AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_operons012_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237645
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0286	135	aminotransferase
#1	HI0468	300	ATP phosphoribosyltransferase (hisG)
#2	HI0469	92	histidinol dehydrogenase (hisD)
#3	HI0470	68	histidinol-phosphate aminotransferase (hisC)
#4	HI0471	111	imidazoleglycerol-phosphate dehydratase / histidinol-phosphatase (hisB)
#5	HI0472	65	amidotransferase (hisH)
#6	HI0473	35	phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA)
#7	HI0621.1	175	conserved hypothetical protein
#8	HI1166	87	histidinol-phosphate aminotransferase (hisH)
#9	HI1167	190	phosphoserine aminotransferase (serC)
#10	HI1181	206	phosphoheptose isomerase (gmhA)
#11	HI1655	71	antigen

Motif 1
TCTCGAAAAATTTATTAGAAACAAAAGGATTTCACT      	0	109	1
CCATCGCGATTTTATTCCCAACAAGGAGCAATCA        	10	182	1
AGGTTTATCATTTGCTTTATACAAACAGTATAAAACTAAATA	4	46	0
AAATTATCTATTTAATCCAAGCAATTAGCAAATATAAGTCAT	7	111	0
AAAAATTGCTTTTTTTAATTTTAAAGTGTATTTTTAAGGCAA	1	45	1
GCACAGTCATTTTATTTATTTTAAAGGGAGTTGTT       	9	3	0
AAAGAATTTTTTTGATTTCAGTAAAAAGCATTGATTATCGAT	9	105	1
    AATGTTTTTCCTATTTTAAAGTTGAGATAAAAGAAAAC	1	272	0
AAAAAAGCAATTTTTTTGAAAAAAATTGTGTTTTTAGTACAT	1	18	0
AAAATCATCATTTCATCGAAAAAAGATGAATTTTTATTTAGG	10	109	1
CTCAAACTTATTTTTTCGATCTAAATCGCAAAAAATCATCAT	10	78	1
AATGGGCGTATTTACTACGCCCAAATTTATTTAAAAATACAT	8	23	1
ATGATGTCTTTTTTATCACTACAAAAATCGATAATCAATGCT	9	131	0
AGCAGTCAAATTTTCATACAACAATACGAAATATGT      	3	42	1
GTAATTTAGCTTTTTTTTAATCAATCGTCAAAATTTACCCTC	9	46	1
GCCCTTTTTATTTATTGTTTTTAAATCTGTTTTGGTATTCTA	7	14	1
TCTCTTACCTTTTATACATGTCAAATTGACAAAAATTATCTA	7	143	0
CCGAGGGGTATTTATTGCTTTTACACTGATTTTTATTACACT	1	213	0
      TGTGTTTTTGAAAATTAAAGGGCTAAGAATTTACGT	10	4	1
TTTCCTTGCTTTTTATGAAAATAATGATGTCTTTTTTATCAC	9	154	0
          ***  *     ***   *  **
MAP Score: 26.1374

Motif 2
GTAATTTAGCTTTTTTTTAATCAATCGTCAAAAT	9	46	1
TGTAAAAAAATTTTTTGTCATTAACAATCTGCGG	0	30	0
AAAATTCATCTTTTTTCGATGAAATGATGATTTT	10	109	0
AAAAAAGCAATTTTTTTGAAAAAAATTGTGTTTT	1	26	0
CTCAAACTTATTTTTTCGATCTAAATCGCAAAAA	10	78	1
TCAGATTATCTTTTTTAGACAGATTAGTTATGAC	7	82	1
          TTTTTTATCCTTTTACAATCGGTC	5	51	0
GGCACAGTCATTTTATTTATTTTAAAGGGAGTTG	9	12	0
TTGATTATCGATTTTTGTAGTGATAAAAAAGACA	9	135	1
AAAGATGAATTTTTATTTAGGCTAGCGAAGAATC	10	130	1
TTTCTAATAAATTTTTCGAGAAAAGTGCGGTTAA	0	96	0
AAAAAATTGCTTTTTTTAATTTTAAAGTGTATTT	1	44	1
 ATAAGCCCTTTTTATTTATTGTTTTTAAATCTG	7	9	1
TGACAAAAAATTTTTTTACAAAATCTTTTCAATA	0	44	1
TAAATAGATAATTTTTGTCAATTTGACATGTATA	7	139	1
AGGGGTTTTCTTTTATCTCAACTTTAAAATAGGA	1	268	1
AGAGCGGTTAATTTTTGTCGTATTTTTGCAAAAT	5	15	1
TTTCCTTGCTTTTTATGAAAATAATGATGTCTTT	9	162	0
CTACGCCCAAATTTATTTAAAAATACATACTAAC	8	37	1
TTACCCTCTATTTTATGAATGATAGAAAGAATTT	9	80	1
GTAGTTGGGGATTTTTCAAGATATGTTTATCTTA	10	45	0
CCATATCAATATTTATAAATACAACT        	8	71	1
TCCGAGGGGTATTTATTGCTTTTACACTGATTTT	1	222	0
ATAGAAAGAATTTTTTTGATTTCAGTAAAAAGCA	9	101	1
          ****** **   **
MAP Score: 19.3573

