AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_profile004_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243403
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	rl33	300	L33 Ribosomal Protein
#1	CT151	35	hypothetical protein
#2	kdsB	300	CMP-2-keto-3-deoxyoctulosonic acid synthetase
#3	leuS	196	Leucyl tRNA Synthetase
#4	yrbH	31	GutQ/KpsF Family Sugar-P Isomerase
#5	sucB_2	245	Dihydrolipoamide Succinyltransferase
#6	pcnB_1	214	PolyA Polymerase
#7	lpxB	60	Lipid A Disaccharide Synthase
#8	lpxC	100	UDP-3-O-Acyl GlcNAc Deacetylase
#9	exbB	152	polysaccharide transporter

Motif 1
GATGCCAGGCAAAAAGAGTTGTTTTATCCAGT	0	16	0
GGTGTAAGAGAAGAAGGATTTTTTTATCAAAA	0	69	1
GACACGGTGAGAAAATGATTTTTTGATAAAAA	0	89	0
TAGTCTTATTAAAAAAGATATTGCTAGAATTT	0	143	1
ATTTTCTTGAGAAAAGGTTCATTC        	0	286	1
GAGAGCCTATGAGAAGGCTTGTAAATATCTAG	2	45	0
CCAATAAGTTAAGAAAGCTAGTAGCTCTGTGA	2	137	1
ATCGCATTAAAAAAAAGATGATGGATTCGCAG	3	57	1
CGCTATATTAAAAAAATGTCTT          	4	0	0
ATCTTTTAACGAAGAGGGTTTTCTCTCTTCGT	5	12	1
CTCAATATGAGAAGAAGATTATCAACTGGCTT	5	179	0
AGTTCTCTCCAGGAAAGCTCTTCCTATAATAG	6	131	0
GTCCTTGAGCAAGAAGGCTTTTAGAGTTCTCT	6	155	0
ATCGATAGGGGAGAAGAATTTTCCCAATTTCA	7	21	0
GCTAAAAAAAAAAAAGGATAATATACGGGGTC	8	60	1
ATTACATACCAAAAAGGATCTTGGTTCTATAC	9	79	1
GGTTCTATACAAGAAATTTGTTAGGATCGTCT	9	101	1
          ******* * **
MAP Score: 15.6023

Motif 2
TTTTGCCTGGCATCAAATAATTATTTGTCG	0	34	1
AGGATTTTTTTATCAAAAAATCATTTTCTC	0	83	1
TGTATAGTCTTATTAAAAAAGATATTGCTA	0	139	1
GCTATACCTATTTTCAAAAATAATCAAGAT	0	239	0
TCAAATACATTATCCAATAAGTTAAGAAAG	2	124	1
ACCAGGATCGCATTAAAAAAAAGATGATGG	3	51	1
TTCACCGCTATATTAAAAAAATGTCTT   	4	7	0
TTTTCTGTGGTTTCAAAAAATGTTTAGTGT	5	65	1
CACCTATATGTTTCTAAAAATTTTCAAGGG	6	74	0
AAGCAAGCGATATCAAAAAATTACTACCTA	8	30	0
TTTAGCAAATCATCAAACAACAGAAGAGTT	9	30	1
          **********
MAP Score: 10.3916

Motif 3
CTTTAGACACGGTGAGAAAATGATTTTTTGATAAAA	0	90	0
TGAATAAATGCGAGAGCAGATCTTGATTATTTTTGA	0	220	1
GAATATGTTTGGTAAGGGCCTACTGTATAAGAAGTT	2	238	1
TAAAGATTGGGGAAAGGGAAGTGTATACCAGGATCG	3	25	1
TTCGCAGACTGGAGAGGACTTGATTTCGATCTCAGA	3	82	1
GCGGTTGTAAGGAGAGAAAACCTTAAAAATAACAAC	3	158	1
ATCTTTTAACGAAGAGGGTTTTCTCTCTTCGTTTTC	5	12	1
ACCGCCTTCAGGTGAGTGTACAGATTTTCATGTTAT	5	112	1
        AAGGAGAGAGAGTCATAAAGCTGTTGAT	6	2	1
GTTCTCTCCAGGAAAGCTCTTCCTATAATAGAAAAA	6	126	0
GAGCTTTCCTGGAGAGAACTCTAAAAGCCTTCTTGC	6	143	1
TTGCTAAACCGGAGAGAGTGTTGTGTTT        	9	2	0
TCAAACAACAGAAGAGTTGTTTTTGTTTTTGCAATT	9	42	1
          ****** *  *  * *
MAP Score: 9.26782

