AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons039_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243656
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0355	51	ferredoxin (fdx-3)
#1	AF0356	127	carbohydrate kinase, pfkB family
#2	AF1208	165	conserved hypothetical protein
#3	AF1210	108	conserved hypothetical protein
#4	AF2099_AF2100	106	AF2099: muconate cycloisomerase II (clcB), AF2100: acetolactate synthase, large subunit (ilvB-4)

Motif 1
TCTGTTAAAGAAAAGGTAAATACTACAAATAG	2	15	0
TTAGCTTCAAAAAAGTTAATTTAAGTATGTTT	2	140	0
TTAACTTTTTTGAAGCTAAATC          	2	153	1
AAACCGGTAAAAAAGGTATTTAAGAGAGAAAA	3	25	0
TATGTGATTTAGAAGATTAATCAAATATAATA	3	66	1
ATCAAATATAATAAGTTAAATCCTATCTGTGA	3	85	1
AACCCATCGAATACGATTAATCAAAAAGAATA	4	77	1
          * *** ******
MAP Score: 4.68215

Motif 2
TAAGAGCTCCGAAGCCTATTGCG       	1	3	0
AATCGATGACGAAGCCTTCTTCATCCTCCC	1	69	0
TCATCGATTTGAAGCTCTCTCCTGGTGGTA	1	90	1
TTGTTCAAGCGAAGCTCGTTTAAACGAGGT	2	56	1
TAACTTTTTTGAAGCTAAATC         	2	154	1
ATGTGATTTAGAAGATTAATCAAATATAAT	3	67	1
          **********
MAP Score: 3.32809

Motif 3
AAAATCTGTTAAAGAAAAGGTAAATACTACAAAT	2	17	0
TGTAGAGTCGAACCACATTGTATAATGATATGTA	2	96	1
AATGATATGTAATGATATTGAAAACATACTTAAA	2	119	1
AACCGGTAAAAAAGGTATTTAAGAGAGAAAAATC	3	22	0
TTAGAAGATTAATCAAATATAATAAGTTAAATCC	3	74	1
CAAGAGTTTAAAACCCATCGAATACGATTAATCA	4	66	1
GAATACGATTAATCAAAAAGAATAAATAATC   	4	85	1
          ** ** ** *** *
MAP Score: 3.10169

Motif 4
GCTTCGTCATCGATTTGAAGCTCTCTCCTG	1	84	1
     AATTTCTATTTGTAGTATTTACCTT	2	5	1
GAGGTGTGGCTGATATGTAGAGTCGAACCA	2	81	1
CATTGTATAATGATATGTAATGATATTGAA	2	111	1
TTAAATTAACTTTTTTGAAGCTAAATC   	2	148	1
          **********
MAP Score: 0.904054