Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01000930.1 Hibiscus syriacus cultivar Beakdansim tig00001855_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: 196410
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


File 2 of 2

Found at i:189217 original size:29 final size:29

Alignment explanation


    Indices: 189175--189258  Score: 123
    Period size: 29  Copynumber: 2.9  Consensus size: 29

     189165 CTCCGAAGAG

                   **           *        
     189175 GATCCCAAACAGAAACATGATGAGAATAT
          1 GATCCCATGCAGAAACATGACGAGAATAT

                                    *    
     189204 GATCCCATGCAGAAACATGACGAGGATAT
          1 GATCCCATGCAGAAACATGACGAGAATAT

                                      
     189233 GATCCCATGCAGAAACATGACAGAGA
          1 GATCCCATGCAGAAACATGAC-GAGA

     189259 TATTGCCATC


Statistics
Matches: 49,  Mismatches: 5, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  29   46  0.94
  30    3  0.06

ACGTcount: A:0.43, C:0.20, G:0.21, T:0.15


Consensus pattern (29 bp):   
GATCCCATGCAGAAACATGACGAGAATAT

Found at i:190103 original size:20 final size:20

Alignment explanation


    Indices: 190078--190152  Score: 123
    Period size: 20  Copynumber: 3.8  Consensus size: 20

     190068 CAATGCTGGT

                        * *     
     190078 AGTATCGATACTACTTAGTG
          1 AGTATCGATACTTCCTAGTG

                                
     190098 AGTATCGATACTTCCTAGTG
          1 AGTATCGATACTTCCTAGTG

                                
     190118 AGTATCGATACTTCCTAGTG
          1 AGTATCGATACTTCCTAGTG

                  *        
     190138 AGTATCAATACTTCC
          1 AGTATCGATACTTCC

     190153 CTTACCTTGG


Statistics
Matches: 52,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   52  1.00

ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35


Consensus pattern (20 bp):   
AGTATCGATACTTCCTAGTG

Found at i:194548 original size:15 final size:15

Alignment explanation


    Indices: 194509--194541  Score: 66
    Period size: 15  Copynumber: 2.2  Consensus size: 15

     194499 AAAAAATTCC

                           
     194509 TTTTGATTTTATTAT
          1 TTTTGATTTTATTAT

                           
     194524 TTTTGATTTTATTAT
          1 TTTTGATTTTATTAT

               
     194539 TTT
          1 TTT

     194542 ATGTTTTTCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76


Consensus pattern (15 bp):   
TTTTGATTTTATTAT

Done.