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):
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GCF_002022765.2_C_virginica-3.0_genomic.fasta.tbl
================================================== 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+