AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons039_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238717
 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
CTTTGAAATATATTCGTTCTGTATTATGGTAG	1	147	1
TAGTAGTCCGTATTCATTTTCTATTCATACAA	1	176	1
ATCCCAAGATTAATCTTTCTGTTTCACTAATG	1	68	0
TGCTATATCATAATCCTTATCTCCAAATGCAT	1	33	1
CATGAACTCCTACTCATTGTATGAATAGAAAA	1	192	0
AGAGTCCTTCGATTCCTGATGTACATTCTTCT	2	139	1
TTAAAAATTCTTTTCTTTTTATACAAAAATCC	1	96	0
CTGGTTGATGTATTCATGAACTCCTACTCATT	1	206	0
TTTAACTTTCTACTATTTATATTTACTGGTTG	1	231	0
GCAATCTATTTCTTAATTTTCTTCGATTTATG	2	196	0
          ***** ** ***
MAP Score: 7.01521

Motif 4
    GGAGGTTAGAATCACAATATATTTGCTATA	1	6	1
TTTTCATTAGTGAAACAGAAAGATTAATCTTGGG	1	64	1
CTTTTTATACAAAAATCCCAAGATTAATCTTTCT	1	80	0
GATTTTTGTATAAAAAGAAAAGAATTTTTAATAA	1	97	1
ATACAATGAGTAGGAGTTCATGAATACATCAACC	1	202	1
TATAAATAGTAGAAAGTTAAAGCTCACTCTACTT	1	242	1
GCTAAGAATCTGAGAAGAAAACATTACAAAGGAG	2	15	0
GAGAAACGATAAGAATGCTAAGAATCTGAGAAGA	2	31	0
AAAAAATCCTAGAAATCAAAAGATAGAATTCTGA	2	73	1
CTTCTGGACAAAGGAGAAAAAGCTCGATAACATA	2	166	1
ACATAAATCGAAGAAAATTAAGAAATAGATTGCT	2	195	1
          *****    *****
MAP Score: 5.60716

Motif 5
AATCACAATATATTTGCTATATCATAATCCTTATCT	1	19	1
GAAAGATTAATCTTGGGATTTTTGTATAAAAAGAAA	1	81	1
GTTCAATGGTTCTTTGAAATATATTCGTTCTGTATT	1	136	1
TGGTAGTAGTCCGTATTCATTTTCTATTCATACAAT	1	173	1
   ACGCTCTCCTTTGTAATGTTTTCTTCTCAGATT	2	7	1
CTTCTCAGATTCTTAGCATTCTTATCGTTTCTCGGT	2	32	1
TTCTTAATTTTCTTCGATTTATGTTATCGAGCTTTT	2	183	0
          **** *  ** *  **
MAP Score: 3.60399