AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_operons013_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237655
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0050	74	conserved hypothetical transmembrane protein
#1	HI0051	38	conserved hypothetical transmembrane protein
#2	HI0052	26	conserved hypothetical protein
#3	HI0053	109	zinc-type alcohol dehydrogenase
#4	HI0154	255	acyl carrier protein (acpP)
#5	HI0156	300	malonyl CoA-acyl carrier protein transacylase (fabD)
#6	HI0157	185	beta-ketoacyl-ACP synthase III (fabH)
#7	HI0876	300	nucleoside diphosphate kinase (ndk)
#8	HI0916	107	outer membrane protein, putative
#9	HI0920	248	conserved hypothetical protein
#10	HI1062	85	(3R)-hydroxymyristol (acyl carrier protein) dehydrase (fabZ)
#11	HI1064	56	conserved hypothetical protein
#12	HI1430	179	short chain dehydrogenase/reductase
#13	HI1533	148	beta-ketoacyl-ACP synthase I (fabB)
#14	HI1734	79	enoyl-(acyl-carrier-protein) reductase (fabI)

Motif 1
AGAAATAACAATAAGAATAAACTACACAAAATAA	0	28	0
AAAACTAACAAATAGGAAAAACAA          	4	241	1
CCGCACTTTAAATCGGATAAAGAACAAATTGGGT	5	27	1
AGGCAAATTCAATGGAACAAAGGAAACAAGGAAA	5	145	1
CAAAGAAAAAGTAAGCAAAAAGAAAGGCGCCCCT	5	182	0
ATTAAAAAACAATAGGACAAAACATA        	5	284	1
AATACCGTAAAATGGCAAAAATTAATAGGGAGAG	9	72	1
ATTGAAAATTTATTGTAAAAAACAACTAAAAAAC	9	123	0
TGCAGAACAGATTAGAACAAAGGAATTCATAGCA	9	160	1
TTTTTAAGCCAGAAGGAAAAAACA          	11	0	0
AACCTCGATCAATTGAAATAAAAATTGGGCAGAT	12	14	1
GTACTATTAAAGTAGTACAAATAAATTTTGATTG	12	128	0
GTACTACTTTAATAGTACAAATAAGCTCAAGATT	12	144	1
TTTCTGAACTGGTCGAACAAATGAATTATTGCTT	13	57	1
TTATTGTTTTATATGTAAAAATAACGACTCAAAA	13	114	0
CCACATTTTTAATTGAACAAAGAAGAAACA    	14	6	0
          *** * *****  *
MAP Score: 20.6232

Motif 2
AGCGATTAAAAAGGAAAAAATCTATGGACT	6	152	0
TTTAAGCCAGAAGGAAAAAACA        	11	2	0
AAGAAAAAGTAAGCAAAAAGAAAGGCGCCC	5	184	0
TTGCTTCGCCAAAGAAAAAGTAAGCAAAAA	5	195	0
TTGGCGAAGCAAAGAAAAAGTAAGCTCGCC	5	213	1
ATAAAACAATAAGGAAGAAGCA        	13	136	1
CATAATCAATAAGGAGAAAGTT        	2	14	1
CAATGGAACAAAGGAAACAAGGAAAAGTAG	5	154	1
GAACACCTATAAGTAAAAAA          	6	0	0
TTAGGCAAGAAAGGAATAAAAA        	13	2	0
AGTTCTGATGAAGAAAAAAGTTCAATTTA 	8	9	0
      GCACAAGCAGAAAATGAACCTTTC	7	4	1
TTAATTGAACAAAGAAGAAACA        	14	2	0
ATAGGGAGAGAAATAAAAAGTGCGGTGGTT	9	96	1
GGGGATTTCTAAGCAATAAAATCATAGCCA	4	29	1
ACCTTACAAAAAATAAACAAATAAAATCTA	10	59	0
TAAATCGGATAAAGAACAAATTGGGTTCCC	5	35	1
          **********
MAP Score: 19.2177

