AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_fusions005_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944254930
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0112	300	855aa long hypothetical replication factor C subunit
#1	PH0452	30	1127aa long hypothetical ATP-dependent protease La

Motif 1
GCTTACCTCTCAAAGGTTCTGGAATTCATATATA	0	24	1
GTCGCCGGTAGTAGGGCCAAGGAAAAGCTAATAC	0	75	1
ACGCTTTCTGCGAAGGATTTGGAAACCTTCGAGA	0	132	1
CTTCGAGATACTAAGGCCATGGAAGAGGTTCTAT	0	158	1
ATTTAGAAAGCTGTGGTTGTGGTATTAAGCCTTA	0	273	0
          * * ** * *****
MAP Score: 7.1788

Motif 2
        CATCCAGCGATCCAGCTTACCTC	0	2	1
AGCTTACCTCTCAAAGGTTCTGGAATTCATA	0	23	1
AAGAATTTGTTCACGCTTTCTGCGAAGGATT	0	120	1
CTTAGTATCTCGAAGGTTTCCAAATCCTTCG	0	142	0
TCTTCCATGGCCTTAGTATCTCGAAGGTTTC	0	153	0
TTTGTAAATTTCCTACTTTCTCCTTCCCTTC	0	202	0
TGGTATTAAGCCTTACTCTCCAGCCCACCTA	0	257	0
ATACCACAACCACAGCTTTCTAAATTAG   	0	282	1
          ** ********
MAP Score: 0.297687