You can clone with
example map for
strenght: .AG. GC.. ...A ..GC | AC.. GT.. T.TC ....
size: CG.. .... ...C ..T. | ..AC .... ...C ..A.
ant 1: TTTC AAAG GGGG GAGC TGTA AGGA TTCT CCAG
ant 2: CCGC GGGC AGGT TTAC TACT TGGA TACC ACTC
Then we match each gene in strength and size against the ant unless it's a '.'
If we have match the score is increased. If we have a similarity (A<->G or C<->T)
the score is not changed and otherwise it's decreased.
For a fully working example script that works with strings:
CCGT TGTA GTAC GACT CCAA GCTT GCGT GTTG
ATCT GGGT GGAC GCAC TTTA TTGG CGCC GCTG
GCAG ACTA CCAT TGTA CCAC CCCC ACGT CAGG
CAGA CCTT CTCC TTAC CCGA CCTA CCAG TATT
GTTG TGTC TTGT CTAA TTCC CGAA TAGC CTTC
TAGT ACTG TCAT TTTG TTCG GTAA TTCG GACT
ACCA GCAA GCCG ATAC CCCT CTTA TCTG TGGA
AAAC CTCG TGGA TCTC TTAG ATAA ACAA CGCA
AGCT CTCG CAAC AGTT TAGC CCTC ATGG CCTA
GCTT CCCC CCAC CATT TACG CTAG TAGA TGGC
GCAA GTCT AAAA CATC GTGC GCAA ATAC TCAC