AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons039_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243649
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0356	127	carbohydrate kinase, pfkB family
#1	AF1208	165	conserved hypothetical protein
#2	AF1210	108	conserved hypothetical protein
#3	AF2099_AF2100	106	AF2099: muconate cycloisomerase II (clcB), AF2100: acetolactate synthase, large subunit (ilvB-4)

Motif 1
TTCTTTAACAGATTTTTCGAATTGTTCAAG	1	35	1
          GATTTAGCTTCAAAAAAGTT	1	155	0
GAGAACGGCAGATTTTTCTCTCTTAAATAC	2	12	1
CTTTTTTACCGGTTTATGTCAATTTATGTG	2	42	1
TATTATATTTGATTAATCTTCTAAATCACA	2	68	0
TCACAGATAGGATTTAACTTATTATATTTG	2	87	0
      ACTCGATTTATGATTATAATTTTA	3	4	1
TATTCTTTTTGATTAATCGTATTCGATGGG	3	79	0
          **********
MAP Score: 4.69061

Motif 2
TTAAGAGCTCCGAAGCCTATTGCG       	0	3	0
AAATCGATGACGAAGCCTTCTTCATCCTCCC	0	69	0
GTCATCGATTTGAAGCTCTCTCCTGGTGGTA	0	89	1
ATTGTTCAAGCGAAGCTCGTTTAAACGAGGT	1	55	1
TATGTAGAGTCGAACCACATTGTATAATGAT	1	94	1
          ******** **
MAP Score: 4.15596

Motif 3
AACCTCGACAAGATTTACACCGTTGACAAAATCCCAAGGGAG	0	32	1
TATTTACCTTTTCTTTAACAGATTTTTCGAATTGTTCAAGCG	1	25	1
CTTAAATACCTTTTTTACCGGTTTATGTCAATTTATGTGATT	2	33	1
TCAATTTATGTGATTTAGAAGATTAATCAAATATAATAAGTT	2	60	1
AACCTTAGCAAACTTTTTAAAATTATAATCATAAATCGAGT 	3	9	0
        GATTATTTATTCTTTTTGATTAATCGTATTCGAT	3	82	0
          *  ****     **     ***
MAP Score: 2.34763

Motif 4
TCCTCCCTTGGGATTTTGTCAACGGTGTAA	0	46	0
GAGAACGGCAGATTTTTCTCTCTTAAATAC	2	12	1
CTTTTTTACCGGTTTATGTCAATTTATGTG	2	42	1
TTGCTAAGGTTGATTTTGTCAGGCTGCAAG	3	40	1
          **********
MAP Score: 1.68627