AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_operons016_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237788
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0183	176	amino acid carrier protein, putative
#1	HI0419	168	protease, putative
#2	HI0726	205	nitrate/nitrite response regulator protein (narP)
#3	HI0837	53	response regulator (cpxR)
#4	HI0839	116	conserved hypothetical protein
#5	HI0883	300	amino acid carrier protein, putative
#6	HI0884	191	aerobic respiration control protein ARCA (arcA)
#7	HI0893	241	transcriptional repressor (Bm3R1)
#8	HI0894	79	lipoprotein, putative
#9	HI1379	300	phosphate regulon transcriptional regulatory protein (phoB)
#10	HI1708	62	transcriptional regulatory protein (ygiX)
#11	HI1709	114	conserved hypothetical protein

Motif 1
CTTGTAAAGGAAAGTGCGGTTAAATTCTTA	1	66	0
TTATCTTAAAAAAGAGCGGTAAAAAATTAT	2	16	1
AAAAATAGAAAAAGTGCGGTAGAAAAATAG	2	46	0
TCTTGCTGAAAAAGTGCGGTTATAATTTGC	4	80	1
CCGAAGCGCAAAAGAGCGGTTAATTTTTCA	5	127	1
AATGGAAAAGAAAGTGCGGTAAAAAAATAA	5	225	0
TAACAATAAAAAAGTGCGGTGATTTTTTAC	6	104	0
TTAATGATGAAAAGTGCGGTTAATTTTGAC	7	34	1
ATAGGAATATAAAATGCAGTCAAAATTAAC	7	52	0
TATTCGCGGTAAAATGGGGTAGTTATTTTG	9	194	1
TTATGGCATAAAAGTGAAGTGAGAAATAAT	9	262	0
TTTTGTTTATAAAGTGCGGTCAATTTTTT 	10	43	1
          **********
MAP Score: 46.9985

Motif 2
TTTTACCTGATTTTCCTTTTTGTGATCTAAA	6	79	0
CTCACCAAACTTTTACTTTTTAATAAGAGAA	9	226	0
TTGTTACGTTTTTTGTTTTTTAACTTGCCAA	7	145	1
TTTATTTATTTTTTGTTTTTTGGCAAGTTAA	7	164	0
TTATAAAATGTTATGCTTTTTAAAGTGGACT	2	162	1
CTACCGCACTTTTTCTATTTTTATCCATCAA	2	54	1
AAGCCAAATTTTTTTTATTTTTAACATT   	4	7	0
AGTGTGGAAATTATTTATTTTTTTACCGCAC	5	211	1
CGGTAAAAAATTATCTATTTTTCTACCGCAC	2	32	1
TGAGCGTTCATTTTATTTATTTTTTGTTTTT	7	175	0
CCGCACTTTCTTTTCCATTGTATCTTTTCGT	5	236	1
ATTAAGAGGACTATACTTTTTTGAAAAGACT	11	13	0
 TTTCCATCCTTATACTTATTTTGGCGTATG	6	171	0
CTTTTACCAATTATTCTTATTGTAGTGTGGT	3	23	0
ATCACCGCACTTTTTTATTGTTACAATAATG	6	111	1
         TCTTTTTATTTTCACCACACTA	3	1	1
TGTGAATTTATTAGATTTTTTCTTGTTTGTG	0	74	1
       AACGTTTCCTTTTTAAGTTAGTTA	11	100	0
TTATTAAGATTTATTTGTTTTAATACACACA	11	47	1
AACCTAAATAATTTCTTTTTTCTTGCTGAAA	4	60	1
          **** ******
MAP Score: 20.316

Motif 3
TTTATTTTGGAAAATATTTAGAATATTGTGAAT	0	48	1
ACAAACAAGAAAAAATCTAATAAATTCACAATA	0	71	0
TTCTTTAGAGAAATTATTAAAAAATCTCGCCTT	0	110	1
TTGATGGATAAAAATAGAAAAAGTGCGGTAGAA	2	52	0
     AATGTTAAAAATAAAAAAAATTTGGCTT	4	5	1
AAGTGCGGTAAAAAAATAAATAATTTCCACACT	5	211	0
CCTCGTCGTTTAAATCAAAATAAACACGACAAG	5	270	0
AACATTATTGTAACAATAAAAAAGTGCGGTGAT	6	111	0
AGCATACGCCAAAATAAGTATAAGGATGGAAA 	6	169	1
TTAAAAAACAAAAAACGTAACAATACTTATCTG	7	135	0
TTAACTTGCCAAAAAACAAAAAATAAATAAAAT	7	164	1
AAACAAAAAATAAATAAAATGAACGCTCATTCA	7	177	1
CTCCGTTATAAAAATAACAACAA          	8	0	0
TTTTATGCCATAAATCAAATGAAGGAGTATT  	9	279	1
TTAAAACAAATAAATCTTAATAAAAGATTAAGA	11	37	0
          ******  ** **
MAP Score: 5.91977