Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_760 ID=scaffold_760-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: 4246
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.33

Warning! 265 characters in sequence are not A, C, G, or T


Found at i:55 original size:39 final size:39

Alignment explanation


    Indices: 1--117  Score: 162
    Period size: 39  Copynumber: 3.0  Consensus size: 39

                 *                         *       
          1 AGTGGCTAATGCTCGTTTGAGCAAGCATTCAATATAATC
          1 AGTGGATAATGCTCGTTTGAGCAAGCATTCAGTATAATC

                                          *       *
         40 AGTGGATAATGCTCGTTTGAGCAAGCATTCGGTATAATT
          1 AGTGGATAATGCTCGTTTGAGCAAGCATTCAGTATAATC

             *  *                    *             
         79 AATGCATAATGCTCGTTTGAGCAAATCATTCAGTATAAT
          1 AGTGGATAATGCTCGTTTGAGC-AAGCATTCAGTATAAT

        118 TGATATTCCA


Statistics
Matches: 69,  Mismatches: 8, Indels: 1
        0.88            0.10        0.01

Matches are distributed among these distances:
  39   55  0.80
  40   14  0.20

ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32


Consensus pattern (39 bp):   
AGTGGATAATGCTCGTTTGAGCAAGCATTCAGTATAATC

Found at i:3435 original size:39 final size:39

Alignment explanation


    Indices: 3373--3580  Score: 281
    Period size: 39  Copynumber: 5.3  Consensus size: 39

       3363 ATAAAATCTT

                       *   * *                     
       3373 ATTCAGTATAACTAGAGGATAATGCTCGTTTGAGCAAGC
          1 ATTCAGTATAATTAGTGCATAATGCTCGTTTGAGCAAGC

                    *   *     *                    
       3412 ATTCAGTACAATCAGTGCTTAATGCTCGTTTGAGCAAGC
          1 ATTCAGTATAATTAGTGCATAATGCTCGTTTGAGCAAGC

                *            *      *              
       3451 ATTCGGTATAATTAGTGGATAATGTTCGTTTGAGCAAGC
          1 ATTCAGTATAATTAGTGCATAATGCTCGTTTGAGCAAGC

                 *           *                     
       3490 ATTCAATATAATTAGTGGATAATGCTCGTTTGAGCAAGC
          1 ATTCAGTATAATTAGTGCATAATGCTCGTTTGAGCAAGC

                          *            *          * 
       3529 ATTCAGTATAATTAATGCATAATGCTCATTTGAGCAAATC
          1 ATTCAGTATAATTAGTGCATAATGCTCGTTTGAGC-AAGC

                        
       3569 ATTCAGTATAAT
          1 ATTCAGTATAAT

       3581 CGATATTCCA


Statistics
Matches: 148,  Mismatches: 20, Indels: 1
        0.88            0.12        0.01

Matches are distributed among these distances:
  39  133  0.90
  40   15  0.10

ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33


Consensus pattern (39 bp):   
ATTCAGTATAATTAGTGCATAATGCTCGTTTGAGCAAGC

Done.