AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons024_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238248
 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
TAGGTTAAGGTAGTCTAAGAAAAACCGAATTTTT	0	23	1
ATATTTATCCTGATCTAAAAATTCGGTTTTTCTT	0	39	0
TGCAAAGTTTTTTTCTAGGAAATCAAGGGTAGAG	0	86	1
GAGGAAATACTTCTCTAAAGAAACGGCTTTAGGG	0	117	1
GGGATTCGTATTATCTTAAATTTCTGTGCAAAAT	0	148	1
TATGTTTTTTTCGTCTCAATAAGCAAAGCAATTT	0	178	0
AAACATACTCTACTCTAGGAAAGCTTTTGTTGTA	0	205	1
GGAAAGCTTTTGTTGTAAAGATTCTGTTGTTAAA	0	222	1
GACAGCATCAAATTCTAAGGAAAATT        	1	27	1
CTAAGCATGCTACTCTAAAAATCCTTTCCTT   	3	7	0
          *  ****** ** *
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

Motif 3
TCTAAGAAAAACCGAATTTTTAGATCAGGATAAATATA	0	36	1
CTATAGTTGCAAAGTTTTTTTCTAGGAAATCAAGGGTA	0	79	1
AATCCCTAAAGCCGTTTCTTTAGAGAAGTATTTCCTCT	0	116	0
TCTGTGCAAAATTGCTTTGCTTATTGAGACGAAAAAAA	0	170	1
CTTTACAACAAAAGCTTTCCTAGAGTAGAGTATGTTTT	0	204	0
CTTTTGTTGTAAAGATTCTGTTGTTAAATGGGGTGGG 	0	228	1
CAGACTGTAGACAGCATCAAATTCTAAGGAAAATT   	1	18	1
      AAGGAAAGGATTTTTAGAGTAGCATGCTTAGC	3	4	1
CCTCGCATTAACGGATTCCGATGCTAAGCATGCTACTC	3	26	0
          *  * ***  * * * **
MAP Score: 8.35528