AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_operons028_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238474
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0682	300	ketol-acid reductoisomerase (ilvC)
#1	HI0737	247	acetohydroxy acid synthase II, putative
#2	HI0738	71	dihydroxyacid dehydratase (ilvD)
#3	HI0986	300	2-isopropylmalate synthase (leuA)
#4	HI0987	85	3-isopropylmalate dehydrogenase (beta-IPM dehydrogenase) (leuB)
#5	HI0988	175	3-isopropylmalate dehydratase, alpha subunit (leuC)
#6	HI0989	23	3-isopropylmalate dehydratase small subunit (leuD)
#7	HI1585	266	acetolactate synthase III large subunit (ilvI)

Motif 1
TTCACCGCACTTTTTTTCGTTTTTTTCTCTCCAAG	1	148	1
TTATATTTGGTTTTTTATATTTTTTTAATTGATTT	7	134	1
      ATTATTTTTCCTATTTTTTACTTCAAAAG	4	66	0
AAAATTTAGTTTTTTATAAATTTTTCCATCAATAA	7	96	0
ACACAGAGGATTTTTATTTATGTTTCGTATTGTTT	3	121	1
GTGCGGTTAGTTTTTTTGTATTTTTCCCCTCTTTG	4	32	0
TTTGCATATTTTTTTGTTGTGGTTTGATTATAGGA	0	230	0
TTTTAATTGATTTTTTTGTTGTTTTAGTGGCTAGA	7	156	1
AATGTTGCGATTTGTGCAATTATTTTTTTTTGTGA	0	158	0
ATATTGAAACTCTTTTCATTTTTTTACATAGGATA	1	14	0
TTTTTACCGCTCTTTTGGCTTATTTATTGACTGAT	1	63	0
AATGCGGCATTTTGTCGCATTTTTTTATTTTTATT	7	66	1
GTCAAACTATTTTTTGGCATTTTATATTAAAAATA	3	51	0
TAGACAAATTTTTTTTACTTTGTATTATGTGAAAC	7	187	1
          TTTTTGTCCTTAATTGTGTAAGGTT	0	285	0
AAAAATAATATTTTTACTATTTTATAAAATGCGGC	7	39	1
    GGTGTTTGTTTCCTGTTGTTTTTATTTTGGG	1	226	0
TAAATCGCTGTTCTTTGCTTTGTTTCAATTTTCTT	0	40	0
AAAAACTAAATTTTCATTTATATTTGGTTTTTTAT	7	117	1
TGCGGTGCGTTTTTCCTGTATTTTTTAGATAAAAA	3	267	0
ATTGACATAATCTGTTCGTTTTTTTAAAAGTGCGG	7	222	1
TTAGGGTTCGTTTGTATGATTAATTTCTTCGTTAA	2	24	0
AATATTATTTTTTATTCAAATTTTTGAATGAGATC	7	16	0
TCCCCCCTGTTTATTGGGGATATTTCTAAATAACT	5	75	0
       TTTTCTTTTTCCTCTTTTGAGCC     	6	5	0
          *****    ** ***
MAP Score: 43.7545

Motif 2
TGAATTTTTACCGCTCTTTTGGCTTATTTA	1	72	0
CCAATTTTCACCGCACTTTTTTTCGTTTTT	1	142	1
AATTTTAAACCCGCACTTTATAAGTTGCGG	3	235	1
GAAAAACGCACCGCACTTTTGGA       	3	287	1
AAAAAACTAACCGCACTTTTGAAGTAAAAA	4	51	1
TTGCCCCCTTCCGCCCTTCAGGCACCTTCC	5	34	0
TGTTTTTCAACCGCACTTTAAATACTTTGT	5	109	0
CGAATTTTAACCGCACTTCCCTTAACGAAT	5	142	1
CGACAAAATGCCGCATTTTATAAAATAGTA	7	53	0
CGGCATTTTGTCGCATTTTTTTATTTTTAT	7	70	1
CTTAAATTCACCGCACTTTTAAAAAAACGA	7	237	0
          **********
MAP Score: 36.1247

Motif 3
GTTCTTTGCTTTGTTTCAATTTTCTTAACGGCAATTTGCTG	0	25	0
TCGCTCGATGAACGACCTACTTTCTTTTACTCGTGTAAAAG	0	103	0
TTGCGATTTGTGCAATTATTTTTTTTTGTGAATTGGCATCG	0	148	0
TGTTGTGGTTTGATTATAGGATTTTTTGTTGTTGCGTAAAG	0	210	0
TATGATGTTGTGTTTGCATATTTTTTTGTTGTGGTTTGATT	0	236	0
ATATTGAAACTCTTTTCATTTTTTTACATAGGATAATTT  	1	8	0
AGCGGTAAAAATTCACTAAATTTTTTAGGGGAAGAACAGGA	1	87	1
AAGCCAATTTTCACCGCACTTTTTTTCGTTTTTTTCTCTCC	1	139	1
GGTGTTTGTTTCCTGTTGTTTTTATTTTGGGGATAAGTTCA	1	216	0
GGGTTCGTTTGTATGATTAATTTCTTCGTTAATTGATAAAA	2	15	0
ATGAAGTGTAAGTAGGTTTATTTTTAATATAAAATGCCAAA	3	33	1
AAAAACTGGCTGTCAAACTATTTTTTGGCATTTTATATTAA	3	56	0
CTCAACCTACTGCTCTCACATTTTGTGTGCGGCTAAGTTGT	3	164	1
GGGTATTTACATCTGACTGTTTTTTTATCCACAACTTAGCC	3	194	0
CGCACTTTATAAGTTGCGGGTTTTTTATCTAAAAAATACAG	3	246	1
ACTTCAAAAGTGCGGTTAGTTTTTTTGTATTTTTCCCCTCT	4	35	0
      ATTATTTTTCCTATTTTTTACTTCAAAAGTGCGGT	4	60	0
TTTAAATACTTTGTCCCCCCTGTTTATTGGGGATATTTCTA	5	82	0
AAATATTATTTTTTATTCAAATTTTTGAATGAGATCACAGT	7	11	0
AAATGCGGCATTTTGTCGCATTTTTTTATTTTTATTGATGG	7	65	1
AAATTTTCATTTATATTTGGTTTTTTATATTTTTTTAATTG	7	124	1
TTTTATATTTTTTTAATTGATTTTTTTGTTGTTTTAGTGGC	7	146	1
TGTTTTAGTGGCTAGACAAATTTTTTTTACTTTGTATTATG	7	175	1
CATTGACATAATCTGTTCGTTTTTTTAAAAGTGCGGTGAAT	7	221	1
          *  *  *   ******    *
MAP Score: 0.106805