AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_sum_all046_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236265
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0263	253	529aa long hypothetical DNA repair protein
#1	PH0452	30	1127aa long hypothetical ATP-dependent protease La
#2	PH0605	42	140aa long hypothetical translation initiation factor eIF-2 beta

Motif 1
         AAGATTTCCAGCTATGCCAATGA	0	1	1
CAAATATCTAACTTTTCTCCCTGAAAAATAAC	0	128	0
GAATATTCTAAGATTTTCGCCTTATTTCCGCC	0	159	1
GATTTTCGCCTTATTTCCGCCTGGTATTTAAA	0	170	1
GAGAAAAGTATATAACCCTGCTAATGTTACCC	0	206	1
ACCCTGCTAATGTTACCCACCTTGAAGCCTCA	0	220	1
TCCAGTTTTATAAACTTCACCTAC        	1	2	0
         TTTTATTCCAGTTTTATAAACTT	1	17	0
ACCTCCGTTTAAAGTTCCTCCTGGAGTTATAT	2	13	0
          * ****** ***
MAP Score: 4.42398

Motif 2
GAGGAGAGATGTAAAGGTTCATGCTCTCAGT	0	46	1
AGGTTAAATAGTGAATTTCATTTCTTTAGTT	0	100	1
AGTTAGATATTTGAATATTCTAAGATTTTCG	0	147	1
CGCCTGGTATTTAAATATTGAGAAAAGTATA	0	187	1
GTTACCCACCTTGAAGCCTCACGGTCATTAG	0	231	1
      GTAGGTGAAGTTTATAAAACTGGAA	1	4	1
TCACCTCCGTTTAAAGTTCCTCCTGGAGTTA	2	16	0
          ****** ****
MAP Score: 1.50149