##########################################
A. cardenasii characteristic markers:
########################################## 

egrep $'^\S+\tBB\tAA\tAA\tAA' Wild_control.txt >> Acar-markers-1.txt
egrep $'^\S+\tAA\tBB\tBB\tBB' Wild_control.txt >> Acar-markers-2.txt


head -7 Tetra_control.txt > Acar-markers.txt
"for i in `cut -f 1 Acar-markers-1.txt` ; do grep ""$i"" Tetra_control.txt | perl -lpe ""s/AB/ab/g"" | perl -lpe ""s/BB/bb/g"" | perl -lpe ""s/AA/aa/g"" >> Acar-markers.txt ; done"
"for i in `cut -f 1 Acar-markers-2.txt` ; do grep ""$i"" Tetra_control.txt | perl -lpe ""s/AB/ab/g"" | perl -lpe ""s/AA/bb/g"" | perl -lpe ""s/BB/aa/g"" >> Acar-markers.txt ; done"

head -7 Acar-markers.txt > Acar-markers-filter.txt
egrep $'^\S+\tbb\tbb\taa\taa' Acar-markers.txt >> Acar-markers-filter.txt

#############################################
A. batizocoi characteristic markers:
############################################# 

egrep $'^\S+\tBB\tAA\tBB\tBB' Wild_control.txt >> Abat-markers-1.txt
egrep $'^\S+\tAA\tBB\tAA\tAA' Wild_control.txt >> Abat-markers-2.txt

head -7 Tetra_control.txt > Abat-markers.txt
"for i in `cut -f 1 Abat-markers-1.txt` ; do grep ""$i"" Tetra_control.txt | perl -lpe ""s/AB/ab/g"" | perl -lpe ""s/BB/bb/g"" | perl -lpe ""s/AA/aa/g"" >> Abat-markers.txt ; done"
"for i in `cut -f 1 Abat-markers-2.txt` ; do grep ""$i"" Tetra_control.txt | perl -lpe ""s/AB/ab/g"" | perl -lpe ""s/AA/bb/g"" | perl -lpe ""s/BB/aa/g"" >> Abat-markers.txt ; done"

head -7 Abat-markers.txt > Abat-markers-filter.txt
egrep $'^\S+\tbb\tbb\taa\taa' Abat-markers.txt >> Abat-markers-filter.txt

#############################################
A. correntina characteristic markers:
############################################# 

egrep $'^\S+\tBB\tBB\tAA\tBB' Wild_control.txt >> Acor-markers-1.txt
egrep $'^\S+\tAA\tAA\tBB\tAA' Wild_control.txt >> Acor-markers-2.txt

head -7 Tetra_control.txt > Acor-markers.txt
"for i in `cut -f 1 Acor-markers-1.txt` ; do grep ""$i"" Tetra_control.txt | perl -lpe ""s/AB/ab/g"" | perl -lpe ""s/BB/bb/g"" | perl -lpe ""s/AA/aa/g"" >> Acor-markers.txt ; done"
"for i in `cut -f 1 Acor-markers-2.txt` ; do grep ""$i"" Tetra_control.txt | perl -lpe ""s/AB/ab/g"" | perl -lpe ""s/AA/bb/g"" | perl -lpe ""s/BB/aa/g"" >> Acor-markers.txt ; done"

head -7 Acor-markers.txt > Acor-markers-filter.txt
egrep $'^\S+\tbb\tbb\taa\taa' Acor-markers.txt >> Acor-markers-filter.txt


#############################################
Amphi-wild characteristic markers:
#############################################
 
egrep $'^\S+\tBB\tBB\tBB\tAA\tBB' Wild_control.txt >> Amphi-wild-markers-1.txt
egrep $'^\S+\tAA\tAA\tAA\tBB\tAA' Wild_control.txt >> Amphi-wild-markers-2.txt

head -7 Tetra_control.txt > Amphi-wild-markers.txt
"for i in `cut -f 1 Amphi-wild-markers-1.txt` ; do grep ""$i"" Tetra_control.txt | perl -lpe ""s/AB/ab/g"" | perl -lpe ""s/BB/bb/g"" | perl -lpe ""s/AA/aa/g"" >> Amphi-wild-markers.txt ; done"
"for i in `cut -f 1 Amphi-wild-markers-2.txt` ; do grep ""$i"" Tetra_control.txt | perl -lpe ""s/AB/ab/g"" | perl -lpe ""s/AA/bb/g"" | perl -lpe ""s/BB/aa/g"" >> Amphi-wild-markers.txt ; done"

head -7 Amphi-wild-markers.txt > Amphi-wild-markers-filter.txt
egrep $'^\S+\tbb\tbb\taa\taa' Amphi-wild-markers.txt >> Amphi-wild-markers-filter.txt

