AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_operons028_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238488
 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)
#8	HI1586	300	conserved hypothetical integral membrane protein

Motif 1
TTCACCGCACTTTTTTTCGTTTTTTTCTCTCCAAG	1	148	1
TTATATTTGGTTTTTTATATTTTTTTAATTGATTT	7	134	1
GTGCGGTTAGTTTTTTTGTATTTTTCCCCTCTTTG	4	32	0
TTGTGTTTATTTTCTTTATATTTTTATTAAAGTTT	8	20	1
AATATTATTTTTTATTCAAATTTTTGAATGAGATC	7	16	0
AAAATTTAGTTTTTTATAAATTTTTCCATCAATAA	7	96	0
  GGTGTTTGTTTCCTGTTGTTTTTATTTTGGGGA	1	224	0
GCGGTGCGTTTTTCCTGTATTTTTTAGATAAAAAA	3	266	0
TTTAATTGATTTTTTTGTTGTTTTAGTGGCTAGAC	7	157	1
TGTCAAACTATTTTTTGGCATTTTATATTAAAAAT	3	52	0
       ATTATTTTTCCTATTTTTTACTTCAAAA	4	67	0
AAATGCGGCATTTTGTCGCATTTTTTTATTTTTAT	7	65	1
TGTTCTTTGCTTTGTTTCAATTTTCTTAACGGCAA	0	32	0
     ATATATTTTTTTGTGTTTATTTTCTTTATA	8	5	1
ATATTGAAACTCTTTTCATTTTTTTACATAGGATA	1	14	0
ATTGACATAATCTGTTCGTTTTTTTAAAAGTGCGG	7	222	1
TGATGTTGTGTTTGCATATTTTTTTGTTGTGGTTT	0	240	0
GCTAGACAAATTTTTTTTACTTTGTATTATGTGAA	7	185	1
TTTATTAAAGTTTATAAAATTTTTATAAAATCTGT	8	42	1
AGGCGCAATTATTATAAGTATTTTTTCAGAGTGGA	8	126	1
TTGTGGTTTGATTATAGGATTTTTTGTTGTTGCGT	0	214	0
TTCGGCAACTATTCCTTTCTTTTTTCTTCTTCGTT	8	162	0
AAAAATAATATTTTTACTATTTTATAAAATGCGGC	7	39	1
ACACAGAGGATTTTTATTTATGTTTCGTATTGTTT	3	121	1
CCCTAAAAAATTTAGTGAATTTTTACCGCTCTTTT	1	82	0
GATTTGTGCAATTATTTTTTTTTGTGAATTGGCAT	0	150	0
TGCGGTTAAAATTCGATGTGTTTTTCAACCGCACT	5	122	0
          *** **    *****
MAP Score: 47.2635

Motif 2
TGAATTTTTACCGCTCTTTTGGCTTATTTA	1	72	0
CCAATTTTCACCGCACTTTTTTTCGTTTTT	1	142	1
AATTTTAAACCCGCACTTTATAAGTTGCGG	3	235	1
GATAAAAAACCCGCAACTTATAAAGTGCGG	3	245	0
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
TATGACAGTGTCGCCCCTTTCGAGCACGCC	8	227	0
          **********
MAP Score: 34.2615

