AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons039_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238728
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	accB	22	Biotin Carboxyl Carrier Protein
#1	rpe	300	Ribulose-P Epimerase
#2	efp_2	221	Elongation Factor P

Motif 1
ATGCATTTGGAGATAAGGATTATGATATAGCAAAT	1	30	0
TTCTTTTTATACAAAAATCCCAAGATTAATCTTTC	1	81	0
GGATTTTTGTATAAAAAGAAAAGAATTTTTAATAA	1	96	1
TACAGAACGAATATATTTCAAAGAACCATTGAACA	1	135	0
TTTTCTATTCATACAATGAGTAGGAGTTCATGAAT	1	192	1
CAACCAGTAAATATAAATAGTAGAAAGTTAAAGCT	1	231	1
TCTGAGAAGAAAACATTACAAAGGAGAGCGT    	2	6	0
CGAGAAACGATAAGAATGCTAAGAATCTGAGAAGA	2	31	0
CTCGGTCATTAAAAAAATCCTAGAAATCAAAAGAT	2	62	1
AAATCAAAAGATAGAATTCTGATAAGGGACAGCTG	2	85	1
AGAATGTACATCAGGAATCGAAGGACTCTCCTTCT	2	133	0
AAGCTCGATAACATAAATCGAAGAAAATTAAGAAA	2	185	1
          * * ** **  ****
MAP Score: 15.8404

Motif 2
TTTCATTAGTGAAACAGAAAGATTAATCTT	1	65	1
GATTTTTGTATAAAAAGAAAAGAATTTTTA	1	97	1
AAAGAATTTTTAATAAGAAATGTTCAATGG	1	115	1
ACTCATTGTATGAATAGAAAATGAATACGG	1	183	0
ATTCATACAATGAGTAGGAGTTCATGAATA	1	198	1
CCAGTAAATATAAATAGTAGAAAGTTAAAG	1	234	1
AAGAAAACATTACAAAGGAGAGCGT     	2	5	0
GCTAAGAATCTGAGAAGAAAACATTACAAA	2	19	0
TGCAATCATTTACATAGAAGGAGAGTCCTT	2	118	1
ATGTACATCAGGAATCGAAGGACTCTCCTT	2	135	0
CATTCTTCTGGACAAAGGAGAAAAAGCTCG	2	162	1
CTCGATAACATAAATCGAAGAAAATTAAGA	2	188	1
          **********
MAP Score: 9.55814

Motif 3
TTTTCATTAGTGAAACAGAAAGATTAATCTTGGGATTTTTG	1	64	1
ACTACTACCATAATACAGAACGAATATATTTCAAAGAACCA	1	142	0
CTTGGGATTTTTGTATAAAAAGAAAAGAATTTTTAATAAGA	1	92	1
AAAAGCTCGATAACATAAATCGAAGAAAATTAAGAAATAGA	2	183	1
CTGCAATCATTTACATAGAAGGAGAGTCCTTCGATTCCTGA	2	117	1
GAAAATGCATTTGGAGATAAGGATTATGATATAGCAAATAT	1	28	0
TTCATTTTCTATTCATACAATGAGTAGGAGTTCATGAATAC	1	188	1
ATCAACCAGTAAATATAAATAGTAGAAAGTTAAAGCTCACT	1	229	1
AAAGAATTTTTAATAAGAAATGTTCAATGGTTCTTTGAAAT	1	115	1
          *   * * ** **  *   **
MAP Score: 6.51042

Motif 4
CATTTGGAGATAAGGATTATGATATAGCAAATA	1	29	0
ATCCCAAGATTAATCTTTCTGTTTCACTAATGA	1	67	0
CATTTCTTATTAAAAATTCTTTTCTTTTTATAC	1	104	0
ATATATTCGTTCTGTATTATGGTAGTAGTCCGT	1	154	1
ATGGTAGTAGTCCGTATTCATTTTCTATTCATA	1	172	1
AGAGTGAGCTTTAACTTTCTACTATTTATATTT	1	239	0
TCTCCTTTGTAATGTTTTCTTCTCAGATTCTTA	2	14	1
TCTCAGATTCTTAGCATTCTTATCGTTTCTCGG	2	34	1
AATTCTATCTTTTGATTTCTAGGATTTTTTTAA	2	70	0
AAATCAAAAGATAGAATTCTGATAAGGGACAGC	2	85	1
AGGAGAGTCCTTCGATTCCTGATGTACATTCTT	2	136	1
CTTAATTTTCTTCGATTTATGTTATCGAGCTTT	2	184	0
          AAAGCAATCTATTTCTTAATTTT	2	208	0
          * ** ****** *
MAP Score: 1.89033

Motif 5
GATAAGGATTATGATATAGCAAATATATTGTGATT	1	19	0
AAAATGCATTTGGAGATAAGGATTATGATATAGCA	1	33	0
GCATTTTCATTAGTGAAACAGAAAGATTAATCTTG	1	61	1
TTGGGATTTTTGTATAAAAAGAAAAGAATTTTTAA	1	93	1
TCATTGTATGAATAGAAAATGAATACGGACTACTA	1	176	0
AAATATAAATAGTAGAAAGTTAAAGCTCACTCTAC	1	239	1
CCGAGAAACGATAAGAATGCTAAGAATCTGAGAAG	2	32	0
TTAAAAAAATCCTAGAAATCAAAAGATAGAATTCT	2	70	1
AAGAATGTACATCAGGAATCGAAGGACTCTCCTTC	2	134	0
TTCTGGACAAAGGAGAAAAAGCTCGATAACATAAA	2	167	1
AAAGCTCGATAACATAAATCGAAGAAAATTAAGAA	2	184	1
TCGAAGAAAATTAAGAAATAGATTGCTTT      	2	202	1
          *  *****  *** *
MAP Score: 1.74089