AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_operons028_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236054
 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
GATAGGTTGATTAAACTCAAAGAGGTAAAG	0	140	0
TTATATTGTGATATACTAAATTTCTGGAGG	1	26	1
CTTGACAAAAATAAACTCAACTTTTAAGTT	2	23	1
ACCAGAGTAAATAACTTAAAAGTTGAGTTT	2	35	0
GTGGGTTAGAATATACTAACCGGAGGTGGA	4	13	0
CATAATAAAAATAAATTAAAGGATAATTAA	4	45	1
AATTCAAGATTTAAATTCAATTTAAGAAAA	5	19	0
 GTGAGTTTTATATATTAAATCATTAATTT	6	10	0
      GCATATAAATTATAGACAAAAGGA	7	46	0
          **********
MAP Score: 10.2545

Motif 3
TGTTGCACTCTTTGCTTTTCCTTTGAAAACTTT	0	29	0
     GAACATTAGAATATTCTTATATTGTGAT	1	5	1
       ATTTTAACATTTTCTTAAATTGAATT	5	3	1
TGCCTTTCCTTTGGGCTTTCCGTCTTCGTCGTT	0	107	0
CCACCTCCGGTTAGTATATTCTAACCCACTACA	4	14	1
       TTACTTAATTATCCTTTAATTTATTT	4	53	0
GCTTTTACAACTCACTTTTTCTAAAGGA     	0	282	1
TGTAAACCTGTGCGATTATCCGTCTTTTATATG	0	246	0
          ** *  *******
MAP Score: 2.35103

Motif 4
CTTTACCTCTTTGAGTTTAATCAACCTATCCCGA	0	140	1
GCGATTATCCGTCTTTTATATGCATCTGTGAAGT	0	234	0
ATTTTGAAACTTGACAAAAATAAACTCAACTTTT	2	14	1
     AAGCCTTATTTTAAATTGATAATTTTGTG	3	5	1
TCCACCTCCGGTTAGTATATTCTAACCCACTACA	4	13	1
TAATTATCCTTTAATTTATTTTTATTATGTAGTG	4	40	0
 ATTTTAACATTTTCTTAAATTGAATTTAAATCT	5	9	1
AAAGTTCTCCTTGTGTTAATTCAAGATTTAAATT	5	32	0
CATGTCAGGGTTAATATTAATTTAGA        	7	2	0
TCTCTTCCTTTTGTCTATAATTTATATGC     	7	41	1
          ** * ******  *
MAP Score: 0.298554