AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions013_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241418
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0220	180	biotin carboxylase (acc)
#1	AF1252	194	oxaloacetate decarboxylase, subunit alpha (oadA)
#2	AF1954	68	Glu-tRNA amidotransferase, subunit A (gatA-1)
#3	AF2086	41	protease inhibitor, putative
#4	AF2089	111	conserved hypothetical protein
#5	AF2219	137	methylmalonyl-CoA mutase, subunit alpha, C-terminus (mcmA2)
#6	AF2327	72	shikimate 5-dehydrogenase (aroE)
#7	AF2328	116	Glu-tRNA amidotransferase, subunit C (gatC)

Motif 1
AGGCTAAAGCCACCGATTTAAAAACCTTTTTTCAAATAGA	0	141	0
AGTTATAAGGCAACCTTTTGAAAAGCGTTTTTAAACTTGA	4	66	1
TAGACCGAGCCAACTTATTTAAAATTATTTGGAATGAACT	5	16	1
GATAAATACTTACCGCTCCGAAAACCCTTTTTTACTGCAT	6	28	1
TTGATACTGCCATCAACCTAAATAAACTTTCCTGAAGAAC	1	24	1
         CCAACTCCCTTAAAAGTAATTACGCTATATT	4	1	1
CCCCAGCCCCCAAAACTAGAAAAACCATTTATTACCCACC	7	72	1
GTGCAAGCAATATTAAAAACAAAAAATTTTTGTATTTCCC	1	84	1
AATTGTTTAATATCTCTGAAGAAACACTTTAAAACATTTC	2	23	0
AATTGTTATCTAAGGCACCGAAAACGATTTACAGCTTAGC	0	13	0
GAGTAGTTGTCATATAGGTAAAAATTTTTCGGATTAATTC	5	98	0
GATAACAATTTATCGAAATAAATAAAATTCTCGGCAACTG	0	43	1
TCCTCCTAAACTTTATGATTAAAAAGCTTTGGTTTT    	3	6	0
TCGGCAACTGCTACAAATCAAATACGTATTCTTGTTGCAA	0	73	1
       AAGCTGAGTAGTAGAAATGTTTTAAAGTGTTTC	2	3	1
          ** *      ****   ***
MAP Score: 17.3292

Motif 2
AAAATTCTCGGCAACTGCTACAAATCAAATACGTA	0	66	1
AAGGCTAAAGCCACCGATTTAAAAACCTTTTTTCA	0	147	0
         ACCATCACCTTGATTTGATACTGCCA	1	1	1
TTTGATACTGCCATCAACCTAAATAAACTTTCCTG	1	23	1
          CTAACCACCTCAATTAATTGTTTAA	2	53	0
          CCAACTCCCTTAAAAGTAATTACGC	4	0	1
TAGTTATAAGGCAACCTTTTGAAAAGCGTTTTTAA	4	65	1
TTAGACCGAGCCAACTTATTTAAAATTATTTGGAA	5	15	1
AATGAACTTCTCATCGCCCAAAATTCAAACCTCAC	5	48	1
AGGCACACCCCCAGCCCCCAAAACTAGAAAAACCA	7	64	1
          *** *  *** ** *
MAP Score: 9.0635