kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 3 -r 11240 11510 >  hs2.l3.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 4 -r 11240 11510 >  hs2.l4.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 5 -r 11240 11510 >  hs2.l5.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 6 -r 11240 11510 >  hs2.l6.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 7 -r 11240 11510 >  hs2.l7.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 8 -r 11240 11510 >  hs2.l8.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 9 -r 11240 11510 >  hs2.l9.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 10 -r 11240 11510 >  hs2.l10.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 11 -r 11240 11510 >  hs2.l11.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 12 -r 11240 11510 >  hs2.l12.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 13 -r 11240 11510 >  hs2.l13.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 14 -r 11240 11510 >  hs2.l14.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 15 -r 11240 11510 >  hs2.l15.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 16 -r 11240 11510 >  hs2.l16.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 17 -r 11240 11510 >  hs2.l17.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 18 -r 11240 11510 >  hs2.l18.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 19 -r 11240 11510 >  hs2.l19.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 20 -r 11240 11510 >  hs2.l20.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 21 -r 11240 11510 >  hs2.l21.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 22 -r 11240 11510 >  hs2.l22.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 23 -r 11240 11510 >  hs2.l23.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 24 -r 11240 11510 >  hs2.l24.list
kunk alignment -I /usr/local/globin/data/align.beta -a 3 -x -l 25 -r 11240 11510 >  hs2.l25.list

cluster hs2.l3.list > hs2.l3.c
error hs2_reference hs2.l3.c
cluster hs2.l4.list > hs2.l4.c
error hs2_reference hs2.l4.c
cluster hs2.l5.list > hs2.l5.c
error hs2_reference hs2.l5.c
cluster hs2.l6.list > hs2.l6.c
error hs2_reference hs2.l6.c
cluster hs2.l7.list > hs2.l7.c
error hs2_reference hs2.l7.c
cluster hs2.l8.list > hs2.l8.c
error hs2_reference hs2.l8.c
cluster hs2.l9.list > hs2.l9.c
error hs2_reference hs2.l9.c
cluster hs2.l10.list > hs2.l10.c
error hs2_reference hs2.l10.c
cluster hs2.l11.list > hs2.l11.c
error hs2_reference hs2.l11.c
cluster hs2.l12.list > hs2.l12.c
error hs2_reference hs2.l12.c
cluster hs2.l13.list > hs2.l13.c
error hs2_reference hs2.l13.c
cluster hs2.l14.list > hs2.l14.c
error hs2_reference hs2.l14.c
cluster hs2.l15.list > hs2.l15.c
error hs2_reference hs2.l15.c
cluster hs2.l16.list > hs2.l16.c
error hs2_reference hs2.l16.c
cluster hs2.l17.list > hs2.l17.c
error hs2_reference hs2.l17.c
cluster hs2.l18.list > hs2.l18.c
error hs2_reference hs2.l18.c
cluster hs2.l19.list > hs2.l19.c
error hs2_reference hs2.l19.c
cluster hs2.l20.list > hs2.l20.c
error hs2_reference hs2.l20.c
cluster hs2.l21.list > hs2.l21.c
error hs2_reference hs2.l21.c
cluster hs2.l22.list > hs2.l22.c
error hs2_reference hs2.l22.c
cluster hs2.l23.list > hs2.l23.c
error hs2_reference hs2.l23.c