA
          1 TATTTATTGTA

                       
       2933 TATTTATTGTA
          1 TATTTATTGTA

               
       2944 TAT
          1 TAT

       2947 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:3569 original size:21 final size:21

Alignment explanation


    Indices: 3530--3569  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       3520 TTTATTTAAA

                       *         
       3530 AATATAAATGATATAGAATAT
          1 AATATAAATGAAATAGAATAT

                          *    
       3551 AATATAAATGAAATGGAAT
          1 AATATAAATGAAATAGAAT

       3570 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:3713 original size:14 final size:14

Alignment explanation


    Indices: 3694--3722  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       3684 TAGATAAATA

                          
       3694 ATAATCTATATAAC
          1 ATAATCTATATAAC

                          
       3708 ATAATCTATATAAC
          1 ATAATCTATATAAC

             
       3722 A
          1 A

       3723 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:5433 original size:19 final size:19

Alignment explanation


    Indices: 5409--5448  Score: 62
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       5399 ATTTTTTTTT

                    *       *  
       5409 ATTAGAATCGAAAAGTTTA
          1 ATTAGAATAGAAAAGTATA

                               
       5428 ATTAGAATAGAAAAGTATA
          1 ATTAGAATAGAAAAGTATA

              
       5447 AT
          1 AT

       5449 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:6099 original size:16 final size:16

Alignment explanation


    Indices: 6078--6110  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       6068 TCTTATTCCT

                       *    
       6078 TTGCTACTATAGAATA
          1 TTGCTACTATAAAATA

                            
       6094 TTGCTACTATAAAATA
          1 TTGCTACTATAAAATA

             
       6110 T
          1 T

       6111 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.