Motif 3
GTTAAATCGCTGTTCTTTGCTTTGTTTCAATTTTCTTAACGGCA	0	33	0
TTGCGATTTGTGCAATTATTTTTTTTTGTGAATTGGCATCGTAT	0	145	0
TGATGTTGTGTTTGCATATTTTTTTGTTGTGGTTTGATTATAGG	0	231	0
TTTAGTGAATTTTTACCGCTCTTTTGGCTTATTTATTGACTGAT	1	63	0
TAAGCCAATTTTCACCGCACTTTTTTTCGTTTTTTTCTCTCCAA	1	138	1
      GGTGTTTGTTTCCTGTTGTTTTTATTTTGGGGATAAGT	1	219	0
AAAAACTGGCTGTCAAACTATTTTTTGGCATTTTATATTAAAAA	3	53	0
CACAGAGGATTTTTATTTATGTTTCGTATTGTTTCTTTATCTCT	3	122	1
  TCCAAAAGTGCGGTGCGTTTTTCCTGTATTTTTTAGATAAAA	3	268	0
ACTTCAAAAGTGCGGTTAGTTTTTTTGTATTTTTCCCCTCTTTG	4	32	0
ATGCGGCATTTTGTCGCATTTTTTTATTTTTATTGATGGAAAAA	7	67	1
CAAATATAAATGAAAATTTAGTTTTTTATAAATTTTTCCATCAA	7	99	0
TAAATTTTCATTTATATTTGGTTTTTTATATTTTTTTAATTGAT	7	123	1
TTTATATTTTTTTAATTGATTTTTTTGTTGTTTTAGTGGCTAGA	7	147	1
  ATATATTTTTTTGTGTTTATTTTCTTTATATTTTTATTAAAG	8	8	1
TGCCAACAGATTTTATAAAAATTTTATAAACTTTAATAAAAATA	8	38	0
TTATAATAATTGCGCCTCTACTTTTGTAGTGATTGGGGAGATTA	8	99	0
TCGGCAACTATTCCTTTCTTTTTTCTTCTTCGTTATCCACTCTG	8	152	0
          ***        **** *     **
MAP Score: 27.1823

Motif 4
GTTAAATCGCTGTTCTTTGCTTTGTTTCAATTT	0	44	0
GTGCAATTATTTTTTTTTGTGAATTGGCATCGT	0	147	0
ATTATAGGATTTTTTGTTGTTGCGTAAAGTGAT	0	206	0
TTTGCATATTTTTTTGTTGTGGTTTGATTATAG	0	232	0
ATTGAAACTCTTTTCATTTTTTTACATAGGATA	1	14	0
TCTTTTGGCTTATTTATTGACTGATGATTAGAT	1	55	0
TTCACCGCACTTTTTTTCGTTTTTTTCTCTCCA	1	148	1
TGTTTCCTGTTGTTTTTATTTTGGGGATAAGTT	1	218	0
        GGTGTTTGTTTCCTGTTGTTTTTAT	1	232	0
GCTGTCAAACTATTTTTTGGCATTTTATATTAA	3	56	0
ACACAGAGGATTTTTATTTATGTTTCGTATTGT	3	121	1
TGTTTCGTATTGTTTCTTTATCTCTCAACCTAC	3	141	1
TACATCTGACTGTTTTTTTATCCACAACTTAGC	3	195	0
AAGTGCGGTTAGTTTTTTTGTATTTTTCCCCTC	4	36	0
AAATTCGATGTGTTTTTCAACCGCACTTTAAAT	5	116	0
    TTTTCTTTTTCCTCTTTTGAGCC      	6	4	0
ATAGTAAAAATATTATTTTTTATTCAAATTTTT	7	26	0
TTTGTCGCATTTTTTTATTTTTATTGATGGAAA	7	76	1
AAAAACTAAATTTTCATTTATATTTGGTTTTTT	7	117	1
TATATTTGGTTTTTTATATTTTTTTAATTGATT	7	135	1
TTTTTAATTGATTTTTTTGTTGTTTTAGTGGCT	7	155	1
GGCTAGACAAATTTTTTTTACTTTGTATTATGT	7	184	1
TGACATAATCTGTTCGTTTTTTTAAAAGTGCGG	7	224	1
       ATATATTTTTTTGTGTTTATTTTCTT	8	3	1
TTTTGTGTTTATTTTCTTTATATTTTTATTAAA	8	18	1
ATCTGTTGGCATTTTGTTTGTTTTACGGTAATC	8	71	1
TTCCTTTCTTTTTTCTTCTTCGTTATCCACTCT	8	153	0
ACAAAACGACTTTTATTTGATTTCGGCAACTAT	8	185	0
          ***** *** * *
MAP Score: 4.60558