Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_686 ID=scaffold_686-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: 6308
ACGTcount: A:0.20, C:0.12, G:0.17, T:0.25

Warning! 1666 characters in sequence are not A, C, G, or T


Found at i:5124 original size:27 final size:27

Alignment explanation


    Indices: 5076--5368  Score: 367
    Period size: 27  Copynumber: 10.9  Consensus size: 27

       5066 AAATAATCGT

                 *       *   *         
       5076 AATACACTCGAAGAGTACAATGACCGA
          1 AATACCCTCGAAGGGTAAAATGACCGA

                     *  *           *  
       5103 AATACCCTCAAAAGGTAAAATGACTGA
          1 AATACCCTCGAAGGGTAAAATGACCGA

                   * *           *  *  
       5130 AATACCCCCAAAGGGTAAAATAACTGA
          1 AATACCCTCGAAGGGTAAAATGACCGA

                              *     *   
       5157 AATACCC-CTGAAGGGTAGAATGATCGA
          1 AATACCCTC-GAAGGGTAAAATGACCGA

                                    *  
       5184 AATACCCTCGAAGGGTAAAATGACTGA
          1 AATACCCTCGAAGGGTAAAATGACCGA

                   * *         *   *   
       5211 AATACCCCCAAAGGGTAAACTGATCGA
          1 AATACCCTCGAAGGGTAAAATGACCGA

                     *                 
       5238 AATACCCTCAAAGGGTAAAATGACCGA
          1 AATACCCTCGAAGGGTAAAATGACCGA

                                       
       5265 AATACCC-CGAAGGGTAAAATGACCGA
          1 AATACCCTCGAAGGGTAAAATGACCGA

              *    *                    
       5291 AAAACCCCCTGAAGGGTAAAATGACCGA
          1 AATACCCTC-GAAGGGTAAAATGACCGA

                                       
       5319 AATACCCTCGAAGGGTAAAATGACCGA
          1 AATACCCTCGAAGGGTAAAATGACCGA

                                    
       5346 AATACCCTCGAAGGGT-AAATGAC
          1 AATACCCTCGAAGGGTAAAATGAC

       5369 TGAANNNNNN


Statistics
Matches: 233,  Mismatches: 29, Indels: 9
        0.86            0.11        0.03

Matches are distributed among these distances:
  26   32  0.14
  27  175  0.75
  28   26  0.11

ACGTcount: A:0.43, C:0.22, G:0.20, T:0.15


Consensus pattern (27 bp):   
AATACCCTCGAAGGGTAAAATGACCGA

Found at i:5201 original size:81 final size:81

Alignment explanation


    Indices: 5076--5372  Score: 413
    Period size: 81  Copynumber: 3.7  Consensus size: 81

       5066 AAATAATCGT

                 *       *   *                  *  *                         
       5076 AATACACTCGAAGAGTACAATGACCGAAATACCCTCAAAAGGTAAAATGACTGAAATACCCCCAA
          1 AATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCCCAA

                      *     
       5141 AGGGTAAAATAACTGA
         66 AGGGTAAAATGACTGA

                              *     *                                        
       5157 AATACCC-CTGAAGGGTAGAATGATCGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCCCA
          1 AATACCCTC-GAAGGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCCCA

                     *        
       5221 AAGGGTAAACTGA-TCGA
         65 AAGGGTAAAATGACT-GA

                     *                                         *    *       *
       5238 AATACCCTCAAAGGGTAAAATGACCGAAATACCC-CGAAGGGTAAAATGACCGAAAAACCCCCTG
          1 AATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCCC-A

                          *  
       5302 AAGGGTAAAATGACCGA
         65 AAGGGTAAAATGACTGA

                                                                   
       5319 AATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGAAGGGT-AAATGACTGAA
          1 AATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACTGAA

       5373 NNNNNNNNNN


Statistics
Matches: 192,  Mismatches: 18, Indels: 12
        0.86            0.08        0.05

Matches are distributed among these distances:
  80   28  0.15
  81  155  0.81
  82    9  0.05

ACGTcount: A:0.43, C:0.22, G:0.20, T:0.15


Consensus pattern (81 bp):   
AATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCCCAA
AGGGTAAAATGACTGA

Found at i:5653 original size:26 final size:26

Alignment explanation


    Indices: 5624--5700  Score: 82
    Period size: 26  Copynumber: 3.0  Consensus size: 26

       5614 TTGCTACATA

                    *                 
       5624 TACTGTTATTGGCAACTTTGCTGCGT
          1 TACTGTTACTGGCAACTTTGCTGCGT

                          *     *     
       5650 TACTGTTACTGGCATCTTTGTTGCGT
          1 TACTGTTACTGGCAACTTTGCTGCGT

            * * *      *  *          
       5676 CATTATTACTGACAGCTTTGCTGCG
          1 TACTGTTACTGGCAACTTTGCTGCG

       5701 ATATTGGTGT


Statistics
Matches: 42,  Mismatches: 9, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  26   42  1.00

ACGTcount: A:0.16, C:0.21, G:0.22, T:0.42


Consensus pattern (26 bp):   
TACTGTTACTGGCAACTTTGCTGCGT

Found at i:5847 original size:30 final size:31

Alignment explanation


    Indices: 5806--5866  Score: 106
    Period size: 30  Copynumber: 2.0  Consensus size: 31

       5796 ACTGCATTGT

                         *                 
       5806 ACTGATTACTGTATTGGGCTAAGGCCCACAC
          1 ACTGATTACTGTAATGGGCTAAGGCCCACAC

                                           
       5837 ACTG-TTACTGTAATGGGCTAAGGCCCACAC
          1 ACTGATTACTGTAATGGGCTAAGGCCCACAC

       5867 TGTACTGATA


Statistics
Matches: 29,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  30   25  0.86
  31    4  0.14

ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25


Consensus pattern (31 bp):   
ACTGATTACTGTAATGGGCTAAGGCCCACAC
Done.