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Part 2 - RepeatMasker results

    Table of contents
    1. 1. Summary:

    Summary:

    We seem to have more than 80% of our sequence as repeats, which is higher than the 66% repeats observed in the overall maize genome. Indeed, as we tried to characterize our predicted genes, we seemed to run into a lot of proteins related to retrotransposons, such as gag and pol proteins.

    ==================================================
    file name: RM2sequpload_1350945846  
    sequences:             1
    total length:     150000 bp  (148800 bp excl N/X-runs)
    GC level:         48.27 %
    bases masked:     120854 bp ( 80.57 %)
    ==================================================
                   number of      length   percentage
                   elements*    occupied  of sequence
    --------------------------------------------------
    Retroelements           48       116503 bp   77.67 %
       SINEs:                0            0 bp    0.00 %
       Penelope              0            0 bp    0.00 %
       LINEs:                0            0 bp    0.00 %
        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             0            0 bp    0.00 %
       LTR elements:        48       116503 bp   77.67 %
         BEL/Pao             0            0 bp    0.00 %
         Ty1/Copia          29        63031 bp   42.02 %
         Gypsy/DIRS1        19        53472 bp   35.65 %
           Retroviral        0            0 bp    0.00 %
    
    DNA transposons          7         3498 bp    2.33 %
       hobo-Activator        1          216 bp    0.14 %
       Tc1-IS630-Pogo        0            0 bp    0.00 %
       En-Spm                0            0 bp    0.00 %
       MuDR-IS905            0            0 bp    0.00 %
       PiggyBac              0            0 bp    0.00 %
       Tourist/Harbinger     1          309 bp    0.21 %
       Other (Mirage,        0            0 bp    0.00 %
        P-element, Transib)
    
    Rolling-circles          0            0 bp    0.00 %
    
    Unclassified:            4          466 bp    0.31 %
    
    Total interspersed repeats:      120467 bp   80.31 %
    
    
    Small RNA:               0            0 bp    0.00 %
    
    Satellites:              0            0 bp    0.00 %
    Simple repeats:          3          219 bp    0.15 %
    Low complexity:          5          168 bp    0.11 %
    ==================================================
    
    * 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
    


    Attached files:

    Results summary (.txt)

    Masked sequence output (.txt)

    Aligned output(.txt)

    kpadmana 09 December 2012

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