Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_90 ID=scaffold_90-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: 15202
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.28

Warning! 373 characters in sequence are not A, C, G, or T


Found at i:12658 original size:44 final size:44

Alignment explanation


    Indices: 12546--12682  Score: 116
    Period size: 44  Copynumber: 3.1  Consensus size: 44

      12536 TAGATCGCAT

                      **  *                        *    
      12546 CAGATTAAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
          1 CAGATTAAAGAAAGTAATCTTATCTCCCTGAGATTACAGTGGAG

                  *   ***      *                        
      12590 CAGATTGAAGCTTGTAATCCTATCTCCCTGAGATTACAGTGGAG
          1 CAGATTAAAGAAAGTAATCTTATCTCCCTGAGATTACAGTGGAG

             *              *          *              *   
      12634 CGGATTAAAAGAAAG-GATCTTATCTCTCTGA-AGTTACAGTAGAG
          1 CAGATT-AAAGAAAGTAATCTTATCTCCCTGAGA-TTACAGTGGAG

            *    
      12678 TAGAT
          1 CAGAT

      12683 CGCATCAGAT


Statistics
Matches: 74,  Mismatches: 17, Indels: 4
        0.78            0.18        0.04

Matches are distributed among these distances:
  43    1  0.01
  44   69  0.93
  45    4  0.05

ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27


Consensus pattern (44 bp):   
CAGATTAAAGAAAGTAATCTTATCTCCCTGAGATTACAGTGGAG

Found at i:12709 original size:142 final size:142

Alignment explanation


    Indices: 12452--12759  Score: 501
    Period size: 142  Copynumber: 2.2  Consensus size: 142

      12442 TCGAATAGGT

                    *             *                       *   *              
      12452 TTGAAGCTGGTAATCCTATCTCACTGAGATTACAGTGGAGCAGATTTAAATAAAGGATCTTATCT
          1 TTGAAGCTTGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAGAAAGGATCTTATCT

                                                                             
      12517 CTCTAAAGTTACAGTAGAGTAGATCGCATCAGATTAAAGCCAGAAATCTTATCTCCCTGAGATTA
         66 CTCTAAAGTTACAGTAGAGTAGATCGCATCAGATTAAAGCCAGAAATCTTATCTCCCTGAGATTA

                        
      12582 CAGCGGAGCAGA
        131 CAGCGGAGCAGA

                                                     *                       
      12594 TTGAAGCTTGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAAGAAAGGATCTTATCT
          1 TTGAAGCTTGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAGAAAGGATCTTATCT

                *                              *         *                   
      12659 CTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAGTCTTATCTCCCTGAGATTA
         66 CTCTAAAGTTACAGTAGAGTAGATCGCATCAGATTAAAGCCAGAAATCTTATCTCCCTGAGATTA

             *          
      12724 CGGCGGAGCAGA
        131 CAGCGGAGCAGA

                      **             
      12736 TTGAAG-TTACAAATCCTATCTCCC
          1 TTGAAGCTT-GTAATCCTATCTCCC

      12760 CGATGTTGCG


Statistics
Matches: 154,  Mismatches: 11, Indels: 2
        0.92            0.07        0.01

Matches are distributed among these distances:
 141    2  0.01
 142  152  0.99

ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28


Consensus pattern (142 bp):   
TTGAAGCTTGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAGAAAGGATCTTATCT
CTCTAAAGTTACAGTAGAGTAGATCGCATCAGATTAAAGCCAGAAATCTTATCTCCCTGAGATTA
CAGCGGAGCAGA

Done.