Motif 3
TGACAAAAAATTTTTTTACAAAATCTTTTCAATA	0	44	1
AAAAACACAATTTTTTTCAAAAAAATTGCTTTTT	1	25	1
AAAAAATTGCTTTTTTTAATTTTAAAGTGTATTT	1	44	1
TTTTAAAGTGTATTTTTAAGGCAATATAAGATCT	1	63	1
ATTTTTGTCGTATTTTTGCAAAATTCGACCGATT	5	25	1
TTTTTATTTATTGTTTTTAAATCTGTTTTGGTAT	7	18	1
TGTCAGATTATCTTTTTTAGACAGATTAGTTATG	7	80	1
ACAAAAATTATCTATTTAATCCAAGCAATTAGCA	7	123	0
GGTTAGTATGTATTTTTAAATAAATTTGGGCGTA	8	38	0
CCCATATCAATATTTATAAATACAACT       	8	70	1
GTAATTTAGCTTTTTTTTAATCAATCGTCAAAAT	9	46	1
AAATTTACCCTCTATTTTATGAATGATAGAAAGA	9	76	1
ATAGAAAGAATTTTTTTGATTTCAGTAAAAAGCA	9	101	1
AATGATGTCTTTTTTATCACTACAAAAATCGATA	9	140	0
TGTATTTCCTTGCTTTTTATGAAAATAATGATGT	9	166	0
        TGTGTTTTTGAAAATTAAAGGGCTAA	10	2	1
TACTCAAACTTATTTTTTCGATCTAAATCGCAAA	10	76	1
   TTTTGTTTGCTTTTAAGTTATGAGATAAGTA	11	7	1
          * ***** *  ***
MAP Score: 4.85817

Motif 4
AATTGTGTTTTTAGTACATTTTTACTA      	1	4	0
TTTTTTCAAAAAAATTGCTTTTTTTAATTTTAA	1	36	1
CCGAGGGGTATTTATTGCTTTTACACTGATTTT	1	222	0
ATGCTGGGTTATCATCCATTTTACGGATACAAA	2	57	1
        TTTTTTATCCTTTTACAATCGGTCG	5	50	0
          ATAAGCCCTTTTTATTTATTGTT	7	0	1
CTTGGATTAAATAGATAATTTTTGTCAATTTGA	7	132	1
         TCTCTTACCTTTTATACATGTCAA	7	161	0
ACTGTGCCGTAATTTAGCTTTTTTTTAATCAAT	9	38	1
AAAATCGATAATCAATGCTTTTTACTGAAATCA	9	117	0
AAAAGCATTGATTATCGATTTTTGTAGTGATAA	9	128	1
TATGAAAATAATGATGTCTTTTTTATCACTACA	9	150	0
     TGTATTTCCTTGCTTTTTATGAAAATAA	9	172	0
AGTTTGAGTAGTTGGGGATTTTTCAAGATATGT	10	53	0
TTTTCGATGAAATGATGATTTTTTGCGATTTAG	10	98	0
CTAAATAAAAATTCATCTTTTTTCGATGAAATG	10	117	0
        TTTTGTTTGCTTTTAAGTTATGAGA	11	2	1
          **  * *******
MAP Score: 3.18502

Motif 5
TCTGCGGTAGAATATGGCTAATTTTTT    	0	6	0
TTTAAAATTAAAAAAAGCAATTTTTTTGAAA	1	39	0
TAAAGTTGAGATAAAAGAAAACCCCTCGAAA	1	263	0
TCTCAACTTTAAAATAGGAAAAACATT    	1	283	1
ATTGATTATTTAAATGGCGAGTCAAAGCTCG	2	18	0
ATACTGTTTGTATAAAGCAAATGATAAACCT	4	57	1
CGACCGATTGTAAAAGGATAAAAAA      	5	50	1
AAACAGATTTAAAAACAATAAATAAAAAGGG	7	15	0
TAATCTGTCTAAAAAAGATAATCTGACATAT	7	77	0
TTGCTTGGATTAAATAGATAATTTTTGTCAA	7	129	1
TTTGACATGTATAAAAGGTAAGAGA      	7	160	1
GATTGATTAAAAAAAAGCTAAATTACGGCAC	9	41	0
TATCATTCATAAAATAGAGGGTAAATTTTGA	9	73	0
TATCACTACAAAAATCGATAATCAATGCTTT	9	129	0
TTGTAGTGATAAAAAAGACATCATTATTTTC	9	149	1
ATTATTTTCATAAAAAGCAAGGAAATACA  	9	171	1
TTTTGAAAATTAAAGGGCTAAGAATTTACGT	10	15	1
TTTTGCGATTTAGATCGAAAAAATAAGTTTG	10	80	0
TGTTGGGAATAAAATCGCGATGGCATTGTAT	10	174	0
ATCTCATAACTTAAAAGCAAACAAAA     	11	5	0
TGCTCCATCATAAACAGACAATAGTCGTAGC	11	47	0
          ******** **
MAP Score: 1.5971