Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01003840.1 Hibiscus syriacus cultivar Beakdansim tig00008229_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: 172728
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33


File 2 of 2

Found at i:162057 original size:12 final size:11

Alignment explanation


    Indices: 162042--162115  Score: 55
    Period size: 12  Copynumber: 6.5  Consensus size: 11

     162032 CTTCTTTTTC

                 *      
     162042 TTTTTCTCTCTT
          1 TTTTTTTCTC-T

                        
     162054 TTTTTTTCTTCT
          1 TTTTTTTC-TCT

                   *   
     162066 TTTTTTTTTCT
          1 TTTTTTTCTCT

                         
     162077 TTTTCATTT-TCT
          1 TTTT--TTTCTCT

                    *   
     162089 ATTTTTTTTTCT
          1 -TTTTTTTCTCT

                       
     162101 TTTTTTT-T-T
          1 TTTTTTTCTCT

                  
     162110 TTTTTT
          1 TTTTTT

     162116 CTTCAAGCAT


Statistics
Matches: 55,  Mismatches: 2, Indels: 13
        0.79            0.03        0.19

Matches are distributed among these distances:
   9    7  0.13
  10    1  0.02
  11   17  0.31
  12   21  0.38
  13    9  0.16

ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85


Consensus pattern (11 bp):   
TTTTTTTCTCT

Found at i:162101 original size:35 final size:34

Alignment explanation


    Indices: 162036--162117  Score: 112
    Period size: 35  Copynumber: 2.4  Consensus size: 34

     162026 TTGACCCTTC

                             *                
     162036 TTTTTCTTTTTCTCTCTTTTTTTTTCTTCTTTTT
          1 TTTTTCTTTTTCTCTCTATTTTTTTCTTCTTTTT

                           *                    
     162070 TTTTTCTTTTTCATTTTCTATTTTTTT-TTCTTTTT
          1 TTTTTCTTTTTC--TCTCTATTTTTTTCTTCTTTTT

                 *       
     162105 TTTTTTTTTTTCT
          1 TTTTTCTTTTTCT

     162118 TCAAGCATAA


Statistics
Matches: 43,  Mismatches: 3, Indels: 5
        0.84            0.06        0.10

Matches are distributed among these distances:
  33    1  0.02
  34   12  0.28
  35   19  0.44
  36   11  0.26

ACGTcount: A:0.02, C:0.13, G:0.00, T:0.84


Consensus pattern (34 bp):   
TTTTTCTTTTTCTCTCTATTTTTTTCTTCTTTTT

Found at i:162107 original size:38 final size:39

Alignment explanation


    Indices: 162033--162115  Score: 118
    Period size: 38  Copynumber: 2.2  Consensus size: 39

     162023 ACCTTGACCC

                      *       *                     
     162033 TTCTTTTTCTTTTTCTCTCTTTTTTTTTCTTCTTTTTTTT
          1 TTCTTTTTC-ATTTCTCTATTTTTTTTTCTTCTTTTTTTT

                                                   
     162073 TTCTTTTTCATTT-TCTATTTTTTTTTCTT-TTTTTTTT
          1 TTCTTTTTCATTTCTCTATTTTTTTTTCTTCTTTTTTTT

                   
     162110 TT-TTTT
          1 TTCTTTT

     162116 CTTCAAGCAT


Statistics
Matches: 41,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
  36    4  0.10
  37   10  0.24
  38   15  0.37
  39    3  0.07
  40    9  0.22

ACGTcount: A:0.02, C:0.13, G:0.00, T:0.84


Consensus pattern (39 bp):   
TTCTTTTTCATTTCTCTATTTTTTTTTCTTCTTTTTTTT

Done.