Genome used: NCBI GCA_002022765.4_C_virginica-3.0

I ran RepeatMasker (v4.07) with RepBase-20170127 and RMBlast 2.6.0 with species set to Crassotrea virginica.

All commands were documented in a Jupyter Notebook (GitHub):


RESULTS:

Output folder:

Output table (GFF):

Summary table (text):

==================================================
file name: GCF_002022765.2_C_virginica-3.0_genomic.fasta
sequences:            11
total length:  684741128 bp  (684675328 bp excl N/X-runs)
GC level:         34.83 %
bases masked:   46637065 bp ( 6.81 %)
==================================================
               number of      length   percentage
               elements*    occupied  of sequence
--------------------------------------------------
Retroelements        43139      8952068 bp    1.31 %
   SINEs:            43139      8952068 bp    1.31 %
   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:         0            0 bp    0.00 %
     BEL/Pao             0            0 bp    0.00 %
     Ty1/Copia           0            0 bp    0.00 %
     Gypsy/DIRS1         0            0 bp    0.00 %
       Retroviral        0            0 bp    0.00 %

DNA transposons       3538      1564942 bp    0.23 %
   hobo-Activator        0            0 bp    0.00 %
   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     0            0 bp    0.00 %
   Other (Mirage,        0            0 bp    0.00 %
    P-element, Transib)

Rolling-circles          0            0 bp    0.00 %

Unclassified:        65151     23982146 bp    3.50 %

Total interspersed repeats:    34499156 bp    5.04 %


Small RNA:           43353      8992879 bp    1.31 %

Satellites:              1          222 bp    0.00 %
Simple repeats:     232627     10544162 bp    1.54 %
Low complexity:      29762      1561018 bp    0.23 %
==================================================

* most repeats fragmented by insertions or deletions
  have been counted as one element
  Runs of >=20 X/Ns in query were excluded in % calcs


The query species was assumed to be crassostrea virginica
RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127
        
run with rmblastn version 2.6.0+

from Sam’s Notebook https://ift.tt/2L8mKKn

Transposable Element Mapping – Crassostrea virginica NCBI Genome Assembly using RepeatMasker 4.07
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