Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gorai.010G043200.1-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, 1000

Length: 2147
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.34


Found at i:686 original size:15 final size:15

Alignment explanation


    Indices: 666--714  Score: 59
    Period size: 15  Copynumber: 3.5  Consensus size: 15

        656 ATGAAAAGTG

                    *     *
        666 CTTCTTCCTCTTCCT
          1 CTTCTTCCCCTTCCC

                           
        681 CTTCTTCCCCTTCCC
          1 CTTCTTCCCCTTCCC

                           
        696 CTTC-T--CCTTCCC
          1 CTTCTTCCCCTTCCC

                   
        708 CTTCTTC
          1 CTTCTTC

        715 TTATTCTCCC


Statistics
Matches: 30,  Mismatches: 2, Indels: 5
        0.81            0.05        0.14

Matches are distributed among these distances:
  12   11  0.37
  13    1  0.03
  14    1  0.03
  15   17  0.57

ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47


Consensus pattern (15 bp):   
CTTCTTCCCCTTCCC

Found at i:728 original size:6 final size:6

Alignment explanation


    Indices: 684--756  Score: 65
    Period size: 6  Copynumber: 11.7  Consensus size: 6

        674 TCTTCCTCTT

                *      *             *            *       *           
        684 CTTCCC CTTCCC CTTCTC CTTCCC CTTCTTC TTATTCTC CCTCTC CTTCTC
          1 CTTCTC CTTCTC CTTCTC CTTCTC CTTC-TC --CTTCTC CTTCTC CTTCTC

                               *     
        735 CTTCTC CTTCTC CTTCTA CTTC
          1 CTTCTC CTTCTC CTTCTC CTTC

        757 ATACCTCTCT


Statistics
Matches: 56,  Mismatches: 8, Indels: 6
        0.80            0.11        0.09

Matches are distributed among these distances:
   6   50  0.89
   7    1  0.02
   8    2  0.04
   9    3  0.05

ACGTcount: A:0.03, C:0.51, G:0.00, T:0.47


Consensus pattern (6 bp):   
CTTCTC

Found at i:739 original size:18 final size:18

Alignment explanation


    Indices: 695--775  Score: 71
    Period size: 18  Copynumber: 4.7  Consensus size: 18

        685 TTCCCCTTCC

                              
        695 CCTTCTCCTTC-CCCT-T
          1 CCTTCTCCTTCTCCCTCT

                  **          
        711 -CTTCTTATTCTCCCTCT
          1 CCTTCTCCTTCTCCCTCT

                          *   
        728 CCTTCTCCTTCTCCTTCT
          1 CCTTCTCCTTCTCCCTCT

                  *      *     
        746 CCTTCTACTTCATACCTCT
          1 CCTTCTCCTTC-TCCCTCT

             *          
        765 CTTTCT-CTTCT
          1 CCTTCTCCTTCT

        776 TCCCAAACAC


Statistics
Matches: 52,  Mismatches: 9, Indels: 7
        0.76            0.13        0.10

Matches are distributed among these distances:
  15    8  0.15
  16    4  0.08
  17    2  0.04
  18   28  0.54
  19   10  0.19

ACGTcount: A:0.05, C:0.46, G:0.00, T:0.49


Consensus pattern (18 bp):   
CCTTCTCCTTCTCCCTCT

Done.