kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 3 -r 7188 7487 >  hs3.l3.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 4 -r 7188 7487 >  hs3.l4.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 5 -r 7188 7487 >  hs3.l5.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 6 -r 7188 7487 >  hs3.l6.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 7 -r 7188 7487 >  hs3.l7.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 8 -r 7188 7487 >  hs3.l8.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 9 -r 7188 7487 >  hs3.l9.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 10 -r 7188 7487 >  hs3.l10.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 11 -r 7188 7487 >  hs3.l11.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 12 -r 7188 7487 >  hs3.l12.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 13 -r 7188 7487 >  hs3.l13.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 14 -r 7188 7487 >  hs3.l14.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 15 -r 7188 7487 >  hs3.l15.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 16 -r 7188 7487 >  hs3.l16.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 17 -r 7188 7487 >  hs3.l17.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 18 -r 7188 7487 >  hs3.l18.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 19 -r 7188 7487 >  hs3.l19.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 20 -r 7188 7487 >  hs3.l20.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 21 -r 7188 7487 >  hs3.l21.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 22 -r 7188 7487 >  hs3.l22.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 23 -r 7188 7487 >  hs3.l23.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 24 -r 7188 7487 >  hs3.l24.list
kkno alignment -I /usr/local/globin/data/align.beta -a 3 -g -l 25 -r 7188 7487 > hs3.l25.list

cluster hs3.l3.list > hs3.l3.c
error hs3_reference hs3.l3.c
cluster hs3.l4.list > hs3.l4.c
error hs3_reference hs3.l4.c
cluster hs3.l5.list > hs3.l5.c
error hs3_reference hs3.l5.c
cluster hs3.l6.list > hs3.l6.c
error hs3_reference hs3.l6.c
cluster hs3.l7.list > hs3.l7.c
error hs3_reference hs3.l7.c
cluster hs3.l8.list > hs3.l8.c
error hs3_reference hs3.l8.c
cluster hs3.l9.list > hs3.l9.c
error hs3_reference hs3.l9.c
cluster hs3.l10.list > hs3.l10.c
error hs3_reference hs3.l10.c
cluster hs3.l11.list > hs3.l11.c
error hs3_reference hs3.l11.c
cluster hs3.l12.list > hs3.l12.c
error hs3_reference hs3.l12.c
cluster hs3.l13.list > hs3.l13.c
error hs3_reference hs3.l13.c
cluster hs3.l14.list > hs3.l14.c
error hs3_reference hs3.l14.c
cluster hs3.l15.list > hs3.l15.c
error hs3_reference hs3.l15.c
cluster hs3.l16.list > hs3.l16.c
error hs3_reference hs3.l16.c

rm  -f  hs3.l*.c  hs3.l*.list