AlignACE 3.0 10/20/99
AlignACE2 -i HP/HP_operons007_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944245876
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HP1255	116	protein translocation protein, low temperature (secG)
#1	HP1259	69	conserved hypothetical protein
#2	HP1260	101	NADH-ubiquinone oxidoreductase, NQO7 subunit (NQO7)

Motif 1
AGAATACACTAAAATTTAGTTTTAATTTCA	0	35	0
TATTCTTAGCAAATTTTAGATAAGATCAAG	0	59	1
TTAAATGCCTAAAATTTAGAAAAAATCACG	0	89	0
          AAAATTTAGTAATCTTAAGC	1	0	1
GCGGGATTAAAACCTTTAGAGACGCTG   	1	52	1
          **********
MAP Score: 10.1992

Motif 2
TTTAGTGTATTCTTAGCAAATTTTAGATAA	0	52	1
TCTTAGCAAATTTTAGATAAGATCAAGCGT	0	62	1
AATGCCTAAAATTTAGAAAAAATCACGCTT	0	86	0
GGGGCTGGTATTTCAGCAGAAAGCGGGATT	1	30	1
ATTTTTATTTTTTCAGCTAACGATTAGCAA	2	24	1
TTAAACCATGTTTTTGCTAATCGTTAGCTG	2	37	0
          **********
MAP Score: 6.88197

Motif 3
AGAATACACTAAAATTTAGTTTTAATTTCAAGCGTG	0	29	0
AATTTTAGTGTATTCTTAGCAAATTTTAGATAAGAT	0	49	1
TTAAATGCCTAAAATTTAGAAAAAATCACGCTTGAT	0	83	0
          AAAATTTAGTAATCTTAAGCGGGGCT	1	0	1
         GAAATGTTAAAATAATTTTTATTTTTT	2	1	1
TTTTTCAGCTAACGATTAGCAAAAACATGGTTTAAT	2	32	1
          **   **** ***  *
MAP Score: 1.57131