##########################################
Amphi-card characteristic markers:
########################################## 

egrep $'^\S+\tBB\tAA\tAA\tAA\tBB' Wild_control.txt >> Amphi-card-markers-1.txt
egrep $'^\S+\tAA\tBB\tBB\tBB\tAA' Wild_control.txt >> Amphi-card-markers-2.txt


head -7 Tetra_control.txt > Amphi-card-markers.txt
"for i in `cut -f 1 Amphi-card-markers-1.txt` ; do grep ""$i"" Tetra_control.txt | perl -lpe ""s/AB/ab/g"" | perl -lpe ""s/BB/bb/g"" | perl -lpe ""s/AA/aa/g"" >> Amphi-card-markers.txt ; done"
"for i in `cut -f 1 Amphi-card-markers-2.txt` ; do grep ""$i"" Tetra_control.txt | perl -lpe ""s/AB/ab/g"" | perl -lpe ""s/AA/bb/g"" | perl -lpe ""s/BB/aa/g"" >> Amphi-card-markers.txt ; done"

head -7 Amphi-card-markers.txt > Amphi-card-markers-filter.txt
egrep $'^\S+\tbb\tbb\taa\taa' Amphi-card-markers.txt >> Amphi-card-markers-filter.txt

##########################################
Amphi-bat characteristic markers:
########################################## 

egrep $'^\S+\tAA\tBB\tAA\tAA\tBB' Wild_control.txt >> Amphi-bat-1.txt
egrep $'^\S+\tBB\tAA\tBB\tBB\tAA' Wild_control.txt >> Amphi-bat-2.txt


head -7 Tetra_control.txt > Amphi-bat.txt
"for i in `cut -f 1 Amphi-bat-1.txt` ; do grep ""$i"" Tetra_control.txt | perl -lpe ""s/AB/ab/g"" | perl -lpe ""s/BB/bb/g"" | perl -lpe ""s/AA/aa/g"" >> Amphi-bat.txt ; done"
"for i in `cut -f 1 Amphi-bat-2.txt` ; do grep ""$i"" Tetra_control.txt | perl -lpe ""s/AB/ab/g"" | perl -lpe ""s/AA/bb/g"" | perl -lpe ""s/BB/aa/g"" >> Amphi-bat.txt ; done"

head -7 Amphi-bat.txt > Amphi-bat-markers-filter.txt
egrep $'^\S+\tbb\tbb\taa\taa' Amphi-bat.txt >> Amphi-bat-markers-filter.txt

##########################################
Amphi-cor characteristic markers:
########################################## 

egrep $'^\S+\tAA\tAA\tBB\tAA\tBB' Wild_control.txt >> Amphi-cor-1.txt
egrep $'^\S+\tBB\tBB\tAA\tBB\tAA' Wild_control.txt >> Amphi-cor-2.txt


head -7 Tetra_control.txt > Amphi-cor.txt
"for i in `cut -f 1 Amphi-cor-1.txt` ; do grep ""$i"" Tetra_control.txt | perl -lpe ""s/AB/ab/g"" | perl -lpe ""s/BB/bb/g"" | perl -lpe ""s/AA/aa/g"" >> Amphi-cor.txt ; done"
"for i in `cut -f 1 Amphi-cor-2.txt` ; do grep ""$i"" Tetra_control.txt | perl -lpe ""s/AB/ab/g"" | perl -lpe ""s/AA/bb/g"" | perl -lpe ""s/BB/aa/g"" >> Amphi-cor.txt ; done"

head -7 Amphi-cor.txt > Amphi-cor-markers-filter.txt
egrep $'^\S+\tbb\tbb\taa\taa' Amphi-cor.txt >> Amphi-cor-markers-filter.txt

##########################################
A. hypogaea characteristic markers:
########################################## 

egrep $'^\S+\tAA\tAA\tAA\tBB\tAA' Wild_control.txt >> Ahyp-1.txt
egrep $'^\S+\tBB\tBB\tBB\tAA\tBB' Wild_control.txt >> Ahyp-2.txt


head -7 Tetra_control.txt > Ahyp.txt
"for i in `cut -f 1 Ahyp-1.txt` ; do grep ""$i"" Tetra_control.txt | perl -lpe ""s/AB/ab/g"" | perl -lpe ""s/BB/bb/g"" | perl -lpe ""s/AA/aa/g"" >> Ahyp.txt ; done"
"for i in `cut -f 1 Ahyp-2.txt` ; do grep ""$i"" Tetra_control.txt | perl -lpe ""s/AB/ab/g"" | perl -lpe ""s/AA/bb/g"" | perl -lpe ""s/BB/aa/g"" >> Ahyp.txt ; done"

head -7 Ahyp.txt > Ahyp-markers.txt
egrep $'^\S+\taa\taa\tbb\tbb' Ahyp.txt >> Ahyp-markers.txt


#########################################
Find mapped markers in Tetra_control
#########################################

awk 'NR==FNR{arr[$1];next} $1 in arr' Map.txt Acor.txt > probeset_names_Acor_intro.txt