/* A more detailed description can be found in man.yama3. */
Usage: yama3 [-r ALL_SIM] [-w width] [-c <score file>] [-p <pattern file>] [-t] [L=??] <input sequence order>

score file format :
	seq1 seq2 60 2 8 -10
	seq2 seq3 50 2 10 -10
	default 60 2 10 -10

	seq2 3 2 4 3
	default 0 0 0 0

Default : to output LAT-format text
	-t : normal text output
	 L : text length

pattern file format :
	<pattern name> <pattern> <pattern score>

	e.g.

	YY1             ATGG            16
	TBP             AATAAA          36
	CBF             CCAAT           25
	silencer        TTGGAAG         49
	CDP             GGTCA           25

input sequence order format:
	"((seq1[20,50] seq2[30,45]) seq3[20,50])"

output scripts:

	lat header ...
	l script1 script2 ...    first sequence
	l script1 script2 ...    second sequence
	l script1 script2 ...    third sequence
	...

	positive script means # of characters
	negative script means # of gap symbols (dashes)