Motif 4
GCCAGGCAAAAAGAGTTGTTTTATCCAGTAATT	0	12	0
GGTGTAAGAGAAGAAGGATTTTTTTATCAAAAA	0	69	1
ACACGGTGAGAAAATGATTTTTTGATAAAAAAA	0	87	0
GTCTTATTAAAAAAGATATTGCTAGAATTTAGG	0	145	1
CCTACTGTATAAGAAGTTTTGCTTCTTAGGTGG	2	256	1
          AAGACATTTTTTTAATATAGCGG	4	0	1
TCTTTTAACGAAGAGGGTTTTCTCTCTTCGTTT	5	13	1
TTTAAGGTTTAAGCGTCTTTTCTGTGGTTTCAA	5	48	1
TTAAACCCTCAAAAGGCATTTTTTATCTGTAAA	5	147	1
TTGCCCTTGTAAACGTAATTTTTTCTATTATAG	6	107	1
GTCCTTGAGCAAGAAGGCTTTTAGAGTTCTCTC	6	154	0
CAAACAACAGAAGAGTTGTTTTTGTTTTTGCAA	9	43	1
GTATAGAACCAAGATCCTTTTTGGTATGTAATG	9	78	0
          *****   *****
MAP Score: 7.34137

Motif 5
TGTTTGACGCTTATTTCTCTCTAAGTGCAAGGCG	3	127	1
TCAAAAGGCATTTTTTATCTGTAAAAGCCAGTTG	5	155	1
ATGTATTTGATTATTTTTCACGAATGAAACGCGG	2	100	0
GAAGAAGGATTTTTTTATCAAAAAATCATTTTCT	0	78	1
GTTTTCTCTCTTCGTTTTCTTTAAGGTTTAAGCG	5	29	1
AAGGCACGTCTTTTTGATCATCAACAGCTTTATG	6	23	0
ACCAAGATCCTTTTTGGTATGTAATGAATTGCAA	9	70	0
AAAAAGGATCTTGGTTCTATACAAGAAATTTGTT	9	89	1
ATTATCCTTTTTTTTTTTTAGCAAGCAAGCGATA	8	48	0
TGTACAGATTTTCATGTTATTAAACCCTCAAAAG	5	128	1
TCTAAAAGCCTTCTTGCTCAAGGACAAAATCCTC	6	162	1
          ** *** ***  **
MAP Score: 5.84613

Motif 6
CCAGGCAAAAAGAGTTGTTTTATCCAGTAA	0	14	0
TAAGAGAAGAAGGATTTTTTTATCAAAAAA	0	73	1
CGGTGAGAAAATGATTTTTTGATAAAAAAA	0	87	0
AAAAATAATCAAGATCTGCTCTCGCATTTA	0	224	0
GGGCTGATTTAGCATTTTCTTGAGAAAAGG	0	273	1
CTGCGAATCCATCATCTTTTTTTTAATGCG	3	59	0
TGTTATTTTTAAGGTTTTCTCTCCTTACAA	3	162	0
TTTAACGAAGAGGGTTTTCTCTCTTCGTTT	5	16	1
TTAAGGTTTAAGCGTCTTTTCTGTGGTTTC	5	49	1
TGTTACACTAAACATTTTTTGAAACCACAG	5	69	0
ACCCTCAAAAGGCATTTTTTATCTGTAAAA	5	151	1
AAGCCAGTTGATAATCTTCTTCTCATATTG	5	179	1
GAAGGCTTTTAGAGTTCTCTCCAGGAAAGC	6	145	0
AAAAGTCTGGAGGATTTTGTCCTTGAGCAA	6	175	0
ATAGGGGAGAAGAATTTTCCCAATTTCAAA	7	19	0
TCTCTTTGTCAGGGTTTTGC          	8	90	1
CTGTTGTTTGATGATTTGCTAAACCGGAGA	9	23	0
AAACAACAGAAGAGTTGTTTTTGTTTTTGC	9	44	1
GAAATTTGTTAGGATCGTCTAGGAACTCGT	9	113	1
          **********
MAP Score: 4.07838

