AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons024_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238253
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ribC	255	Riboflavin Synthase
#1	CPn0869	43	CT728 hypothetical protein
#2	serS_ribD	43	serS: Seryl tRNA Synthetase-2, ribD: Riboflavin Deaminase
#3	ribA/ribB	60	GTP Cyclohydratase & DHBP Synthase

Motif 1
AAAAATTCGGTTTTTCTTAGACTACCTTAACCTA	0	23	0
AAGAAAAACCGAATTTTTAGATCAGGATAAATAT	0	39	1
CTCTACCCTTGATTTCCTAGAAAAAAACTTTGCA	0	86	0
CCCTAAAGCCGTTTCTTTAGAGAAGTATTTCCTC	0	117	0
ATTTTGCACAGAAATTTAAGATAATACGAATCCC	0	148	0
AAATTGCTTTGCTTATTGAGACGAAAAAAACATA	0	178	1
TACAACAAAAGCTTTCCTAGAGTAGAGTATGTTT	0	205	0
TTTAACAACAGAATCTTTACAACAAAAGCTTTCC	0	222	0
        AATTTTCCTTAGAATTTGATGCTGTC	1	27	0
   AAGGAAAGGATTTTTAGAGTAGCATGCTTAG	3	7	1
          * ** ******  *
MAP Score: 14.8248

Motif 2
GACTATAGTTGCAAAGTTTTTTTCTAGGAAATC	0	77	1
GTCTCAATAAGCAAAGCAATTTTGCACAGAAAT	0	167	0
CTTTCCTAGAGTAGAGTATGTTTTTTTCGTCTC	0	195	0
CTCTACTCTAGGAAAGCTTTTGTTGTAAAGATT	0	212	1
AGCTTTTGTTGTAAAGATTCTGTTGTTAAATGG	0	226	1
        AAGGAAAGGATTTTTAGAGTAGCAT	3	2	1
          * **** ** ***
MAP Score: 10.5041