Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g00693.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: 1935
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30


Found at i:29 original size:14 final size:15

Alignment explanation


    Indices: 10--38  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

          1 GATTTTTCT

                           
         10 AAAAAAGAAA-TAAA
          1 AAAAAAGAAACTAAA

                           
         24 AAAAAAGAAACTAAA
          1 AAAAAAGAAACTAAA

         39 CAATTTAAAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14   10  0.71
  15    4  0.29

ACGTcount: A:0.83, C:0.03, G:0.07, T:0.07


Consensus pattern (15 bp):   
AAAAAAGAAACTAAA

Found at i:304 original size:9 final size:9

Alignment explanation


    Indices: 279--322  Score: 52
    Period size: 9  Copynumber: 4.9  Consensus size: 9

        269 CCGATGAGGA

                   * 
        279 AACAGCAAC
          1 AACAGCAGC

               *     
        288 AACTGCAGC
          1 AACAGCAGC

                     
        297 AACAGCAGC
          1 AACAGCAGC

             *       
        306 AGCAGCAGC
          1 AACAGCAGC

             *      
        315 AGCAGCAG
          1 AACAGCAG

        323 ATGACTACGA


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   9   31  1.00

ACGTcount: A:0.41, C:0.32, G:0.25, T:0.02


Consensus pattern (9 bp):   
AACAGCAGC

Found at i:305 original size:3 final size:3

Alignment explanation


    Indices: 292--322  Score: 53
    Period size: 3  Copynumber: 10.3  Consensus size: 3

        282 AGCAACAACT

                    *                                
        292 GCA GCA ACA GCA GCA GCA GCA GCA GCA GCA G
          1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA G

        323 ATGACTACGA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.35, C:0.32, G:0.32, T:0.00


Consensus pattern (3 bp):   
GCA

Found at i:307 original size:12 final size:12

Alignment explanation


    Indices: 281--321  Score: 55
    Period size: 12  Copynumber: 3.4  Consensus size: 12

        271 GATGAGGAAA

                    * * 
        281 CAGCAACAACTG
          1 CAGCAACAGCAG

                        
        293 CAGCAACAGCAG
          1 CAGCAACAGCAG

                 *      
        305 CAGCAGCAGCAG
          1 CAGCAACAGCAG

                 
        317 CAGCA
          1 CAGCA

        322 GATGACTACG


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  12   26  1.00

ACGTcount: A:0.39, C:0.34, G:0.24, T:0.02


Consensus pattern (12 bp):   
CAGCAACAGCAG
Done.