Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_93 ID=scaffold_93-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: 14630
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32


Found at i:1628 original size:12 final size:12

Alignment explanation


    Indices: 1611--1647  Score: 56
    Period size: 12  Copynumber: 3.1  Consensus size: 12

       1601 GCCCTTTTAC

                   *    
       1611 AGAAAAATGAAA
          1 AGAAAAAAGAAA

                        
       1623 AGAAAAAAGAAA
          1 AGAAAAAAGAAA

                    *   
       1635 AGAAAAAATAAA
          1 AGAAAAAAGAAA

             
       1647 A
          1 A

       1648 TCCCTCCCCC


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  12   23  1.00

ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05


Consensus pattern (12 bp):   
AGAAAAAAGAAA

Found at i:2371 original size:87 final size:87

Alignment explanation


    Indices: 2224--2548  Score: 425
    Period size: 87  Copynumber: 3.7  Consensus size: 87

       2214 GTTGTATTTG

                      *       *  *  *    *     *  *      * *  *    *         
       2224 TGGCTTAAATATGTTTCCTTATTCTTGGGAAAGATAAGGTTCGCCATTTTGGATCTGCTCCACTA
          1 TGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCACTA

                              ** *
       2289 TTGCTTAGGGAGATAGAACCAG
         66 TTGCTTAGGGAGATAGAATTAA

                       *     *                  *                            
       2311 TGGCTTAAATCAGTTTCGCTACTCCTGGGGAAGATGGGATTCGCCGTCTTCGATCCGCTCCACTA
          1 TGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCACTA

                                  
       2376 TTGCTTAGGGAGATAGAATTAA
         66 TTGCTTAGGGAGATAGAATTAA

                      *                     *                                
       2398 TGGCTTAAATTTGTTTCCCTACTCCTGGGGAAAATGAGATTCGCCGTCTTCGATCCGCTCCACTA
          1 TGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCACTA

                            *     
       2463 TTGCTTAGGGAGATAGGATTAA
         66 TTGCTTAGGGAGATAGAATTAA

                                               *     * **          *        
       2485 TGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTTGTTGTCTTCGATCTGCTCCACT
          1 TGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCACT

       2549 GTTAACGCAG


Statistics
Matches: 208,  Mismatches: 30, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  87  208  1.00

ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33


Consensus pattern (87 bp):   
TGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCACTA
TTGCTTAGGGAGATAGAATTAA

Done.