AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons002_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241634
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	pfrA	187	Peptide Chain Releasing Factor (RF-1)
#1	rl19	25	L19 Ribosomal Protein
#2	rnhB_2	63	Ribonuclease HII
#3	flhA	181	Flagellar Secretion Protein
#4	yscU	256	YopS Translocation Protein U
#5	rnc	108	Ribonuclease III
#6	CT309	166	hypothetical protein
#7	elaC	300	Sulphohydrolase/Glycosulfatase
#8	xerC	61	Integrase/recombinase
#9	sohB	102	Protease
#10	yscL	275	Yop Translocation L
#11	topA	300	DNA Topoisomerase I-Fused to SWI Domain
#12	CT663	300	hypothetical protein
#13	CT665	43	hypothetical protein
#14	CT666	26	hypothetical protein
#15	fliI	73	Flagellum-specific ATP Synthase
#16	fliF	272	Flagellar M-Ring Protein
#17	CT763	157	hypothetical protein
#18	ftsY	69	Cell Division Protein FtsY
#19	xerD	248	Integrase/recombinase

Motif 1
TCATAACGAGCTTTTTCTTGTGTTTAGGCT	7	86	1
ACTAATCTTGCTTTTTCTTTAGAATTTCTT	4	71	0
TTTGGTGCTTCTTTTTTTTGTATATATGGG	10	41	0
AAAAAAAAACCTTTTTCTTATACGATTATA	11	228	0
AGTTGTACAGCTTTTTCTTAAGGCTAACAC	4	19	1
 TTACAGTATCTTTCTCTTGTCTAGTATAT	3	162	0
CTAATCTTTTCTTTTTCCTTCTGGAGTCCT	3	10	0
TTTAGAATTTCTTTTTCCTTAATAATAAAA	4	54	0
TTCACACCCACTTTTTGTTTAATGAAACAG	11	108	0
CGCACAAAAGCTTTTTTTTAAAAAAAAAAC	11	248	0
TTAATAGCCTCTTTTTGTTACAGAAGACAA	16	67	1
CCCTATGAGCCGTTTTCTTTGAGGACTTCC	11	47	0
GAACCCCTTACTCTTTGTTTATAAATGGGA	4	146	1
TCTCTAATGACTCTTTTTTAAAAAATTACG	11	142	0
TTGAACAGAACTTTCTGTTATCTAGAGAAA	0	11	1
GTTTTAGTACCGTTTTGTTGCTA       	9	89	1
GCATTAAGCCCTTTCTGCTGTTCTCAACGT	2	26	1
TTTAATAAGTCTCTCTTTTTGAATCTGACT	0	69	1
TAATGCCGCTCTCTTTTCTTTA        	2	2	0
AGGAAATACGCTTTCTTCTATTCTAAAAAT	19	169	1
ACGAACGACTCGTTCTTTTGATTTCTAAAG	12	68	0
AAAAAGAAGGCTTCTTCTTGTGAACAAGAA	16	158	0
GATGAGAAATCGTTTTTCTTTTTAAAGTAG	12	177	1
   AGATACCCTCTCTTTTACCGTTTACA 	14	9	0
GCGAACACCCCGCTTTTTTTGTTTTAATAA	0	47	1
TAACAAGCGACTTCCTCTTGCTTGCAAGGT	7	229	0
AAAATATTGACGCTTTTTTAGAATTTCATA	17	68	1
CATCTGCCACCTTCTTTCTTGAGAAAAACA	4	180	1
CTAACACAGCCTTTTTATTATTAAGGAAAA	4	42	1
TTTTATTATTCTTTTTACTTCAATCAACTT	18	39	1
          **********
MAP Score: 33.5574

