AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_profile003_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243371
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	rl28	148	L28 Ribosomal Protein
#1	sycE	37	Secretion Chaperone
#2	yscU	256	YopS Translocation Protein U
#3	rl33	300	L33 Ribosomal Protein
#4	CT165	300	hypothetical protein
#5	CT167	55	hypothetical protein
#6	CT168	65	hypothetical protein
#7	trpR	55	Trp Operon Repressor
#8	dsbD	152	Thio:disulfide Interchange Protein
#9	amn	219	AMP Nucleosidase
#10	mrsA	245	Phosphoglucomutase
#11	tyrP_1	51	Tyrosine Transport

Motif 1
CTCTTCTAAGCTTTGTCCAGAAGAATGTCGCGA	9	53	1
AGAAGGATTTTTTTATCAAAAAATCATTTTCTC	3	80	1
 GAATGAACCTTTTCTCAAGAAAATGCTAAATC	3	278	0
ATATAAATGTTTTTCTCAAGAAAGAAGGTGGCA	2	184	0
TAGAGAATCTTTTTTTCTAAAAACATAGTATGA	9	174	0
AGTTGTACAGCTTTTTCTTAAGGCTAACACAGC	2	19	1
ACTAATCTTGCTTTTTCTTTAGAATTTCTTTTT	2	68	0
CTAGCAATATCTTTTTTAATAAGACTATACATA	3	137	0
TTTTCTATGATGTTTTCAACAAGGTTGGATTAG	4	114	0
ACCCCTTACTCTTTGTTTATAAATGGGATGAGC	2	148	1
AAAAATATTCCGTTCTCTAAAGAACCCCTTACT	2	125	1
TTTTCTGCCACTTTTTCACGAAAACTTCTTCCC	0	41	1
AACACAGCCTTTTTATTATTAAGGAAAAAGAAA	2	44	1
CCTTGAGTACTTTTATTTTGAAACACATTTTCT	0	14	1
GAACGGAATATTTTTTTTAAAGAGCGTTTTTCA	2	107	0
TGGAACAAGTTGTTCTCGTGAGGGTAATAGTTG	9	138	0
AAAAGAGTTGTTTTATCCAGTAATTTA      	3	4	0
AGGAAAACTTCTTTATCAACTGGATTTCAATAA	4	83	0
CTGTGAGGAATTTTCTCTTGTAGCAACAATCGG	4	277	0
GATTACGATTTGTTTTTAACAGGTAATAACAAA	4	230	1
CGCTTTCCCTCTTTCTTGCAAAAGAAAACTATA	9	92	1
TCTATGTTATCGTTCTCTTCTAAGCTTTGTCCA	9	39	1
ATCTACAGTTTTTTCTCTCTTGATGAATAGCAT	11	11	1
          **** ** * ***
MAP Score: 24.6608

Motif 2
CTTCCCGATATATTAAAAAAGGTCTAACATA	0	68	1
TGTATAGTCTTATTAAAAAAGATATTGCTAG	3	139	1
TTTTCCTTAATAATAAAAAGGCTGTGTTAGC	2	41	0
TCATCCCATTTATAAACAAAGAGTAAGGGGT	2	148	0
TTTTTATTATTAAGGAAAAAGAAATTCTAAA	2	53	1
AAAGAAATTCTAAAGAAAAAGCAAGATTAGT	2	70	1
TATTATAGCATTACAAAAAGGTGCGAT    	7	38	1
GTAAAAACTGTAATAAAAAGAGCGCACTTCC	1	13	1
AGGGCAACTGTAACAAAAAGAAACTATGTTA	0	92	0
TACTATGTTTTTAGAAAAAAAGATTCTCTAA	9	177	1
TGTGTTAGCCTTAAGAAAAAGCTGTACAACT	2	19	0
AGGATTTTTTTATCAAAAAATCATTTTCTCA	3	83	1
ATTCATTACATACCAAAAAGGATCTTGGTTC	8	66	0
AAAAACGCTCTTTAAAAAAAATATTCCGTTC	2	109	1
AAATAAGAAGTAAGAAAATAATTATCGAAAA	10	36	0
TATTACCTGTTAAAAACAAATCGTAATCACC	4	227	0
TTTTAACAGGTAATAACAAATACCCGTTCCG	4	243	1
TCTATGATGTTTTCAACAAGGTTGGATTAGG	4	113	0
CTTGATTATTTTTGAAAATAGGTATAGCATA	3	241	1
        AAAAACAAAAAAAATAAATCATT	10	2	1
AAAAATACGAAAACAAAAAAATCCCGCTCAA	4	164	0
AGAAAATGTGTTTCAAAATAAAAGTACTCAA	0	16	0
          *** *******
MAP Score: 14.1727

