Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01001941.1 Hibiscus syriacus cultivar Beakdansim tig00003934_pilon, whole genome shotgun sequence

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: 155000
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


File 2 of 2

Found at i:145455 original size:18 final size:18

Alignment explanation


    Indices: 145406--145468  Score: 63
    Period size: 18  Copynumber: 3.5  Consensus size: 18

     145396 ATCAAATCCT

                 *     *      
     145406 AAACCCAAACCCGAACCC
          1 AAACCTAAACCTGAACCC

            *     *  *       *
     145424 GAACCTGAATCTGAACCT
          1 AAACCTAAACCTGAACCC

               *              
     145442 AAATCTAAACCTGAACCC
          1 AAACCTAAACCTGAACCC

                     
     145460 AAACCTAAA
          1 AAACCTAAA

     145469 TACAAACTAT


Statistics
Matches: 33,  Mismatches: 12, Indels: 0
        0.73            0.27        0.00

Matches are distributed among these distances:
  18   33  1.00

ACGTcount: A:0.44, C:0.35, G:0.08, T:0.13


Consensus pattern (18 bp):   
AAACCTAAACCTGAACCC

Found at i:145463 original size:12 final size:12

Alignment explanation


    Indices: 145358--145468  Score: 78
    Period size: 12  Copynumber: 9.2  Consensus size: 12

     145348 CCTTAACCCG

                      * 
     145358 AACCCAAACCCA
          1 AACCCAAACCTA

                      * 
     145370 AACCCAAACCCA
          1 AACCCAAACCTA

                 *      
     145382 AACCCGAACCTA
          1 AACCCAAACCTA

              **         
     145394 AAATCAAATCCTA
          1 AACCCAAA-CCTA

                      **
     145407 AACCCAAACCCG
          1 AACCCAAACCTA

                 *     *
     145419 AACCCGAACCTG
          1 AACCCAAACCTA

              * **      
     145431 AATCTGAACCTA
          1 AACCCAAACCTA

              * *      *
     145443 AATCTAAACCTG
          1 AACCCAAACCTA

                        
     145455 AACCCAAACCTA
          1 AACCCAAACCTA

              
     145467 AA
          1 AA

     145469 TACAAACTAT


Statistics
Matches: 79,  Mismatches: 19, Indels: 2
        0.79            0.19        0.02

Matches are distributed among these distances:
  12   69  0.87
  13   10  0.13

ACGTcount: A:0.46, C:0.38, G:0.05, T:0.11


Consensus pattern (12 bp):   
AACCCAAACCTA

Found at i:148234 original size:23 final size:22

Alignment explanation


    Indices: 148204--148248  Score: 72
    Period size: 23  Copynumber: 2.0  Consensus size: 22

     148194 TGCTTTCTTA

                                  
     148204 ATGCATGATGCTTGCTGAATTG
          1 ATGCATGATGCTTGCTGAATTG

                           *       
     148226 ATGCAATGATGCTTGTTGAATTG
          1 ATGC-ATGATGCTTGCTGAATTG

     148249 GTTCTATATA


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  22    4  0.19
  23   17  0.81

ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38


Consensus pattern (22 bp):   
ATGCATGATGCTTGCTGAATTG

Found at i:148500 original size:13 final size:13

Alignment explanation


    Indices: 148481--148518  Score: 51
    Period size: 13  Copynumber: 2.8  Consensus size: 13

     148471 TAATTTAGTG

                         
     148481 ATTATAAATAA-A
          1 ATTATAAATAAGA

                           
     148493 ATTTATAATATAAGA
          1 A-TTATAA-ATAAGA

                       
     148508 ATTATAAATAA
          1 ATTATAAATAA

     148519 TATAAAGAAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 5
        0.82            0.00        0.18

Matches are distributed among these distances:
  12    1  0.04
  13   10  0.43
  14   10  0.43
  15    2  0.09

ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37


Consensus pattern (13 bp):   
ATTATAAATAAGA

Done.