Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g01245.M1

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: 3373
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29


Found at i:458 original size:150 final size:150

Alignment explanation


    Indices: 288--592  Score: 513
    Period size: 150  Copynumber: 2.0  Consensus size: 150

        278 CAATGAGGAG

                                                                *  *         
        288 GAAGAGGAAGAGGTGAGAGAGGTTGTTAGATTGAAAAGAGAACGGATATCTTCGGTAAGGGAGAG
          1 GAAGAGGAAGAGGTGAGAGAGGTTGTTAGATTGAAAAGAGAACGGATATCTTAGGAAAGGGAGAG

                                          *                                  
        353 GAAGATT-CTGGATAAAAAATCTGTAAAGCGGGAAAGCATGTCTGTTGAAGAAGATGAAGACAAG
         66 GAAGATTGC-GGATAAAAAATCTGTAAAGCAGGAAAGCATGTCTGTTGAAGAAGATGAAGACAAG

                *                
        417 GATTTTGAGGAGGAAGAAGAA
        130 GATTATGAGGAGGAAGAAGAA

                                         *                       *           
        438 GAAGAGGAAGAGGTGAGAGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTATGAAAGGGAGAG
          1 GAAGAGGAAGAGGTGAGAGAGGTTGTTAGATTGAAAAGAGAACGGATATCTTAGGAAAGGGAGAG

                                    *            *                           
        503 GAAGATTGCGGATAAAAAATCTGTCAAGCAGGAAAGCTTGTCTGTTGAAGAAGATGAAGACAAGG
         66 GAAGATTGCGGATAAAAAATCTGTAAAGCAGGAAAGCATGTCTGTTGAAGAAGATGAAGACAAGG

                         *      
        568 ATTATGAGGAGGAGGAAGAA
        131 ATTATGAGGAGGAAGAAGAA

                 
        588 GAAGA
          1 GAAGA

        593 AAAGGAAGAT


Statistics
Matches: 145,  Mismatches: 9, Indels: 2
        0.93            0.06        0.01

Matches are distributed among these distances:
 150  144  0.99
 151    1  0.01

ACGTcount: A:0.40, C:0.06, G:0.35, T:0.19


Consensus pattern (150 bp):   
GAAGAGGAAGAGGTGAGAGAGGTTGTTAGATTGAAAAGAGAACGGATATCTTAGGAAAGGGAGAG
GAAGATTGCGGATAAAAAATCTGTAAAGCAGGAAAGCATGTCTGTTGAAGAAGATGAAGACAAGG
ATTATGAGGAGGAAGAAGAA

Found at i:613 original size:30 final size:30

Alignment explanation


    Indices: 552--613  Score: 70
    Period size: 30  Copynumber: 2.1  Consensus size: 30

        542 GTCTGTTGAA

                 *     *     **           
        552 GAAGATGAAGACAAGGATTATGAGGAGGAG
          1 GAAGAAGAAGAAAAGGAAGATGAGGAGGAG

                                   *  *   
        582 GAAGAAGAAGAAAAGGAAGATGATGATGAG
          1 GAAGAAGAAGAAAAGGAAGATGAGGAGGAG

              
        612 GA
          1 GA

        614 GTTCACTCCA


Statistics
Matches: 26,  Mismatches: 6, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  30   26  1.00

ACGTcount: A:0.48, C:0.02, G:0.39, T:0.11


Consensus pattern (30 bp):   
GAAGAAGAAGAAAAGGAAGATGAGGAGGAG

Found at i:646 original size:36 final size:36

Alignment explanation


    Indices: 606--722  Score: 171
    Period size: 36  Copynumber: 3.2  Consensus size: 36

        596 GGAAGATGAT

                    *             *   *         
        606 GATGAGGAGTTCACTCCAGATGTAGAAGATTGTTTG
          1 GATGAGGAATTCACTCCAGATGAAGAGGATTGTTTG

                       *                        
        642 GATGAGGAATTTACTCCAGATGAAGAGGATTGTTTG
          1 GATGAGGAATTCACTCCAGATGAAGAGGATTGTTTG

                 *           *                 *
        678 GATGAAGAATTCACTCCGGATGAAGAGGATTGTTTA
          1 GATGAGGAATTCACTCCAGATGAAGAGGATTGTTTG

                     
        714 GATGAGGAA
          1 GATGAGGAA

        723 GAGGAATTGA


Statistics
Matches: 72,  Mismatches: 9, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  36   72  1.00

ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28


Consensus pattern (36 bp):   
GATGAGGAATTCACTCCAGATGAAGAGGATTGTTTG
Done.