Motif 3
GAGCTTATAATGTTACTATTATTTTGTGTAGTTTATTCTTAT	0	10	1
TGTAGTTTATTCTTATTGTTATTTCTTGGTGTACCTGTAGCA	0	36	1
         AACTTTCTCCTTATTGATTATGTTTT       	2	3	0
CCAAAAAGAGTTTTTATGTTTCATAATCATATCATAGTTAAA	3	30	1
      TTGTTTTTCCTATTTGTTAGTTTTAACTCATAAAAG	4	229	0
GGGGCGCCTTTCTTTTTGCTTACTTTTTCTTTGGCGAAGCAA	5	183	1
TGTTTTGTCCTATTGTTTTTTAATTGAAAATTCTTCTTCGGT	5	266	0
        TTTTTTACTTATAGGTGTTCACTTGAACCGTCTA	6	2	1
TAGTCCATAGATTTTTTCCTTTTTAATCGCTTATCTTATTGA	6	151	1
CTTTTGCCGATATTGCTAATATTGGTTCGGTTCCAGTTGGAG	7	80	1
ATGCAACCAATTTTGTTTATAATTTTTTACAAAATACGATAA	7	148	0
TTTTTATTTCTCTCCCTATTAATTTTTGCCATTTTACGGTAT	9	73	0
          TATTTTTATTATTGAGAGACCTCTATAAATTT	9	226	0
ATTGAGTGCGTTTTATTTTTAGCTATAAATATCGTATAATCC	10	15	1
ATCCGATAGATTTTATTTGTTTATTTTTTGTAAGGTATCAAC	10	53	1
      TGTTTTTTCCTTCTGGCTTAAAAAATTGGCTTATTC	11	4	1
          TTTTTCTCCTAAATCTTGAGCTTATTTGTACT	12	157	0
         TTTTTATTCCTTTCTTGCCTAATGAAATTTGCG	13	1	1
TTGCTTGAAATATTTTTATTTCGTAGTAATTTTGAGTCGTTA	13	85	1
      TGCTTCTTCCTTATTGTTTTATATGTAAAAATAACG	13	122	0
          TGTTTCTTCTTTGTTCAATTAAAAATGTGGAC	14	0	1
          * ** **  **  *  *    *
MAP Score: 14.8546

Motif 4
GTTACTATTATTTTGTGTAGTTTATTCTTATTGTTATTTCTT	0	21	1
       AACTTTCTCCTTATTGATTATGTTTT         	2	1	0
TAACAAGTAATTTTATTCTGTCAATGGCATATAAGGAGTCTA	3	74	1
CGAGCGGGATTTTAGCATTATCTAAAATCTTTGGCTATGATT	4	48	0
       TTGTTTTTCCTATTTGTTAGTTTTAACTCATAAAA	4	230	0
CTTTTCCTTGTTTCCTTTGTTCCATTGAATTTGCCTTAACGG	5	139	0
      TATGTTTTGTCCTATTGTTTTTTAATTGAAAATTCT	5	274	0
GTCCATAGATTTTTTCCTTTTTAATCGCTTATCTTATTGAGT	6	153	1
CATTTGAAGATTTTCATCGTTCACAAATTAATTCATCTTTTG	7	44	1
CAACGGCATTTTTATCGTATTTTGTAAAAAATTATAAACAAA	7	137	1
AAATTGAACTTTTTTCTTCATCAGAACTCAAAAACAACGTTC	8	11	1
AAATGATGGGTTTAATATTTTCTCTGCCCAATTAAATTAGGC	8	56	0
TTTTTGCCATTTTACGGTATTCTATGCCACATTTTCTATTGT	9	51	0
CACCGCACTTTTTATTTCTCTCCCTATTAATTTTTGCCATTT	9	81	0
GTGCGGTGGTTTTTTAGTTGTTTTTTACAATAAATTTTCAAT	9	115	1
TATGAATTCCTTTGTTCTAATCTGTTCTGCAAAAATTGAAAA	9	149	0
ATCCGATAGATTTTATTTGTTTATTTTTTGTAAGGTATCAAC	10	53	1
CTGCCCAATTTTTATTTCAATTGATCGAGGTTAATC      	12	4	0
         TTTTTATTCCTTTCTTGCCTAATGAAATTTGCG	13	1	1
TTCGTAGTAATTTTGAGTCGTTATTTTTACATATAAAACAAT	13	104	1
ATGTGGACTATTTTCCCTGATTTTAGGTTTTTGCTCAAACGA	14	34	1
          ***    *  **  *  *  **
MAP Score: 14.5273

