Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_1073 ID=scaffold_1073-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, 664

Length: 1107
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37


Found at i:1010 original size:26 final size:28

Alignment explanation


    Indices: 956--1019  Score: 87
    Period size: 28  Copynumber: 2.4  Consensus size: 28

        946 TAAGAATAAG

                *    *   *              
        956 AATTTTATTAAATTATATATTATTATTA
          1 AATTATATTTAATAATATATTATTATTA

                                        
        984 AATTATATTTAATAATA-ATTATT-TTA
          1 AATTATATTTAATAATATATTATTATTA

                      
       1010 AATTATATTT
          1 AATTATATTT

       1020 TATAGTGTTA


Statistics
Matches: 33,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  26   13  0.39
  27    6  0.18
  28   14  0.42

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (28 bp):   
AATTATATTTAATAATATATTATTATTA

Found at i:1087 original size:110 final size:106

Alignment explanation


    Indices: 868--1076  Score: 287
    Period size: 110  Copynumber: 1.9  Consensus size: 106

        858 AATAAAGTAG

                                                          *                  
        868 ATTATAAATTATAATTTAATAATAATTAGTTAAATTATATTTTATATTATTATATATTATGATTT
          1 ATTATAAATTATAATTTAATAATAATTAGTTAAATTATATTTTATAGTATTATATATTATGATTT

                                                        
        933 TAGTAAATTCATATAAGAATAAGAATTTTATTAAATTATATATT
         66 TAGTAAATTCATAT---AATAAGAATTTTATTAAATTATATATT

                                          *                   *              
        977 ATTATTAAATTAT-ATTTAATAATAATTATTTTAAATTATATTTTATAGTGTTATATATTATGAT
          1 ATTA-TAAATTATAATTTAATAATAATTA-GTTAAATTATATTTTATAGTATTATATATTATGA-

                                *                
       1041 TTTATTAGTAAATTCATAT-TTAAGAATATTTATTAA
         63 -TT-TTAGTAAATTCATATAATAAGAAT-TTTATTAA

       1077 TCATTTTATT


Statistics
Matches: 90,  Mismatches: 4, Indels: 11
        0.86            0.04        0.10

Matches are distributed among these distances:
 109   26  0.29
 110   47  0.52
 112    2  0.02
 113   15  0.17

ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51


Consensus pattern (106 bp):   
ATTATAAATTATAATTTAATAATAATTAGTTAAATTATATTTTATAGTATTATATATTATGATTT
TAGTAAATTCATATAATAAGAATTTTATTAAATTATATATT
Done.