AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_fusions003_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944234376
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	trpD1	53	phosphoribosylanthranilate transferase
#1	nirB	120	nitrite reductase (NAD(P)H) large subunit
#2	guaA	45	GMP synthase
#3	nuoD1	43	NADH dehydrogenase I chain D
#4	frdB1	35	fumarate reductase iron-sulfur subunit
#5	trpE	300	anthranilate synthase component I
#6	aq_1791	40	putative protein
#7	ntrC2	209	transcriptional regulator (NtrC family)

Motif 1
TATAATAGCCTTTAAAAAGTAAGCTTGTAGAA	0	24	0
TTACAGAGGTTGTAAAATGAAAGTTATACGTA	1	25	0
TGTAAGGACTTACAAAACATAACTACCCGGAA	1	52	1
  AATTCCGTTTGAAAAATTTATCCCCCAGAC	4	8	1
GAAGAGGAGCTTGAAAACTTAAGGGCAACACA	5	110	0
ATAAAACGAAGGCAAAAACTAACGGGATAATT	5	186	1
AGGACTCAGAGGGAAAAAATACTACTTATAAT	5	215	0
 ACAAAAAATTTTAAAATTTAATGGAGAGGGG	5	279	0
ATTCCGAATATTGAAAGGATAACTCCGCAAAT	7	24	0
GGATAGGCTTTGTAAAAGCAAAAGAGCGCAGG	7	102	0
GTTTTAAACAGTGAAAAGGTAAGGCGCTTCGT	7	150	1
AAGAAAGTTCTTGAAAAGCTAAATTAAAAATA	7	186	1
          *******  ***
MAP Score: 13.3165

Motif 2
GTAAGTCCTTACAGAGGTTGTAAAATGAAA	1	35	0
GAAGAAGATAAAAGAGCTTGAAGCACAAAT	5	50	0
CCTGATTGCGAAGAAGCTTGCTCTGGAGAA	5	77	0
AAAACTGGAAGAGGAGCTTGAAAACTTAAG	5	119	0
TTTTCGCTTAAAAGAGGTTGTATGAAGTTC	5	152	1
ACCACACGAAACGGAGGTTCGGAA      	6	26	1
AGGAATGAAAAAGGGGCTTGACGGAATTAT	7	75	0
GTGAAAAGGTAAGGCGCTTCGTTCCGAAGA	7	160	1
          **********
MAP Score: 12.843

Motif 3
TTAATAATATTTCTACAAGCTTACTTTTTAAA	0	14	1
ACAAGCTTACTTTTTAAAGGCTATTATAAAAG	0	28	1
TTAAAGGCTATTATAAAAGTGT          	0	41	1
GCAAAAAACGTGCCAAAAAGTTCCGGGTAGTT	1	72	0
GGCACGTTTTTTGCAAGAGTTTCCTCAGGAGG	1	90	1
GTCGTTATTATTAATAAAGGTTTAATTTCAGG	3	11	1
   AATTCCGTTTGAAAAATTTATCCCCCAGA	4	7	1
GGAGAAGAAGATAAAAGAGCTTGAAGCACAAA	5	51	0
AATTCCTGATTGCGAAGAAGCTTGCTCTGGAG	5	79	0
CTCTTTTCGCTTAAAAGAGGTTGTATGAAGTT	5	149	1
CATTAAACCATTCAAAGAATTTTCCATAGTCC	5	249	1
CTCCATTAAATTTTAAAATTTTTTGT      	5	284	1
TTAAAACCTTTTTCACAAAGTTCGGATAGGCT	7	125	0
TAATTTAGCTTTTCAAGAACTTTCTTCGGAAC	7	180	0
          **  ********
MAP Score: 8.99298