


IES=internal_eliminated_sequence_PGM_IES51.fa

awk '$4=="internal_eliminated_sequence" { print ">"$1"\n"$16 }' /data/PARAMECIUM/GENOMIC/tetraurelia/micronucleus/IES/51/internal_eliminated_sequence_PGM_IES51.pt_51.gff3.tab | perl -p -e 's/(.{60})/$1\n/g' > $IES


makeblastdb -in $IES -dbtype nucl

blastn -evalue 1e-8 -query $IES -db $IES -dust yes -task blastn -max_target_seqs 1000 -num_threads 15 -perc_identity 90 -outfmt 6 | awk '$1!=$2 { print $0 }' > internal_eliminated_sequence_PGM_IES51.VS.itself.blastn


DB=/data/DATABASES/PARAMECIUM/tetraurelia/blast/ptetraurelia_mac_51
blastn -evalue 1e-8 -query $IES -db $DB -dust yes -task blastn -max_target_seqs 1000 -num_threads 15 -perc_identity 100 -outfmt 6 > internal_eliminated_sequence_PGM_IES51.VS.ptetraurelia_mac_51.blastn



R>

