AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_operons028_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236063
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	aq_467	300	putative protein
#1	aq_699	53	hypothetical protein
#2	dnaJ2	70	chaperone DnaJ
#3	truB	30	tRNA pseudouridine 55 synthase
#4	acrD4	69	cation efflux (AcrB/AcrD/AcrF family)
#5	aq_1133	68	putative protein
#6	proB	29	glutamate 5-kinase
#7	moeB	60	molybdopterin biosynthesis protein MoeB

Motif 1
    GGCACTTGAGGAAGAGATGAAAGTTT	0	6	1
GAAAGTTTTCAAAGGAAAAGCAAAGAGTGC	0	28	1
CGGAAAGCCCAAAGGAAAGGCACTTTACCT	0	118	1
TTAAACTCAAAGAGGTAAAGTGCCTTTCCT	0	130	0
TGTGGGGTATAAGGGAAAAGGCGAGAAGCG	0	174	1
GCGTAGTTAAAAAAGAAGAGGAGTCCTTCA	0	201	1
CTAAATTTCTGGAGGAAGAGGT        	1	41	1
TCTGGTAAACGGAGGAAAGTT         	2	59	1
AAAATAAATTAAAGGATAATTAAGTAA   	4	52	1
ATTATAGACAAAAGGAAGAGAGTTTCCATG	7	32	0
          **********
MAP Score: 16.0412

Motif 2
GAAAGTTTTCAAAGGAAAAGCAAAGAGTGCAA	0	28	1
GTTTTATCACGAACGACGAAGACGGAAAGCCC	0	96	1
CGGAAAGCCCAAAGGAAAGGCACTTTACCTCT	0	118	1
GGTATAAGGGAAAAGGCGAGAAGCGTAGTTAA	0	179	1
GCGTAGTTAAAAAAGAAGAGGAGTCCTTCAAG	0	201	1
AGATGCATATAAAAGACGGATAATCGCACAGG	0	241	1
TTACTCTGGTAAACGGAGGAAAGTT       	2	55	1
ATTATAGACAAAAGGAAGAGAGTTTCCATGTC	7	30	0
          *** ****** *
MAP Score: 7.83357

Motif 3
TGAGGAAGAGATGAAAGTTTTCAAAGGAAAAG	0	16	1
CTGTTGCACTCTTTGCTTTTCCTTTGAAAACT	0	31	0
CAAAGAGTGCAACAGCCTTTCCGAACCCGGAA	0	48	1
CAAAGAGGTAAAGTGCCTTTCCTTTGGGCTTT	0	121	0
TTTGAGTTTAATCAACCTATCCCGATGTGGGG	0	149	1
TAACTACGCTTCTCGCCTTTTCCCTTATACCC	0	178	0
ACAGGTTTACAGGAGCTTTTACAACTCACTTT	0	268	1
AGCTTTTACAACTCACTTTTTCTAAAGGA   	0	281	1
      GAACATTAGAATATTCTTATATTGTG	1	4	1
        TTACTTAATTATCCTTTAATTTAT	4	55	0
        ATTTTAACATTTTCTTAAATTGAA	5	2	1
AGACAAAAGGAAGAGAGTTTCCATGTCAGGGT	7	25	0
          * **** *****
MAP Score: 5.25765

Motif 4
TTTACCTCTTTGAGTTTAATCAACCTATCC	0	141	1
TTAGAAAAAGTGAGTTGTAAAAGCTCCTGT	0	276	0
        TGTGATTTTGAAACTTGACAAA	2	2	1
ACTTAAAAGTTGAGTTTATTTTTGTCAAGT	2	22	0
     AAGCCTTATTTTAAATTGATAATTT	3	5	1
ATCCTTTAATTTATTTTTATTATGTAGTGG	4	39	0
TTTCTTAAATTGAATTTAAATCTTGAATTA	5	20	1
         GTGAGTTTTATATATTAAATC	6	18	0
          **********
MAP Score: 4.95983

Motif 5
   GGCACTTGAGGAAGAGATGAAAGTTTT	0	7	1
GAAAGTTTTCAAAGGAAAAGCAAAGAGTGC	0	28	1
TTTTATCACGAACGACGAAGACGGAAAGCC	0	97	1
CGGAAAGCCCAAAGGAAAGGCACTTTACCT	0	118	1
TGTGGGGTATAAGGGAAAAGGCGAGAAGCG	0	174	1
AAGCGTAGTTAAAAAAGAAGAGGAGTCCTT	0	199	1
TAAATTTCTGGAGGAAGAGGT         	1	42	1
TACTCTGGTAAACGGAGGAAAGTT      	2	56	1
TGAATTAACACAAGGAGAACTTTACATATT	5	43	1
TTATAGACAAAAGGAAGAGAGTTTCCATGT	7	31	0
          **********
MAP Score: 2.21459