Motif 5
TATGGTCTGGTCGCACCACAAAATAGGCAATGTGA	4	153	0
TTTTCCACCTTTGTGGAATTGAATTTGTAGGAAAT	5	68	1
CTTGTTTCCTTTGTTCCATTGAATTTGCCTTAACG	5	140	0
TATGGTCTGTTGGGGCAACAGGAATTGGTGTGCAA	7	230	1
AATATTTTCTCTGCCCAATTAAATTAGGCAGAGAA	8	50	0
CAGAACAGATTAGAACAAAGGAATTCATAGCAAGC	9	162	1
  GATTAACCTCGATCAATTGAAATAAAAATTGGG	12	8	1
ACTATTAAAGTAGTACAAATAAATTTTGATTGCAA	12	125	0
TATTCCTTTCTTGCCTAATGAAATTTGCGTATAAT	13	14	1
TCTGAACTGGTCGAACAAATGAATTATTGCTTGAA	13	59	1
TGTTTCTTCTTTGTTCAATTAAAAATGTGGACTAT	14	10	1
TTTTAGGTTTTTGCTCAAACGAATTTGCAAATAAA	14	54	1
          * *  ***  *****
MAP Score: 12.0397

Motif 6
TACATTGCGAGCGGGATTTTAGCATTATCT	4	67	0
TTGAGTTTTGACCGCACTTTAAATCGGATA	5	16	1
CATCGGCGAAACCCGATTTTAATTACCGAA	5	242	1
ATAAGACCACACCGGATTATTTTCCGATGT	6	107	0
AAGCACTGCAACGGCATTTTTATCGTATTT	7	129	1
TTAAATTTTAACCGCACTTTTGCAGCATTT	9	19	1
CCGCACTTTTGCAGCATTTTGACAATAGAA	9	30	1
GGTATTCTATGCCACATTTTCTATTGTCAA	9	48	0
CTAAAAAACCACCGCACTTTTTATTTCTCT	9	102	0
GATATAATCTGCCCAATTTTTATTTCAATT	12	24	0
GCGTATAATAACGCGATTTTCTGAACTGGT	13	40	1
GGGAAAATAGTCCACATTTTTAATTGAACA	14	21	0
          **********
MAP Score: 10.9876

Motif 7
CATACACTAACCACTCTTTTATGAGTTAAA	4	214	1
TGAGTTTTGACCGCACTTTAAATCGGATAA	5	17	1
AAATTGGGTTCCCTTCTTTTCCACCTTTGT	5	52	1
AGAAAGGCGCCCCTACTTTTCCTTGTTTCC	5	166	0
AGTAGGGGCGCCTTTCTTTTTGCTTACTTT	5	179	1
CTTTCTTTTTGCTTACTTTTTCTTTGGCGA	5	190	1
CCGATGGCGAGCTTACTTTTTCTTTGCTTC	5	218	0
TAAATTTTAACCGCACTTTTGCAGCATTTT	9	20	1
TAAAAAACCACCGCACTTTTTATTTCTCTC	9	101	0
GGAAAATAGTCCACATTTTTAATTGAACAA	14	20	0
          **********
MAP Score: 10.2803

Motif 8
CTACAGGTACACCAAGAAATAACAATAAGAA	0	45	0
GTCTGGTCGCACCACAAAATAGGCAATGTGA	4	153	0
GTGCGACCAGACCATAAAATAGTTGCAAGTT	4	172	1
GTTGCAAGTTACTAAAAAATACATACACTAA	4	193	1
AAAACTAACAAATAGGAAAAACAA       	4	241	1
GTGCGGTCAAAACTCAAAATATT        	5	2	0
GAGCGTAGCGAGTTCAGAAAATTTCCGTTAA	5	115	1
GAACAAAGGAAACAAGGAAAAGTAGGGGCGC	5	159	1
TCTTTGCTTCGCCAAAGAAAAAGTAAGCAAA	5	197	0
TCTTTGGCGAAGCAAAGAAAAAGTAAGCTCG	5	210	1
CATTCCTTTAACATCGGAAAATAATCCGGTG	6	97	1
ATAAGCGATTAAAAAGGAAAAAATCTATGGA	6	154	0
AATTTAATTGGGCAGAGAAAATATTAAACCC	8	60	1
CAGCATTTTGACAATAGAAAATGTGGCATAG	9	41	1
TAGAAAATGTGGCATAGAATACCGTAAAATG	9	55	1
TAATAGGGAGAGAAATAAAAAGTGCGGTGGT	9	94	1
CAATTTTTGCAGAACAGATTAGAACAAAGGA	9	153	1
TTTTTAAGCCAGAAGGAAAAAACA       	11	3	0
TTTTCCTTCTGGCTTAAAAAATTGGCTTATT	11	14	1
TCATTAGGCAAGAAAGGAATAAAAA      	13	4	0
ACTCAAAATTACTACGAAATAAAAATATTTC	13	91	0
AAAACCTAAAATCAGGGAAAATAGTCCACAT	14	34	0
          **** ******
MAP Score: 1.87438