AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_operons017_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237830
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0136	300	GTP-binding protein
#1	HI0567	150	DNA gyrase, subunit B (gyrB)
#2	HI0993	191	chromosomal replication initiator protein (dnaA)
#3	HI0998	180	ribosomal protein L34 (rpL34)
#4	HI1225.1	65	conserved hypothetical protein
#5	HI1227	104	uracil permease (uraA)
#6	HI1264	300	DNA gyrase, subunit A (gyrA)
#7	HI1527	84	lipid A biosynthesis lauroyl acyltransferase (htrB)
#8	HI1528	73	topoisomerase IV, subunit B (parE)
#9	HI1529	66	topoisomerase IV, subunit A (parC)

Motif 1
TGTAATAGAGAAAAGTGCGGTAAAAATTGTC	2	150	0
GAATTAACTTAAAAGTGCGGTCAGTTTTTCT	5	63	0
AATTCTATCAAAAAGTGCGGTGATATTCGAC	8	17	0
GAAGCAAAGAAAAAGTAAGGCGCCATCAGGC	6	199	1
TTGAATAACCAAAATTGTGGCGATTTTACCA	7	26	1
TTTTTGATCAAAAATTGTGGCGGATTATAGC	6	269	0
GGAAACAAGGAAAAGTAGGGTCGCCTTTCTT	6	147	1
ATTATAGCATAAAATTGTGGATATGTGGTTT	6	246	0
GAGATACCTCAAAAGTTAGGTTACAACTTTT	3	15	0
TTTTGTAAATAAAAATTGGGCGAGATTATAG	1	115	0
AAAGTAAGTAAAAAGAAAGGCGACCCTACTT	6	159	0
TCCTTTCCCGAAAAGCATCGCCAAAACGGCG	1	76	1
TTATTTTGTCAAAAATGGCGACTATTATATC	0	269	0
TCAAATTTAAAAAATTAACGAATAACCTCAC	8	51	1
ATTATAGCAAAAAATCGCCGTTTTGGCGATG	1	91	0
GTTTTTTTTAAAAATTTCCGTTTCTTATTTG	3	88	1
ACAAAGGTGGAAAAGAAGGGAACCCAATTTG	6	33	0
AACGCACGGAAAAAAGACGGCTTAAATGCCG	5	24	0
GGAAAACGATAAAAAAAGGGCGAATAATTTC	1	48	0
CATTTATTGTAAAATCTCCGACAATTTTTAC	2	131	1
ATAGAACAGAAAAAAATGCGCCAGTATTGTA	2	48	0
    TGCACTAAAAAATTGGAAAAAATAACA	1	6	1
          ******* ***
MAP Score: 32.4605

Motif 2
ATCATTTCATAAAGAAAAGAAAAAGCCACAGGATACAA	0	208	0
   TGCACTAAAAAATTGGAAAAAATAACAAGTTATGG	1	7	1
CCGTGCGTTGAAACACAAGAAAAACTGACCGCACTTTT	5	46	1
CTTGTGTTTCAACGCACGGAAAAAAGACGGCTTAAATG	5	27	0
ATCCTCTTCAAACGTTGCGAAAAAGCGCAACACTCGCT	0	91	1
AAACGATAAAAAAAGGGCGAATAATTTCGCCCCATAAC	1	38	0
ACCACAACTCAAATTTACGATAAACTACGCCCCTAACT	7	53	1
CAAATTTAAAAAATTAACGAATAACCTCACC       	8	52	1
TCGGAAGTTAAAGGATTGGTAAAAAATCATTTCATAAA	0	233	0
TTTCTTTGGCGAAGCAAAGAAAAAGTAAGGCGCCATCA	6	189	1
GGCTACGCTCAAACAGACGAAAATTTCCTACAAATTCA	6	69	0
TCGCCAAAGAAAAAGTAAGTAAAAAGAAAGGCGACCCT	6	163	0
TTAATTTTTTAAATTTGAGAAAATTCTATCAAAAAGTG	8	31	0
TCGTAAATTTGAGTTGTGGTAAAATCGCCACAATTTTG	7	35	0
TTATAACGTTAAGTTGTAGATAAATAAACAGTATTTAG	0	158	1
GTAATAGAGAAAAGTGCGGTAAAAATTGTCGGAGATTT	2	142	0
TGAAGAGGATAAGAAAATGATTAAGATCATTATCCTTG	0	63	0
ATAAGAAACGGAAATTTTTAAAAAAAACTTCAAACGAA	3	78	0
CTCTCTGTTTGAATTAACTTAAAAGTGCGGTCAGTTTT	5	66	0
          ***     ******   *
MAP Score: 18.753

