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+