Motif 3
ATATCGGGAAGAAGTTTTCGTGAAAAAGTGGCA	0	46	0
TATTAAGGAAAAAGAAATTCTAAAGAAAAAGCA	2	60	1
ACCGTATATAAATGTTTTTCTCAAGAAAGAAGG	2	189	0
GGTAACTTGCGAAGTATTCCTTATAGCGCTTAA	2	219	1
GTAAGAGAAGAAGGATTTTTTTATCAAAAAATC	3	72	1
ACGGTGAGAAAATGATTTTTTGATAAAAAAATC	3	85	0
CCTATCCACTAAGGTTTTATTGAAATCCAGTTG	4	67	1
AGTTGATAAAGAAGTTTTCCTAATCCAACCTTG	4	95	1
TTTGGTATGTAATGAATTGCAAAAACAAAAACA	8	80	1
TCTGTTGTTTGATGATTTGCTAAACCGGAGAGA	8	118	1
TTTTAGAAAAAAAGATTCTCTAACCATTATAAT	9	185	1
AGTTTTCGATAATTATTTTCTTACTTCTTATTT	10	34	1
GGCGAATTGCAAAGATTTTGATAAAAATAGGGA	10	156	1
TTTTGAGCCAAAGGATATTCTTAGGGATAGAGC	10	221	1
          ** ***** ** *
MAP Score: 9.21335

Motif 4
TTCTGCCACTTTTTCACGAAAACTTCTTCCCG	0	43	1
GGCTGTGTTAGCCTTAAGAAAAAGCTGTACAA	2	21	0
GAAAAAGAAATTCTAAAGAAAAAGCAAGATTA	2	67	1
CAAGATTAGTGCTTCATGAAAAACGCTCTTTA	2	91	1
GAAAAACGCTCTTTAAAAAAAATATTCCGTTC	2	108	1
GCCACCTTCTTTCTTGAGAAAAACATTTATAT	2	185	1
GAAAATGATTTTTTGATAAAAAAATCCTTCTT	3	79	0
AGTATGTATAGTCTTATTAAAAAAGATATTGC	3	135	1
GCTATACCTATTTTCAAAAATAATCAAGATCT	3	237	0
AATGAACCTTTTCTCAAGAAAATGCTAAATCA	3	277	0
TCATACTATGTTTTTAGAAAAAAAGATTCTCT	9	174	1
GCCATTCACTTTTTAAATAAGAAGTAAGAAAA	10	49	0
CCAGATTGATGTTTGAGGAAAGGTCTTAAGAA	10	124	1
TTGAGGAAAGGTCTTAAGAAGGCGAATTGCAA	10	136	1
ATTGCAAAGATTTTGATAAAAATAGGGAATAT	10	161	1
GTTTTTTCTCTCTTGATGAATAGCATAAGCGT	11	18	1
          **** * *****
MAP Score: 8.4002

Motif 5
       AACACGCTTAACCCGTTATCTTTTCTC	9	3	1
CGCGAAACAAACGCTTTCCCTCTTTCTTGCAAAA	9	81	1
AAGGTGGCAGATGCTCATCCCATTTATAAACAAA	2	159	0
TAAGATACAGACGCTTATGCTATTCATCAAGAGA	11	26	0
ATCAGCCCCTATGCTATACCTATTTTCAAAAATA	3	247	0
CTTAAGATTGATGCTTCCTCTGTTTTCTACTCCT	5	19	0
TAATCAAGATCTGCTCTCGCATTTATTCAAAGAG	3	215	0
AAAAGAAACTATGTTAGACCTTTTTTAATATATC	0	74	0
TGATAAAAAAATCCTTCTTCTCTTACACCTAAAA	3	64	0
AGAGTTGTTTTTGTTTTTGCAATTCATTACATAC	8	84	0
AGCATAGGGGCTGATTTAGCATTTTCTTGAGAAA	3	266	1
AGATGGCCAGTTGCTTAAGCGCTATAAGGAATAC	2	232	0
          ******  **  **
MAP Score: 3.90082