Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01000419.1 Hibiscus syriacus cultivar Beakdansim tig00000766_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: 196632
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


File 2 of 2

Found at i:179850 original size:70 final size:70

Alignment explanation


    Indices: 179721--179851  Score: 183
    Period size: 70  Copynumber: 1.9  Consensus size: 70

     179711 CTTATACAAC

                                                 *              * *          
     179721 TAAAGTATTGATGTGACACTAATATATGTACATACTTGATTATATGACACATGCCATGTGTTTAA
          1 TAAAGTATTGATGTGACACTAATATATGTACATACTTAATTATATGACACATACAATGTGTTTAA

                 
     179786 AGTGT
         66 AGTGT

                            * * *                                 *       
     179791 TAAAGTATTGATGTGATATTGATATATGTACATAAC-TAATTATATGACACATATAATGTGT
          1 TAAAGTATTGATGTGACACTAATATATGTACAT-ACTTAATTATATGACACATACAATGTGT

     179852 CTAGAGTGAT


Statistics
Matches: 53,  Mismatches: 7, Indels: 2
        0.85            0.11        0.03

Matches are distributed among these distances:
  70   51  0.96
  71    2  0.04

ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38


Consensus pattern (70 bp):   
TAAAGTATTGATGTGACACTAATATATGTACATACTTAATTATATGACACATACAATGTGTTTAA
AGTGT

Found at i:179891 original size:25 final size:25

Alignment explanation


    Indices: 179863--179918  Score: 67
    Period size: 25  Copynumber: 2.2  Consensus size: 25

     179853 TAGAGTGATG

                *      *   *         
     179863 ATATGTCATAAGATAGTAATAAAAT
          1 ATATATCATAAAATAATAATAAAAT

                  **                 
     179888 ATATATTTTAAAATAATAATAAAAT
          1 ATATATCATAAAATAATAATAAAAT

                  
     179913 ATATAT
          1 ATATAT

     179919 TTTAAAGTTA


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  25   26  1.00

ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38


Consensus pattern (25 bp):   
ATATATCATAAAATAATAATAAAAT

Found at i:179893 original size:27 final size:25

Alignment explanation


    Indices: 179870--179924  Score: 74
    Period size: 25  Copynumber: 2.2  Consensus size: 25

     179860 ATGATATGTC

                *   *                
     179870 ATAAGATAGTAATAAAATATATATT
          1 ATAAAATAATAATAAAATATATATT

            *                        
     179895 TTAAAATAATAATAAAATATATATT
          1 ATAAAATAATAATAAAATATATATT

            *    
     179920 TTAAA
          1 ATAAA

     179925 GTTAAGATAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  25   27  1.00

ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38


Consensus pattern (25 bp):   
ATAAAATAATAATAAAATATATATT

Found at i:179901 original size:14 final size:14

Alignment explanation


    Indices: 179882--179924  Score: 56
    Period size: 14  Copynumber: 3.3  Consensus size: 14

     179872 AAGATAGTAA

                          
     179882 TAAAATATATATTT
          1 TAAAATATATATTT

                         *
     179896 TAAAATA-ATA--A
          1 TAAAATATATATTT

                          
     179907 TAAAATATATATTT
          1 TAAAATATATATTT

                
     179921 TAAA
          1 TAAA

     179925 GTTAAGATAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 6
        0.75            0.06        0.19

Matches are distributed among these distances:
  11    7  0.29
  12    3  0.12
  13    3  0.12
  14   11  0.46

ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42


Consensus pattern (14 bp):   
TAAAATATATATTT

Found at i:179985 original size:30 final size:31

Alignment explanation


    Indices: 179895--180046  Score: 143
    Period size: 31  Copynumber: 4.9  Consensus size: 31

     179885 AATATATATT

                     *                 *   
     179895 TTAAAATAATAATAAAATATATATTTTAAAG
          1 TTAAAATAAGAATAAAATATATATTTTTAAG

                *                           
     179926 TTAAGATAAGAAT-AAATAATATATTTTTAAG
          1 TTAAAATAAGAATAAAAT-ATATATTTTTAAG

                           *   *           
     179957 TTAAAATAAGAATAATATACAT-TTTTTAAG
          1 TTAAAATAAGAATAAAATATATATTTTTAAG

                *   *                **    
     179987 TTAATATACGAATAAAATATAT-TTAGTAAG
          1 TTAAAATAAGAATAAAATATATATTTTTAAG

                                            
     180017 TTACGTAAA-AA-AATAAAATATATACTTTTT
          1 TTA---AAATAAGAATAAAATATATA-TTTTT

     180047 GAATAGTCTA


Statistics
Matches: 98,  Mismatches: 16, Indels: 12
        0.78            0.13        0.10

Matches are distributed among these distances:
  30   39  0.40
  31   50  0.51
  32    4  0.04
  33    5  0.05

ACGTcount: A:0.52, C:0.03, G:0.07, T:0.39


Consensus pattern (31 bp):   
TTAAAATAAGAATAAAATATATATTTTTAAG

Done.