Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_235 ID=scaffold_235-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: 9106
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33


Found at i:6567 original size:25 final size:25

Alignment explanation


    Indices: 6529--6585  Score: 87
    Period size: 25  Copynumber: 2.3  Consensus size: 25

       6519 TCATTAGGGT

                    **               
       6529 TATCGATTTGTAGCTCGTGAGAGCA
          1 TATCGATTCATAGCTCGTGAGAGCA

                                     
       6554 TATCGATTCATAGCTCGTGAGAGCA
          1 TATCGATTCATAGCTCGTGAGAGCA

              *    
       6579 TACCGAT
          1 TATCGAT

       6586 CTTCAGCTCA


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  25   29  1.00

ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30


Consensus pattern (25 bp):   
TATCGATTCATAGCTCGTGAGAGCA

Found at i:6593 original size:25 final size:26

Alignment explanation


    Indices: 6540--6631  Score: 88
    Period size: 25  Copynumber: 3.7  Consensus size: 26

       6530 ATCGATTTGT

                             *      *  
       6540 AGCTCGTGA-GAGCATATCGATTCAT-
          1 AGCTCGTGATGAGCATACCGA-TCTTC

                                      
       6565 AGCTCGTGA-GAGCATACCGATCTTC
          1 AGCTCGTGATGAGCATACCGATCTTC

                  **                   
       6590 AGCTC-AAATGAGCATACCGAT-TTAC
          1 AGCTCGTGATGAGCATACCGATCTT-C

                              
       6615 AGCTCGT-ATGAGCATAC
          1 AGCTCGTGATGAGCATAC

       6632 ATGTACATGA


Statistics
Matches: 58,  Mismatches: 5, Indels: 8
        0.82            0.07        0.11

Matches are distributed among these distances:
  24    6  0.10
  25   52  0.90

ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25


Consensus pattern (26 bp):   
AGCTCGTGATGAGCATACCGATCTTC

Found at i:7864 original size:12 final size:12

Alignment explanation


    Indices: 7847--7876  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

       7837 TCAGGCTGTT

                        
       7847 ACACGGCCTAGC
          1 ACACGGCCTAGC

                     *  
       7859 ACACGGCCTGGC
          1 ACACGGCCTAGC

                  
       7871 ACACGG
          1 ACACGG

       7877 GCGTTTGGTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07


Consensus pattern (12 bp):   
ACACGGCCTAGC
Done.