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Results from RepeatMasker

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    We identified and masked the repetitive regions in our sequence using RepeatMasker. The program determined that 55.47% of our sequence was repetitive (83,201 bp / 150,000 bp). These repetitive regions included 50 retroelements (82.5% of repetitive sequence) and 28 DNA transposons (13.0% of repetitive sequence). A vast majority of the retroelements located were Ty1/Copia and Gypsy/DIRS1 LTR elements. The three types of DNA transposons found in our sequence are hobo-Activator, Tourist/Harbinger, and En-Spm.

    Summary of RepeatMasker Results for Sequence 6:

    sequences:             1
    total length:     150000 bp  (148200 bp excl N/X-runs)
    GC level:         46.20 %
    bases masked:      83201 bp ( 55.47 %)
    ==================================================
                   number of      length   percentage
                   elements*    occupied  of sequence
    --------------------------------------------------
    Retroelements           50        68653 bp   45.77 %
       SINEs:                2          224 bp    0.15 %
       Penelope              0            0 bp    0.00 %
       LINEs:                2          841 bp    0.56 %
        CRE/SLACS            0            0 bp    0.00 %
         L2/CR1/Rex          0            0 bp    0.00 %
         R1/LOA/Jockey       0            0 bp    0.00 %
         R2/R4/NeSL          0            0 bp    0.00 %
         RTE/Bov-B           0            0 bp    0.00 %
         L1/CIN4             2          841 bp    0.56 %
       LTR elements:        46        67588 bp   45.06 %
         BEL/Pao             0            0 bp    0.00 %
         Ty1/Copia          22        20824 bp   13.88 %
         Gypsy/DIRS1        24        46764 bp   31.18 %
           Retroviral        0            0 bp    0.00 %
    
    DNA transposons         28        10814 bp    7.21 %
       hobo-Activator        5         1339 bp    0.89 %
       Tc1-IS630-Pogo        0            0 bp    0.00 %
       En-Spm                1          187 bp    0.12 %
       MuDR-IS905            0            0 bp    0.00 %
       PiggyBac              0            0 bp    0.00 %
       Tourist/Harbinger     2          328 bp    0.22 %
       Other (Mirage,        0            0 bp    0.00 %
        P-element, Transib)
    
    Rolling-circles          0            0 bp    0.00 %
    
    Unclassified:            9         2977 bp    1.98 %
    
    Total interspersed repeats:       82444 bp   54.96 %
    
    
    Small RNA:               2          224 bp    0.15 %
    
    Satellites:              0            0 bp    0.00 %
    Simple repeats:         10          459 bp    0.31 %
    Low complexity:          4          298 bp    0.20 %
    ==================================================
    
    * most repeats fragmented by insertions or deletions
      have been counted as one element
                                                          
    
    The query species was assumed to be zea           
    RepeatMasker version open-3.3.0 , default mode
                                       
    run with blastp version 3.0SE-AB [2009-10-30] [linux26-x64-I32LPF64 2009-10-30T17:06:09]
    RepBase Update 20110920, RM database version 20110920

     

    To see a side-by-side comparison of sequence 6 without repetitive regions masked and sequence 6 with repetitive regions masked click here.

    To see more details on the repeats identified by RepeatMasker click here.

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