AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_operons029_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238509
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0478	29	ATP synthase F1, subunit epsilon (atpC)
#1	HI0483	49	ATP synthase F0, subunit b (atpF)
#2	HI0484	55	ATP synthase F0, subunit c (atpE)
#3	HI0485	36	ATP synthase F0, subunit a (atpB)
#4	HI0485.1	125	H. influenzae predicted coding region HI0485.1
#5	HI0486	139	glucose-inhibited division protein (gidB)
#6	HI0487	115	H. influenzae predicted coding region HI0487

Motif 1
ATCACACTTTTAGAAAATAATTTATCTATTTGT	4	16	0
AAGTGTTATATAAATCACACTTTTAGAAAATAA	4	29	0
AAGTGTGATTTATATAACACTTTTTATGTGTTT	4	40	1
    CACTTTTACAAAATAATTTTAGCCCGCCG	4	106	0
TGTCCAGTTTTACACCATAAATTGAATGCACCT	5	19	0
ATTAAGGAAATTTACCGCACTTTTAAGTAAAAT	5	88	1
TTTTAAGTAAAATAGCGTAATTTTTCAAAGAGA	5	108	1
AAACAGTGCATAGATCACAGTTTTGTAGCAAAA	6	38	0
TGTTCGCTAATTTACCGCACTTTACTGAAATAA	6	70	0
          ** * **** ***
MAP Score: 13.5684

Motif 2
TTTGCTTATCAACGTAAAACAAGCATAGTAAGGAGGA	1	18	1
CTCTAGGGCTAAAACTTAACTTCTATTGGAGAAAATT	2	28	1
          AAAGTAACAAATAGATAAATTATTTTC	4	0	1
TATAAATCACACTTTTAGAAAATAATTTATCTATTTG	4	17	0
TCAACTTAAAAACACATAAAAAGTGTTATATAAATCA	4	45	0
GTTGAATCTAAAGCCAGCAAAGGTATAATCGGCGGGC	4	77	1
         CACTTTTACAAAATAATTTTAGCCCGCC	4	107	0
TTTATGGTGTAAAACTGGACATTGATTCGGTAAATAA	5	31	1
ATAATTCATCAAATTACTAAAAACATTAAGGAAATTT	5	64	1
AAAATAGCGTAATTTTTCAAAGAGATAATAAAT    	5	116	1
GTTTTGTAGCAAAATGGTAAAAAAATTTGTAAGGATG	6	15	0
TTACTGAAATAAAACAGTGCATAGATCACAGTTTTGT	6	45	0
AAAGTGCGGTAAATTAGCGAACAAATTTTGAACTAAC	6	80	1
          **  **  ***   ***
MAP Score: 8.71414

Motif 3
       TCGTTTTTTATTAACCGGCTCTAGG	2	3	1
ACTTAACTTCTATTGGAGAAAATT        	2	41	1
AATAGATAAATTATTTTCTAAAAGTGTGATTT	4	19	1
CGGGCTAAAATTATTTTGTAAAAGTG      	4	109	1
TGCATTCAATTTATGGTGTAAAACTGGACATT	5	22	1
AACTGGACATTGATTCGGTAAATAATTCATCA	5	43	1
ATTCGGTAAATAATTCATCAAATTACTAAAAA	5	55	1
ATTTACCGCACTTTTAAGTAAAATAGCGTAAT	5	97	1
TAAAATAGCGTAATTTTTCAAAGAGATAATAA	5	115	1
AAAAAATTTGTAAGGATGTAAAA         	6	1	0
TAGATCACAGTTTTGTAGCAAAATGGTAAAAA	6	29	0
TGCACTGTTTTATTTCAGTAAAGTGCGGTAAA	6	61	1
AGCGAACAAATTTTGAACTAACAAAAACAA  	6	95	1
          * *** ******
MAP Score: 8.55169