AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_fusions003_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944234387
 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
TTTCATTTTACAACCTCTGTAAGGACTTAC	1	35	1
ATTTGTGCTTCAAGCTCTTTTATCTTCTTC	5	50	1
TTCTCCAGAGCAAGCTTCTTCGCAATCAGG	5	77	1
CTTAAGTTTTCAAGCTCCTCTTCCAGTTTT	5	119	1
GAACTTCATACAACCTCTTTTAAGCGAAAA	5	152	0
      TTCCGAACCTCCGTTTCGTGTGGT	6	26	0
ATAATTCCGTCAAGCCCCTTTTTCATTCCT	7	75	1
TCTTCGGAACGAAGCGCCTTACCTTTTCAC	7	160	0
          **********
MAP Score: 12.843

Motif 2
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

Motif 3
TATTTTTAATTTAGCTTTTCAAGAACTTTCTTCGGAACG	7	179	0
TTAGTCTCAATTTGTGCTTCAAGCTCTTTTATCTTCTTC	5	41	1
CTGCGCTCTTTTGCTTTTACAAAGCCTATCCGAACTTTG	7	103	1
ACGTATAACTTTCATTTTACAACCTCTGTAAGGACTTAC	1	26	1
GCCTTACCTTTTCACTGTTTAAAACCTTTTTCACAAAGT	7	136	0
TTTCTACAAGCTTACTTTTTAAAGGCTATTATAAAAGTG	0	23	1
AAGTAGTATTTTTTCCCTCTGAGTCCTTTCATTAAACCA	5	220	1
GACGGAATTATCGGTAGTATAAGACCTATAATTCCGAAT	7	47	0
TTTATGGCTGAACTTCATACAACCTCTTTTAAGCGAAAA	5	152	0
GTCCTTTCATTAAACCATTCAAAGAATTTTCCATAGTCC	5	242	1
          **  *  * ***   ** *
MAP Score: 8.23023

Motif 4
ATTAATAATATTTCTACAAGCTTACTTTTTAAAGG	0	13	1
     ACACTTTTATAATAGCCTTTAAAAAGTAAG	0	33	0
ACGTATAACTTTCATTTTACAACCTCTGTAAGGAC	1	26	1
TTCACCTCCCTTTATTCATCCATCTATATATTATT	2	13	1
GCCCTTAAGTTTTCAAGCTCCTCTTCCAGTTTTCT	5	116	1
ATGGCTGAACTTCATACAACCTCTTTTAAGCGAAA	5	153	0
TCTGAGTCCTTTCATTAAACCATTCAAAGAATTTT	5	237	1
TCAAAGAATTTTCCATAGTCCCCTCTCCATTAAAT	5	260	1
  TAAAATATATTAGTCCACCACACGAAACGGAGG	6	8	1
CTACCGATAATTCCGTCAAGCCCCTTTTTCATTCC	7	69	1
AAGCCCCTTTTTCATTCCTGCGCTCTTTTGCTTTT	7	86	1
     TTATTTTTAATTTAGCTTTTCAAGAACTTT	7	189	0
          **** *  *** * *
MAP Score: 4.60928

Motif 5
        CTTATTAATAATATTTCTACAAGCTT	0	2	1
TTACCTCCCGTATACGTATAACTTTCATTTTACA	1	13	1
TATTCATCCATCTATATATTATTTATCCTT    	2	25	1
 AGTCGTTATTATTAATAAAGGTTTAATTTCAGG	3	9	1
          TATATTTAGTAATTCCTCAAGAGA	5	0	1
ACGGGATAATTATAAGTAGTATTTTTTCCCTCTG	5	207	1
          ****  ** ** **
MAP Score: 0.423089