Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_238 ID=scaffold_238-JGI_221_v2.0

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: 9078
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.32


Found at i:2844 original size:30 final size:30

Alignment explanation


    Indices: 2808--2871  Score: 78
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       2798 TTAGTAAAGG

                                            
       2808 TAAAATTAT-ATTTTAA-CCTCTTAAAAATGA
          1 TAAAATTATGA-TTTAATCCT-TTAAAAATGA

                   *                    * 
       2838 TAAAATTTTGATTTAATCCTTTAAAAATTA
          1 TAAAATTATGATTTAATCCTTTAAAAATGA

                
       2868 TAAA
          1 TAAA

       2872 GATGTAAGCT


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  30   26  0.87
  31    4  0.13

ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42


Consensus pattern (30 bp):   
TAAAATTATGATTTAATCCTTTAAAAATGA

Found at i:6083 original size:27 final size:27

Alignment explanation


    Indices: 6053--6106  Score: 90
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       6043 TTTGGATCAC

                   *                   
       6053 TGATTTGGCACTCATTACCCTTGAACT
          1 TGATTTGACACTCATTACCCTTGAACT

                         *             
       6080 TGATTTGACACTCCTTACCCTTGAACT
          1 TGATTTGACACTCATTACCCTTGAACT

       6107 CTACAGAATA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  27   25  1.00

ACGTcount: A:0.22, C:0.28, G:0.13, T:0.37


Consensus pattern (27 bp):   
TGATTTGACACTCATTACCCTTGAACT
Done.