Motif 2
GTTCGCCCCGCTTTTCTCTAGATAACAGAAAG	0	21	0
TAATGCCGCTCTCTTTTCTTTA          	2	0	0
CTTAACTAATCTTTTCTTTTTCCTTCTGGAGT	3	13	0
TTTAGAATTTCTTTTTCCTTAATAATAAAAAG	4	52	0
CTAATCTTGCTTTTTCTTTAGAATTTCTTTTT	4	68	0
AGAACGGAATATTTTTTTTAAAGAGCGTTTTT	4	109	0
CATCTGCCACCTTCTTTCTTGAGAAAAACATT	4	180	1
GAGATAGTTCTTCTTTTCTCAACGCATACAAA	6	96	0
TTCTTATCCTCTCTTATTTATAAAACTTTTTA	7	11	1
GAAGTTATAATTTTTCTCTGAAACTGTGGAGA	7	121	1
CTTGAGAGATCTCTTCCTTAAAGAGGATATTG	7	277	1
CCAGGTCCTTTTCTTCTCAAGA          	9	0	0
TATTTAAAAATTCTTTTTATAATCCCCCTGTT	9	60	1
TTTGGTGCTTCTTTTTTTTGTATATATGGGAG	10	39	0
AAGGATCGCATTCTTTTTTACACAGAGATCGA	10	137	0
TTCACACCCACTTTTTGTTTAATGAAACAGCA	11	106	0
TCTCTAATGACTCTTTTTTAAAAAATTACGGT	11	140	0
ATATTAGTCCCTCTTCATTTAACTTTTATGAT	11	199	0
AAGAAAAAGGTTTTTTTTTTAAAAAAAAGCTT	11	239	1
TCGTGCCCGATTTTTTTCTAAAATTCTTTTGT	12	94	1
TGAGAAATCGTTTTTCTTTTTAAAGTAGGTAT	12	179	1
TTTTAATAGCCTCTTTTTGTTACAGAAGACAA	16	65	1
AAAAGAAGGCTTCTTCTTGTGAACAAGAAGAA	16	155	0
CTTTTTCATCCTTTTCTTTGTAGGATACTTAG	16	182	1
AAAATATTGACGCTTTTTTAGAATTTCATATA	17	68	1
ATTTCATATATTCTTCCCACAATCTTGGGCAA	17	90	1
TTTTATTATTCTTTTTACTTCAATCAACTTTG	18	39	1
          *********  *
MAP Score: 14.245

Motif 3
AGAACTTTCTGTTATCTAGAGAAAAGCGGGGCG	0	17	1
CCCCGCTTTTTTTGTTTTAATAAGTCTCTCTTT	0	54	1
TACTCTAGTATCTCTCTAACAAAGACCAGAGTG	0	145	0
CTAATCTTGCTTTTTCTTTAGAATTTCTTTTTC	4	67	0
CAAGATTAGTGCTTCATGAAAAACGCTCTTTAA	4	91	1
CATGAAAAACGCTCTTTAAAAAAAATATTCCGT	4	105	1
AAAATATTCCGTTCTCTAAAGAACCCCTTACTC	4	126	1
AACCCCTTACTCTTTGTTTATAAATGGGATGAG	4	147	1
TCTGCCACCTTCTTTCTTGAGAAAAACATTTAT	4	182	1
TGGTTAAATCGTTATTGGGAAAATTCGTTGACG	6	36	1
CTTATCCTCTCTTATTTATAAAACTTTTTAACT	7	13	1
CAGGTAGGAGTTTCTAGTTAAAAAGTTTTATAA	7	28	0
 TCAATATCCTCTTTAAGGAAGAGATCTCTCAA	7	278	0
GGTCTTTTAATTTTTATTTAAAAATTCTTTTTA	9	46	1
TTCTCCGATGGCTATGTTAAAAACGAGAGCGAT	10	87	1
AAAACCTCGATCTCTGTGTAAAAAAGAATGCGA	10	131	1
TCTAATGACTCTTTTTTAAAAAATTACGGTTCT	11	137	0
GAAAAAGGTTTTTTTTTTAAAAAAAAGCTTTTG	11	241	1
GGGATCTTAGTCTCTCGCACAAAAGCTTTTTTT	11	260	0
TCGTGCCCGATTTTTTTCTAAAATTCTTTTGTA	12	94	1
TATGCCAATACCTACTTTAAAAAGAAAAACGAT	12	185	0
CCTTTTGTCTTCTGTAACAAAAAGAGGCTATTA	16	68	0
TATACGTAGAGCTTTTGTAAGAACTTACTTCAT	16	244	1
   AGAGGTTTCTATCTCTAGAATTTTTCACCA	17	7	1
TATGGGCTAATTTATGGTGAAAAATTCTAGAGA	17	21	0
GTAGGAGGTCGCTATGTTGATAATAACGTTTCT	19	103	0
TGCTCGTGCTTTTATCTTGCAAATATTCCTAAT	19	218	1
          *** * * *****
MAP Score: 3.08414