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Seq191 Supplemental Information

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    seq191

     

    Nucleotide Freq. Table		
    Base	Number	Freq.
    T	112615	0.28
    A	109653	0.28
    C	88519	0.22
    G	86613	0.22
    A/T	222268	0.56
    G/C	175132	0.44
    
    Two Word Freq. Table			
    Pair	Bases	Freq.	Ratio
    TT	36295	0.091	1.46139773
    AA	34599	0.087	1.393109245
    AT	29355	0.074	1.181962539
    TG	26729	0.067	1.076228128
    CA	26422	0.066	1.063866946
    TC	25989	0.065	1.046432445
    CT	25943	0.065	1.044580281
    GA	25028	0.063	1.007738321
    AG	24917	0.063	1.003268969
    TA	23595	0.059	0.950039384
    CC	22193	0.056	0.893588643
    GT	21016	0.053	0.846197401
    GG	21003	0.053	0.845673964
    AC	20775	0.052	0.836493672
    GC	19560	0.049	0.787572382
    CG	13954	0.035	0.56184995
    

    Summary:
    
    ==================================================
    file name: RM2sequpload_1285092130  
    sequences:             1
    total length:     400000 bp  (397400 bp excl N/X-runs)
    GC level:         44.07 %
    bases masked:     321186 bp ( 80.30 %)
    ==================================================
                   number of      length   percentage
                   elements*    occupied  of sequence
    --------------------------------------------------
    Retroelements          136       312602 bp   78.15 %
       SINEs:                0            0 bp    0.00 %
       Penelope              0            0 bp    0.00 %
       LINEs:                6         5552 bp    1.39 %
        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           2          902 bp    0.23 %
         L1/CIN4             4         4650 bp    1.16 %
       LTR elements:       130       307050 bp   76.76 %
         BEL/Pao             0            0 bp    0.00 %
         Ty1/Copia          79       178773 bp   44.69 %
         Gypsy/DIRS1        48       127600 bp   31.90 %
           Retroviral        0            0 bp    0.00 %
    
    DNA transposons         26         7474 bp    1.87 %
       hobo-Activator       11         2197 bp    0.55 %
       Tc1-IS630-Pogo        1          186 bp    0.05 %
       En-Spm                4         1665 bp    0.42 %
       MuDR-IS905            3          810 bp    0.20 %
       PiggyBac              0            0 bp    0.00 %
       Tourist/Harbinger     0            0 bp    0.00 %
       Other (Mirage,        0            0 bp    0.00 %
        P-element, Transib)
    
    Rolling-circles          0            0 bp    0.00 %
    
    Unclassified:            0            0 bp    0.00 %
    
    Total interspersed repeats:      320076 bp   80.02 %
    
    
    Small RNA:               0            0 bp    0.00 %
    
    Satellites:              0            0 bp    0.00 %
    Simple repeats:          9          420 bp    0.10 %
    Low complexity:         17          690 bp    0.17 %
    ==================================================
    
    * most repeats fragmented by insertions or deletions
      have been counted as one element
                                                          
    
    The query species was assumed to be zea           
    RepeatMasker version open-3.2.9 , default mode
                                       
    run with blastp version 3.0SE-AB [2009-10-30] [linux26-x64-I32LPF64 2009-10-30T17:06:09]
    RepBase Update 20090604, RM database version 20090604
    
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    Files 13

    FileSizeDateAttached by 
    191a Protein BLAST.png
    No description
    340.21 kB16:40, 10 Dec 2010mpopelkaActions
    191b Protein BLAST.png
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    145.85 kB16:40, 10 Dec 2010mpopelkaActions
    191c Protein Blast.png
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    147.65 kB16:40, 10 Dec 2010mpopelkaActions
     cpgplot.1.png
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    8.78 kB13:16, 21 Sep 2010mpopelkaActions
     Double Word Count Table.txt
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    497 bytes14:05, 21 Sep 2010mpopelkaActions
    FGENESH Gene Models for 191Masked.pdf
    No description
    137.84 kB12:50, 8 Oct 2010mpopelkaActions
     GeneMark Gene Prediction.docx
    No description
    33.22 kB11:34, 10 Dec 2010mpopelkaActions
     Predicted protein summary.xlsx
    No description
    12.68 kB16:30, 10 Dec 2010mpopelkaActions
     Protein Sequence 191p.png
    No description
    532.08 kB13:12, 10 Dec 2010amoralesActions
     Repeat Summary.txt
    No description
    2.54 kB14:25, 21 Sep 2010amoralesActions
     seq191composition.png
    No description
    164 kB16:22, 30 Nov 2010amoralesActions
     Seq191Masked.txt
    Sequence 191 with repeats masked
    398.45 kB14:10, 21 Sep 2010amoralesActions
     Single Word Count Table.txt
    No description
    141 bytes14:03, 21 Sep 2010mpopelkaActions
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