Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gorai.006G093900.2-JGI_221_v2.1

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, 910

Length: 1518
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25


Found at i:403 original size:27 final size:27

Alignment explanation


    Indices: 364--443  Score: 124
    Period size: 27  Copynumber: 3.0  Consensus size: 27

        354 TACTACCCCG

                *                      
        364 ACATCACCGGACACAAATCCGACTCCA
          1 ACATTACCGGACACAAATCCGACTCCA

                    *     *            
        391 ACATTACCAGACACCAATCCGACTCCA
          1 ACATTACCGGACACAAATCCGACTCCA

                                 *    
        418 ACATTACCGGACACAAATCCGGCTCC
          1 ACATTACCGGACACAAATCCGACTCC

        444 CACCGGCCCT


Statistics
Matches: 47,  Mismatches: 6, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  27   47  1.00

ACGTcount: A:0.35, C:0.40, G:0.11, T:0.14


Consensus pattern (27 bp):   
ACATTACCGGACACAAATCCGACTCCA

Found at i:475 original size:24 final size:24

Alignment explanation


    Indices: 448--563  Score: 124
    Period size: 24  Copynumber: 4.8  Consensus size: 24

        438 GGCTCCCACC

                       *            
        448 GGCCCTACCACGACTCCTCCGACT
          1 GGCCCTACCACAACTCCTCCGACT

                                    
        472 GGCCCTACCACAACTCCTCCGACT
          1 GGCCCTACCACAACTCCTCCGACT

                      **        *   
        496 GGCCCTACCATGACTCCTCCAACT
          1 GGCCCTACCACAACTCCTCCGACT

              ** *              *  *
        520 GGGACAACCACAACTCCTCCAACA
          1 GGCCCTACCACAACTCCTCCGACT

              ** *              
        544 GGGACAACCACAACTCCTCC
          1 GGCCCTACCACAACTCCTCC

        564 AACAGGGACA


Statistics
Matches: 82,  Mismatches: 10, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   82  1.00

ACGTcount: A:0.25, C:0.47, G:0.14, T:0.15


Consensus pattern (24 bp):   
GGCCCTACCACAACTCCTCCGACT

Found at i:500 original size:48 final size:48

Alignment explanation


    Indices: 448--578  Score: 145
    Period size: 48  Copynumber: 2.7  Consensus size: 48

        438 GGCTCCCACC

                                *      * *                  
        448 GGCCCTACCACGACTCCTCCGACTGGCCCTACCACAACTCCTCCGACT
          1 GGCCCTACCACGACTCCTCCAACTGGCACAACCACAACTCCTCCGACT

                      *               *                 *  *
        496 GGCCCTACCATGACTCCTCCAACTGGGACAACCACAACTCCTCCAACA
          1 GGCCCTACCACGACTCCTCCAACTGGCACAACCACAACTCCTCCGACT

              ** *     *           *  *        
        544 GGGACAACCACAACTCCTCCAACAGGGACAACCAC
          1 GGCCCTACCACGACTCCTCCAACTGGCACAACCAC

        579 GAGTCCAGGA


Statistics
Matches: 70,  Mismatches: 13, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  48   70  1.00

ACGTcount: A:0.27, C:0.45, G:0.15, T:0.13


Consensus pattern (48 bp):   
GGCCCTACCACGACTCCTCCAACTGGCACAACCACAACTCCTCCGACT

Found at i:564 original size:24 final size:24

Alignment explanation


    Indices: 508--578  Score: 133
    Period size: 24  Copynumber: 3.0  Consensus size: 24

        498 CCCTACCATG

                       *            
        508 ACTCCTCCAACTGGGACAACCACA
          1 ACTCCTCCAACAGGGACAACCACA

                                    
        532 ACTCCTCCAACAGGGACAACCACA
          1 ACTCCTCCAACAGGGACAACCACA

                                   
        556 ACTCCTCCAACAGGGACAACCAC
          1 ACTCCTCCAACAGGGACAACCAC

        579 GAGTCCAGGA


Statistics
Matches: 46,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  24   46  1.00

ACGTcount: A:0.35, C:0.42, G:0.13, T:0.10


Consensus pattern (24 bp):   
ACTCCTCCAACAGGGACAACCACA

Done.