Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_176 ID=scaffold_176-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: 9954
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31


Found at i:2616 original size:42 final size:43

Alignment explanation


    Indices: 2505--2666  Score: 143
    Period size: 43  Copynumber: 3.8  Consensus size: 43

       2495 AAAAGCTCAT

                      *    * * *           *           
       2505 ACAATGCCAACGTCCCAAATATGGTCTTACATGTAATCAAATA
          1 ACAATGCCAATGTCCTAGACATGGTCTTACACGTAATCAAATA

                     *         * *                 *   
       2548 ACAATGCCACTGTCCTAGATAGGGTCTTACACGTAATCATAT-
          1 ACAATGCCAATGTCCTAGACATGGTCTTACACGTAATCAAATA

              *             *                             
       2590 ACGATGCCAATGTCCTTGACATGGTCTTACACGTAAATCTCAAAT-
          1 ACAATGCCAATGTCCTAGACATGGTCTTACACGT-AA--TCAAATA

                      *          *            
       2635 -CAATGCCAACGTACC-AGACGTGGTCTTACACG
          1 ACAATGCCAATGT-CCTAGACATGGTCTTACACG

       2667 ATATCTCATA


Statistics
Matches: 98,  Mismatches: 17, Indels: 7
        0.80            0.14        0.06

Matches are distributed among these distances:
  42   29  0.30
  43   37  0.38
  44   25  0.26
  45    7  0.07

ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26


Consensus pattern (43 bp):   
ACAATGCCAATGTCCTAGACATGGTCTTACACGTAATCAAATA

Found at i:3761 original size:13 final size:13

Alignment explanation


    Indices: 3743--3767  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       3733 ACAAACGATA

                         
       3743 AAATTTTCACACG
          1 AAATTTTCACACG

                        
       3756 AAATTTTCACAC
          1 AAATTTTCACAC

       3768 ACTTTAATTC


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32


Consensus pattern (13 bp):   
AAATTTTCACACG
Done.