Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01008070.1 Hibiscus syriacus cultivar Beakdansim tig00110568_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: 35652
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.32

Warning! 623 characters in sequence are not A, C, G, or T


Found at i:1901 original size:18 final size:18

Alignment explanation


    Indices: 1864--1902  Score: 53
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       1854 TGTAGGAGTC

                        *     
       1864 TTTTCTTTCTCTTTTGTT
          1 TTTTCTTTCTCTGTTGTT

                               
       1882 TTTTCTTTCT-TGTTGCTT
          1 TTTTCTTTCTCTGTTG-TT

               
       1900 TTT
          1 TTT

       1903 GTTGTAGCAC


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  17    4  0.21
  18   15  0.79

ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77


Consensus pattern (18 bp):   
TTTTCTTTCTCTGTTGTT

Found at i:23076 original size:15 final size:15

Alignment explanation


    Indices: 23056--23095  Score: 55
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      23046 CCTTTGATAA

                        *  
      23056 CATTTCTTTCCATTT
          1 CATTTCTTTCCAATT

                            
      23071 CATTTCTTAT-CAATT
          1 CATTTCTT-TCCAATT

                      
      23086 CATTTCTTTC
          1 CATTTCTTTC

      23096 ATAATTTCTT


Statistics
Matches: 22,  Mismatches: 1, Indels: 4
        0.81            0.04        0.15

Matches are distributed among these distances:
  14    1  0.05
  15   20  0.91
  16    1  0.05

ACGTcount: A:0.17, C:0.25, G:0.00, T:0.57


Consensus pattern (15 bp):   
CATTTCTTTCCAATT

Found at i:28490 original size:23 final size:24

Alignment explanation


    Indices: 28448--28500  Score: 81
    Period size: 23  Copynumber: 2.2  Consensus size: 24

      28438 TTTCTTTCTT

                                    
      28448 TTTCTTCTTTTCGAGTGCTTTCAA
          1 TTTCTTCTTTTCGAGTGCTTTCAA

                                 * *
      28472 TTTCTTCTTTT-GAGTGCTTTTAT
          1 TTTCTTCTTTTCGAGTGCTTTCAA

                  
      28495 TTTCTT
          1 TTTCTT

      28501 TTCTGATTTT


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  23   16  0.59
  24   11  0.41

ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62


Consensus pattern (24 bp):   
TTTCTTCTTTTCGAGTGCTTTCAA

Found at i:32699 original size:24 final size:24

Alignment explanation


    Indices: 32637--32696  Score: 86
    Period size: 23  Copynumber: 2.5  Consensus size: 24

      32627 ACTTTTCTTT

                 *                  
      32637 CTTTCTTTTTCTTCTTTTCGAGTG
          1 CTTTCATTTTCTTCTTTTCGAGTG

                  *                 
      32661 CTTTCAATTTCTTCTTTT-GAGTG
          1 CTTTCATTTTCTTCTTTTCGAGTG

                *        
      32684 CTTTTATTTTCTT
          1 CTTTCATTTTCTT

      32697 TCTAATTTTT


Statistics
Matches: 32,  Mismatches: 4, Indels: 1
        0.86            0.11        0.03

Matches are distributed among these distances:
  23   16  0.50
  24   16  0.50

ACGTcount: A:0.08, C:0.18, G:0.10, T:0.63


Consensus pattern (24 bp):   
CTTTCATTTTCTTCTTTTCGAGTG
Done.