Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01001991.1 Hibiscus syriacus cultivar Beakdansim tig00004072_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: 2373627
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


File 13 of 13

Found at i:2360115 original size:17 final size:17

Alignment explanation


    Indices: 2360070--2360126  Score: 57
    Period size: 17  Copynumber: 3.5  Consensus size: 17

    2360060 ATATAATAGT

                             
    2360070 AATAAATAAATAA--AA
          1 AATAAATAAATAACTAA

             *        *      
    2360085 ATTAAA-AAAAAACTAA
          1 AATAAATAAATAACTAA

                            *
    2360101 AATAAATAAATAACTAT
          1 AATAAATAAATAACTAA

                     
    2360118 AATCAAATA
          1 AAT-AAATA

    2360127 TGTACGTATA


Statistics
Matches: 33,  Mismatches: 5, Indels: 5
        0.77            0.12        0.12

Matches are distributed among these distances:
  14    5  0.15
  15    5  0.15
  16    7  0.21
  17   11  0.33
  18    5  0.15

ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23


Consensus pattern (17 bp):   
AATAAATAAATAACTAA

Found at i:2360507 original size:2 final size:2

Alignment explanation


    Indices: 2360494--2360567  Score: 57
    Period size: 2  Copynumber: 39.0  Consensus size: 2

    2360484 TAACGATGAT

                   *                       *                *        *    
    2360494 TA TA TG TA TA TA TA TA TA TA TG TA TA -A TA -A AA TA -A AA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

            *  *        *                                        
    2360533 AA AA TA TA CA TA -A TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

    2360568 AATAAAGGAA


Statistics
Matches: 58,  Mismatches: 10, Indels: 8
        0.76            0.13        0.11

Matches are distributed among these distances:
   1    4  0.07
   2   54  0.93

ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41


Consensus pattern (2 bp):   
TA

Found at i:2362478 original size:105 final size:105

Alignment explanation


    Indices: 2362355--2362814  Score: 893
    Period size: 105  Copynumber: 4.4  Consensus size: 105

    2362345 GTATTGTTCA

                                                                             
    2362355 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
          1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC

                                                    
    2362420 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
         66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG

                                                                             
    2362460 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
          1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC

                         *                          
    2362525 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
         66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG

                                                                *            
    2362565 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATATTTGTTGACAAC
          1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC

                                                    
    2362630 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
         66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG

                                                                             
    2362670 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
          1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC

                                                    
    2362735 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
         66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG

            *                                       
    2362775 TAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
          1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG

    2362815 GGTGAAACCT


Statistics
Matches: 350,  Mismatches: 5, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 105  350  1.00

ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35


Consensus pattern (105 bp):   
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG

Found at i:2363018 original size:15 final size:15

Alignment explanation


    Indices: 2362998--2363032  Score: 52
    Period size: 15  Copynumber: 2.3  Consensus size: 15

    2362988 TCTTCAAATG

                           
    2362998 TTTGATGATTTTTTT
          1 TTTGATGATTTTTTT

                  **       
    2363013 TTTGATTTTTTTTTT
          1 TTTGATGATTTTTTT

                 
    2363028 TTTGA
          1 TTTGA

    2363033 AGATGCTCCT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.11, C:0.00, G:0.11, T:0.77


Consensus pattern (15 bp):   
TTTGATGATTTTTTT

Found at i:2363020 original size:12 final size:12

Alignment explanation


    Indices: 2363003--2363027  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

    2362993 AAATGTTTGA

                        
    2363003 TGATTTTTTTTT
          1 TGATTTTTTTTT

                        
    2363015 TGATTTTTTTTT
          1 TGATTTTTTTTT

             
    2363027 T
          1 T

    2363028 TTTGAAGATG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84


Consensus pattern (12 bp):   
TGATTTTTTTTT

Done.