Motif 3
TCCTTGAAAGCGAGATTATTATAACGTTAA	0	140	1
TGTCAAAAATGGCGACTATTATATCGGAAG	0	264	0
TGACAAAATAAGAGATTTTTT         	0	289	1
AGTTATGGGGCGAAATTATTCGCCCTTTTT	1	37	1
CGAAATTATTCGCCCTTTTTTTATCGTTTT	1	47	1
TCGCCAAAACGGCGATTTTTTGCTATAATC	1	93	1
AAAAATTGGGCGAGATTATAGCAAAAAATC	1	106	0
TATAATCTCGCCCAATTTTTATTTACAAAA	1	116	1
TAATCTATCTGGCGCATTTTAAT       	2	3	0
ATACAATACTGGCGCATTTTTTTCTGTTCT	2	47	1
AAGATCTTTTCACGCATTTATTGTAAAATC	2	117	1
AAAAATTGTCGGAGATTTTACAATAAATGC	2	130	0
TAAAATCTCCGACAATTTTTACCGCACTTT	2	140	1
CAATTTTTACCGCACTTTTCTCTATTACAA	2	152	1
AATAAGAAACGGAAATTTTTAAAAAAAACT	3	87	0
ATTTGACGAACGCGTATTTTATGACTAGAA	3	114	1
TAAAATAGAGCGCAATTCTAGTCATAAAAT	3	129	0
AAAAACTGACCGCACTTTTAAGTTAATTCA	5	65	1
          CGCACTTTAAATCGGATAAA	6	0	1
TGAATTTGTAGGAAATTTTCGTCTGTTTGA	6	69	1
GAAAAGTAGGGTCGCCTTTCTTTTTACTTA	6	156	1
ACCACATATCCACAATTTTATGCTATAATC	6	248	1
TATAATCCGCCACAATTTTTGATCAAAAAA	6	271	1
CCAAAATTGTGGCGATTTTACCACAACTCA	7	34	1
CGAATATCACCGCACTTTTTGATAGAATTT	8	19	1
          **********
MAP Score: 12.4802

Motif 4
ATGATCTTAATCATTTTCTTATCCTCTTCAAA	0	71	1
TGTATCCTGTGGCTTTTTCTTTTCTTTATGAA	0	209	1
TATAATAGTCGCCATTTTTGACAAAATAAGAG	0	271	1
GAAATTATTCGCCCTTTTTTTATCGTTTTCCT	1	48	1
CCTTTTTTTATCGTTTTCCTTTCCCGAAAAGC	1	60	1
CGCCAAAACGGCGATTTTTTGCTATAATCTCG	1	94	1
  AATTTATCTCATTCTTTTGTAAATAAAAAT	1	130	0
CAATACTGGCGCATTTTTTTCTGTTCTATAAT	2	50	1
AATTTTTACCGCACTTTTCTCTATTACAAAAA	2	153	1
ATATTCGTTTGAAGTTTTTTTTAAAAATTTCC	3	75	1
TTTAAAAATTTCCGTTTCTTATTTGACGAACG	3	94	1
TTATCATTTAGCCCTTTCTTACTTAATCTGTA	4	31	1
CGGCATTTAAGCCGTCTTTTTTCCGTGCGTTG	5	24	1
    TTAGTTTCAACTCTCTGTTTGAATTAAC	5	86	0
CAAATTGGGTTCCCTTCTTTTCCACCTTTGTG	6	33	1
GCCAGGTCCGGCAATTTCCGTTAAGGAAATTC	6	104	1
AAGTAGGGTCGCCTTTCTTTTTACTTACTTTT	6	159	1
TCTTTTTACTTACTTTTTCTTTGGCGAAGCAA	6	174	1
    TGGTATTCCTTTTTTGATCAAAAATTGT	6	282	0
GAATATCACCGCACTTTTTGATAGAATTTTCT	8	20	1
          *** ****** *
MAP Score: 11.9082

Motif 5
AAGTTAAAGGATTGGTAAAAAATCATTTCATAA	0	234	0
AAATCTCTTATTTTGTCAAAAATGGCGACTATT	0	274	0
          TGCACTAAAAAATTGGAAAAAAT	1	0	1
GGGAAAGGAAAACGATAAAAAAAGGGCGAATAA	1	52	0
TGGGCGAGATTATAGCAAAAAATCGCCGTTTTG	1	97	0
CTCATTCTTTTGTAAATAAAAATTGGGCGAGAT	1	120	0
CGTGAAAAGATCTTCTAAAAAATCCAAGTTTGA	2	98	0
TAGAGAAAAGTGCGGTAAAAATTGTCGGAGATT	2	143	0
CGCACTTTTCTCTATTACAAAAACAATAAGGAT	2	162	1
ACTTCAAACGAATATTAAAAAATATATGCACTT	3	57	0
GAAACGGAAATTTTTAAAAAAAACTTCAAACGA	3	79	0
GTATTCCTTTTTTGATCAAAAATTGTGGCGGAT	6	275	0
TTGAGAAAATTCTATCAAAAAGTGCGGTGATAT	8	22	0
AGCAAATCCGAATTTTAATAAATTAAGAATATA	9	24	1
          * *  ********
MAP Score: 1.37096