AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons023_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238223
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	guaB	300	Inosine 5'-monophosphase dehydrogenase
#1	ubiA	300	Benzoate Octaphenyltransferase
#2	rl28	216	L28 Ribosomal Protein
#3	CPn0328	26	CT085 hypothetical protein
#4	CPn0329	92	Phopholipase D  Superfamily

Motif 1
AACATTTAAGTCTTTTTATAGTAAGAACCT	2	22	1
AGGGGGTTCGTCTTTTTATGCCTCTACTGT	1	177	0
ATCCCCCCAATCTTTTTAGAACCCCCTATG	1	209	0
ACTTCGCTCATATTTTTATGTAAGATTCCC	0	174	0
ATAGCTTTTTTGTTTTTATATATTTTTAAA	4	58	0
ATGAAGGAATTCTTTTAAGAAAGACGGTCG	2	70	0
TTAAATTAGTTATTTTTATTTTTAAAAATA	4	38	1
TCTATATAATTATTTTTTTATTTATAAAAA	1	269	0
ACAAAAAAGCTATTTTAAGAGTAAAAA   	4	75	1
     GATGTTCTTTTAATCCCCCAATATT	0	5	1
GAGAGGAGTATATTTTTTTTATAAATAAAA	1	254	1
AAGACTTAAATGTTTTATTGCTATCC    	2	6	0
TGTTTTTATATATTTTTAAAAATAAAAATA	4	48	0
AAAGAATCGGTATATTTAGAGAGAGGGTTT	0	80	0
          **********
MAP Score: 12.5259

Motif 2
CGGCCATTTCAAAAACCCTCTCTCTAAATAT	0	68	1
GCGAAGTAGAACAAAGCTCATCTGTGAGAAA	0	197	1
AGAAAAATTAAAGAAGCCTATCCTTAAGCTC	0	223	1
TTGTCAAAACAAAAATCCTTTTA        	1	2	0
TGGTCCTTAAACAAAACTCCTAACGCCAAGA	1	55	0
GCATAAAAAGACGAACCCCCTAACATAGGGG	1	186	1
CCAATCTTTTTAGAACCCCCTATGTTAGGGG	1	202	0
TTTTTATAGTAAGAACCTTATAATAATTTCC	2	34	1
ACATTTTCTAAGAAAACCTCTTCCCCATATA	2	118	1
         TAAGAATCTTATTCTATTAAAC	4	1	1
ATATAAAAACAAAAAAGCTATTTTAAGAGTA	4	67	1
          ***** *****
MAP Score: 10.72

Motif 3
AATATTGGGGGATTAAAAGAACATC         	0	1	0
TCAGAAGGAAGTATTTCAGAATATTGGGGGATTA	0	20	0
AACAAAGCTCATCTGTGAGAAAAATTAAAGAAGC	0	206	1
ATTATGAAGTGCTTGTCAAAACAAAAATCCTTTT	1	11	0
GGAACTTTTTGGATTTAAGAAAAATGTATCGCAC	1	126	1
TAACATAGGGGGTTCTAAAAAGATTGGGGGGATC	1	206	1
TTATTTTTTTATTTATAAAAAAAATATACTCCTC	1	256	0
ATGAAGGAATTCTTTTAAGAAAGACGGTCGTTCC	2	66	0
GGGGAAGAGGTTTTCTTAGAAAATGTGATTGTCT	2	110	0
TTTATTGAGCGGATGTTAGAGAATTCATAGGAAG	2	189	1
TTAATTAAACGTTTAATAGAATAAGATTCTTA  	4	8	0
GTTTTTATATATTTTTAAAAATAAAAATAACTAA	4	43	0
ATTTTTAAAAATATATAAAAACAAAAAAGCTATT	4	55	1
ACAAAAAAGCTATTTTAAGAGTAAAAA       	4	75	1
          * ** * **** **
MAP Score: 10.1393

Motif 4
GTTCTTTTAATCCCCCAATATTCTGAAATA	0	13	1
CATTTCAAAAACCCTCTCTCTAAATATACC	0	72	1
CACAAGAACTACCCTCTATACGAAAGAACA	1	95	1
AAAAAGACGAACCCCCTAACATAGGGGGTT	1	190	1
TCTTTTTAGAACCCCCTATGTTAGGGGGTT	1	199	0
CGGGGGTGATCCCCCCAATCTTTTTAGAAC	1	217	0
TGGGGGGATCACCCCCGATGAATAGAGAGG	1	230	1
GAAAACCTCTTCCCCATATATTCGAAAAGC	2	129	1
          **********
MAP Score: 8.74394

Motif 5
GATGTTCTTTTAATCCCCCAATATTCTGAAA	0	10	1
AGCCTATCCTTAAGCTCCCATAGGAGCCGCT	0	237	1
ATGCGCTCTTGAAATTCCTAAAGGACCAATG	0	273	0
GTCCTTAAACAAAACTCCTAACGCCAAGACA	1	53	0
ATAAAAAGACGAACCCCCTAACATAGGGGGT	1	188	1
AATCTTTTTAGAACCCCCTATGTTAGGGGGT	1	200	0
CATCGGGGGTGATCCCCCCAATCTTTTTAGA	1	219	0
TTCTTCCTATGAATTCTCTAACATCCGCTCA	2	194	0
       AAATATTTCCCTATACTTAAGTTA	3	12	0
          *** *******
MAP Score: 8.47942

Motif 6
ATGTTCTTTTAATCCCCCAATATTCTGAAA	0	11	1
ATTCTGAAATACTTCCTTCTGAAGTGTCCT	0	32	1
CCATTTCAAAAACCCTCTCTCTAAATATAC	0	71	1
TAAATATACCGATTCTTTCAGCTGCTATGG	0	92	1
AGATTCCCAAACCACCTTCTTGAGCTAAAG	0	152	0
GCTTTGTTCTACTTCGCTCATATTTTTATG	0	184	0
GCGCTCTTGAAATTCCTAAAGGACCAATGC	0	272	0
TCAAAACAAAAATCCTTTTA          	1	0	0
ATGCACAAGAACTACCCTCTATACGAAAGA	1	92	1
TAAAAAGACGAACCCCCTAACATAGGGGGT	1	189	1
ATCTTTTTAGAACCCCCTATGTTAGGGGGT	1	200	0
CATCGGGGGTGATCCCCCCAATCTTTTTAG	1	220	0
AAAAAAATATACTCCTCTCTATTCATCGGG	1	243	0
TTCTTAAAAGAATTCCTTCATTATCAACAA	2	79	1
TCTTCCTATGAATTCTCTAACATCCGCTCA	2	194	0
          **********
MAP Score: 3.96698

Motif 7
TGGGAATCTTACATAAAAATATGAGCGAAGT	0	173	1
GTGCTTGTCAAAACAAAAATCCTTTTA    	1	6	0
AATGGTCCTTAAACAAAACTCCTAACGCCAA	1	57	0
TTTATTTATAAAAAAAATATACTCCTCTCTA	1	252	0
TTTTTTTTATAAATAAAAAAATAATTATATA	1	266	1
ATATTTTTAAAAATAAAAATAACTAATTTAA	4	38	0
          *** *******
MAP Score: 2.10377