Motif 7
GAAGAAGGATTTTTTTATCAAAAAATCATT	0	78	1
TAGCAATATCTTTTTTAATAAGACTATACA	0	139	0
AACGTTGCACTTTCTGAACCAAGATCTTAC	0	177	0
ATCTTGATTATTTTTGAAAATAGGTATAGC	0	239	1
AGCTACTAGCTTTCTTAACTTATTGGATAA	2	133	0
CACTAAACATTTTTTGAAACCACAGAAAAG	5	64	0
TCAAAAGGCATTTTTTATCTGTAAAAGCCA	5	155	1
AATCTCCTTATTTCTGAACTCGAAGGCTTT	5	224	0
AAGGCACGTCTTTTTGATCATCAACAGCTT	6	27	0
ATCCTCCAGACTTTTTAACTTTCAATGTCA	6	190	1
   CCATTCCTATTTGAAATTGGGAAAATT	7	7	1
ATAGCAAGTGTTTTAGAACTAGGTAGTAAT	8	11	1
AGGTAGTAATTTTTTGATATCGCTTGCTTG	8	31	1
GTTGTTTTTGTTTTTGCAATTCATTACATA	9	57	1
          **********
MAP Score: 3.93931

Motif 8
TAAGAGAAGAAGGATTTTTTTATCAAAAAATCATTT	0	73	1
TGTATGATTTATGATGTTATTTACTATTTTTC    	2	6	0
CATCCTAACAAGGAGATCGTTAACAATCAAGATTAT	2	169	0
CTTCTTAGGTGGGACGTCATTAATGGGGGTGCG   	2	277	1
ATTGGGGAAAGGGAAGTGTATACCAGGATCGCATTA	3	30	1
TCTAAGTGCAAGGCGGTTGTAAGGAGAGAAAACCTT	3	146	1
AGTGTAACATAGGGAGTGCTTAACCGCCTTCAGGTG	5	90	1
ATGCCTTTTGAGGGTTTAATAACATGAAAATCTGTA	5	130	0
AACCCTCAAAAGGCATTTTTTATCTGTAAAAGCCAG	5	150	1
CTGAACTCGAAGGCTTTAGTATTCTGTTAACTCAAT	5	205	0
TTTCTATTATAGGAAGAGCTTTCCTGGAGAGAACTC	6	128	1
TTTTAGAACTAGGTAGTAATTTTTTGATATCGCTTG	8	21	1
CTGTTGTTTGATGATTTGCTAAACCGGAGAGAGTGT	9	17	0
          ***  **  *** * *
MAP Score: 2.71661

Motif 9
AGAGAGCCTATGAGAAGGCTTGTAAATATCTAG	2	45	0
TCCAATAAGTTAAGAAAGCTAGTAGCTCTGTGA	2	136	1
TGTACACTCACCTGAAGGCGGTTAAGCACTCCC	5	101	0
TATTAAACCCTCAAAAGGCATTTTTTATCTGTA	5	145	1
TATTTCTGAACTCGAAGGCTTTAGTATTCTGTT	5	213	0
GGAGAGAGAGTCATAAAGCTGTTGATGATCAAA	6	12	1
GAGTTCTCTCCAGGAAAGCTCTTCCTATAATAG	6	131	0
TGTCCTTGAGCAAGAAGGCTTTTAGAGTTCTCT	6	155	0
          *  ******* **
MAP Score: 2.56277