blat -out=axt ../RepeatBrowserConsensus/L1PA4.fa nomLeu3_L1PA4_full.fa nomLeu3_L1PA4.axt 
java extract_aligned nomLeu3_L1PA4.axt 811 832
grep ">" matches811-832nomLeu3_L1PA4.fa | sed "s/:/\t/" | sed "s/-/\t/" | sed "s/>//" > nomLeu3_L1PA4_mapped.bed
bedtools intersect -b nomLeu3_L1PA4_mapped.bed -a nomLeu3_L1PA4_full.bed -v > nomLeu3_L1PA4_unmapped.bed
twoBitToFa -bed=nomLeu3_L1PA4_unmapped.bed -bedPos https://hgdownload.soe.ucsc.edu/gbdb/nomLeu3/nomLeu3.2bit nomLeu3_L1PA4_unmapped.fa
blat ../RepeatBrowserConsensus/L1PA4.fa nomLeu3_L1PA4_unmapped.fa nomLeu3_L1PA4_unmapped.psl
blat -out=axt ../RepeatBrowserConsensus/L1PA4.fa nomLeu3_L1PA4_unmapped.fa nomLeu3_L1PA4_unmapped.axt
psl2cov.sh nomLeu3_L1PA4_unmapped.ps

bedtools intersect -b nomLeu3_L1PA4_mapped.bed -a nomLeu3_L1PA4_full.bed  > temp.bed
mv temp.bed nomLeu3_L1PA4_mapped.bed
twoBitToFa -bed=nomLeu3_L1PA4_mapped.bed -bedPos https://hgdownload.soe.ucsc.edu/gbdb/nomLeu3/nomLeu3.2bit nomLeu3_L1PA4_mapped.fa
blat ../RepeatBrowserConsensus/L1PA4.fa nomLeu3_L1PA4_mapped.fa nomLeu3_L1PA4_mapped.psl
blat -out=axt ../RepeatBrowserConsensus/L1PA4.fa nomLeu3_L1PA4_mapped.fa nomLeu3_L1PA4_mapped.axt
psl2cov.sh nomLeu3_L1PA4_mapped.psl

java extract_aligned nomLeu3_L1PA4_mapped.axt 579 598
grep ">" matches579-598nomLeu3_L1PA4_mapped.fa | sed "s/:/\t/" | sed "s/-/\t/" | sed "s/>//" > nomLeu3_L1PA4_mapped_579_598.bed
#969/1118 map

java extract_aligned nomLeu3_L1PA4_unmapped.axt 579 598
grep ">" matches579-598nomLeu3_L1PA4_unmapped.fa | sed "s/:/\t/" | sed "s/-/\t/" | sed "s/>//" > nomLeu3_L1PA4_unmapped_579_598.bed
#441/1351 map

blat -out=axt ../RepeatBrowserConsensus/L1PA4.fa ponAbe3_L1PA3_full.fa ponAbe3_L1PA3.axt 
java extract_aligned ponAbe3_L1PA3.axt 232 242
grep ">" matches232-242ponAbe3_L1PA3.fa  | sed "s/:/\t/" | sed "s/-/\t/" | sed "s/>//" > ponAbe3_L1PA3_mapped_232_242.bed
bedtools intersect -b ponAbe3_L1PA3_mapped_232_242.bed -a ponAbe3_L1PA3_full.bed -v > ponAbe3_L1PA3_unmapped_232_242.bed

java extract_aligned ponAbe3_L1PA4.axt 773 908
grep ">" matches773-908ponAbe3_L1PA3.fa  | sed "s/:/\t/" | sed "s/-/\t/" | sed "s/>//" > ponAbe3_L1PA3_mapped_773_908.bed
bedtools intersect -b ponAbe3_L1PA3_mapped_773_908.bed -a ponAbe3_L1PA3_full.bed -v > ponAbe3_L1PA3_unmapped_773_908.bed
bedtools intersect -b ponAbe3_L1PA3_unmapped_773_908.bed -a ponAbe3_L1PA3_unmapped_232_242.bed -v


blat -out=axt ../RepeatBrowserConsensus/L1PA2.fa gorGor5_L1PA2_full.fa gorGor5_L1PA2.axt 
java extract_aligned gorGor5_L1PA2.axt 100 700
grep ">" matches100-700gorGor5_L1PA2.fa  | sed "s/:/\t/" | sed "s/-/\t/" | sed "s/>//" > gorGor5_L1PA2_mapped_100_700.bed 
bedtools intersect -b gorGor5_L1PA2_mapped_100_700.bed -a gorGor5_L1PA2_full.bed -v > gorGor5_L1PA2_unmapped_100_700.bed
twoBitToFa -bed=gorGor5_L1PA2_unmapped_100_700.bed -bedPos https://hgdownload.soe.ucsc.edu/gbdb/gorGor5/gorGor5.2bit gorGor5_L1PA2_unmapped_100_700.fa

bedtools
awk '$3-$2>5000' temp2.bed  > temp2_full.bed
twoBitToFa -bed=temp2_full.bed -bedPos https://hgdownload.soe.ucsc.edu/gbdb/gorGor5/gorGor5.2bit temp2_full.fa
blat ../RepeatBrowserConsensus/L1PA2.fa temp2_full.fa temp2_full.psl
psl2cov.sh temp2_full.psl