AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_operons005_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944234899
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	mtfB	300	mannosyltransferase B
#1	spsK	63	spore coat polysaccharide biosynthesis protein SpsK
#2	lpdA	85	dihydrolipoamide dehydrogenase
#3	aq_737	63	hypothetical protein
#4	aq_796	41	putative protein
#5	flgG2	43	flagellar hook basal-body protein FlgG
#6	minC	23	septum site-determining protein MinC
#7	motA	42	flagellar motor protein MotA
#8	aq_1211	37	putative protein
#9	aq_1400	300	hypothetical protein
#10	flgH	59	flagellar L-ring protein FlgH
#11	aq_1858	216	flagellar hook assembly protein
#12	fliP	231	flagellar biosynthetic protein FliP
#13	fliQ	300	flagellar biosynthesis protein FliQ
#14	aq_2013	74	hypothetical protein
#15	vacB	29	VacB protein (ribonuclease II family)

Motif 1
TGAGAGATGGCTGTGGTGGAGTTGATGTGGACGA	0	177	1
TGTGGTGGAGTTGATGTGGACGAGAAAATAATCA	0	188	1
GGACTTGGACTTGCAGTGGTGTAACTGATCTAAG	1	33	1
TCCGATTTGATCGGAGTGGACATAAAGTTTAAAG	9	201	1
ATACAGTGTCTTGCAGAGGAGGGGCAGCGTGAAA	9	237	1
TTTGCAAAATTCGTGGTGGAGGAGGTTAAATCCA	11	176	1
          CCGTAGTGGAGTTGAAACGTAATG	13	0	1
TCCTAATGTACCGTAGTGGAGTTGAAACGTAGAA	13	66	1
TCCTAATGTACCGTAGTGGAGTTGAAACTGTATT	13	132	1
TCCTAATGTACCGTAGTGGAGTTGAAACTGACTT	13	199	1
          ***  ******  *
MAP Score: 27.295

Motif 2
CACATGCTCATTCCTTATGTTACCAAGCCT	0	104	0
      TCGCTTCCTCCTTTTAAGGCAAAT	2	4	1
      GAAGCTCCTCCTGAAAAGGGGTTT	2	71	0
     TTACTTACCTCCTTTAGGAAATATG	3	48	0
GACTGTTTATTTCCTTCCTTAACTTCTTTC	9	10	1
TTTACAAACCTTCTTCTTGTACTTCTTTTT	9	141	0
AGTACTTAGTCTCCTTCTTTTA        	9	288	1
    AACTCCTACCTCCTTTAAAGTTTAAT	11	6	1
CTTCTTTTTTCTCTTCATTTAACTTTTAAA	11	122	0
CGTAGTTCTCGTCCTCCTTTACTTTGCACT	12	53	1
GGGGAAGAACTTCCTCAAGTTTTAGGTTTT	12	124	0
GGTAAAACTTCTTCTCCTTTATCCTTACAC	12	178	0
TGGATTTCCCTTCCTTATTTTAATGTTCAT	13	31	0
AATCCAGCAGTTCCTAATGTACCGTAGTGG	13	55	1
AACGTAGAATTTCCTCATGTCTTTCCCATC	13	91	1
TCTTTCCCATCTCCTCACTTGTTCCTAATG	13	110	1
TCCTCACTTGTTCCTAATGTACCGTAGTGG	13	121	1
TTTACAAGAACTCCTTTTTTGAATGCTAAA	13	164	1
GCTAAATAAGTTCCTAATGTACCGTAGTGG	13	188	1
ATTTTCTTTGTTCCTAATGTACCGTGTGGA	13	256	1
          **********
MAP Score: 26.1284

Motif 3
CCATACACCACTTTCTCCTTCCAC       	0	3	0
TGGCTTATTGAGAGCTTCTTTTCAACCTTCG	0	41	1
ACTTTAAACACATGCTCATTCCTTATGTTAC	0	111	0
TATCCGATATCATGCTCCTTTGGGACTTGGA	1	11	1
       TCGCTTCCTCCTTTTAAGGCAAAT	2	3	1
      TTACTTACCTCCTTTAGGAAATATG	3	48	0
        AACCACCTCCCTCTAGGTACTTA	5	30	0
ATTTCCTTCCTTAACTTCTTTCTGGAGAGAG	9	18	1
ACCTTCTTCTTGTACTTCTTTTTCAAAGCCA	9	133	0
TAGAATTTACAAACCTTCTTCTTGTACTTCT	9	145	0
CTCTACTTTCCGAGCTTTTTTCCGATTTGAT	9	181	1
AAGTACTTAGTCTCCTTCTTTTA        	9	287	1
     AACTCCTACCTCCTTTAAAGTTTAAT	11	5	1
ACTCTCTTTTTTAGCTTCTTTTTTCTCTTCA	11	135	0
TCGTAGTTCTCGTCCTCCTTTACTTTGCACT	12	52	1
AGGTAAAACTTCTTCTCCTTTATCCTTACAC	12	178	0
CTGGATTTCCCTTCCTTATTTTAATGTTCAT	13	31	0
TGTATTTACAAGAACTCCTTTTTTGAATGCT	13	160	1
GATTTTTACCATAGCTTCTTCCACACGGTAC	13	274	0
CTCAGAAAGTCGTGCACCTTTAAGTCTTTAA	14	24	0
          * *********
MAP Score: 23.322

Motif 4
ATGGCTGTGGTGGAGTTGATGTGGACGAGAA	0	183	1
GGACAGAGCATGGAATTTATAACCCTCTGGG	0	249	1
          TTGAATTTATAGGTATTCAGT	0	289	0
     TTTTATGGATTTTATACTACCCGTGT	4	5	1
  GTTAAGCTTAAATTTTAAAATAAGTACCT	5	8	1
ATTTCCTTTTTAAAATTTAAATT        	7	2	0
GCCATAGCTCTGGCTTTGAAAAAGAAGTACA	9	123	1
TAGAGTTTCGTAGAATTTACAAACCTTCTTC	9	155	0
GGAGTGGACATAAAGTTTAAAGAGATACAGT	9	213	1
TTTAGTAAATTAAACTTTAAAGGAGGTAGGA	11	13	0
TTTAATTTACTAAAGATTAAAAGTATACAAC	11	30	1
TCTCTTCATTTAACTTTTAAATTTATCCCCG	11	112	0
    CCGTAGTGGAGTTGAAACGTAATGAAC	13	6	1
TGAAACGTAATGAACATTAAAATAAGGAAGG	13	22	1
TGTACCGTAGTGGAGTTGAAACGTAGAATTT	13	72	1
TGTACCGTAGTGGAGTTGAAACTGTATTTAC	13	138	1
TGTACCGTAGTGGAGTTGAAACTGACTTCGG	13	205	1
    GGCGAATAGAGTTTATAATTTAAAGCA	15	6	1
          **** ******
MAP Score: 23.0029

Motif 5
AAGTTGGGATAATGATCATGATGATGAGGTCAGGTGGTA	0	138	1
GTGGACGAGAAAATAATCAGGTCAGGGAGATCATAACAG	0	203	1
ATATACTAATAATTTGCCTTAAAAGGAGGAAGCGA    	2	6	0
AAAGGCAATTAAAACCCCTTTTCAGGAGGAGCTTC    	2	60	1
TAAATTTTAAAATAAGTACCTAGAGGGAGGTGGTT    	5	18	1
       CTTAACTATTATTATAAGGAAGT         	6	1	0
TTTCTCTCTCCAGAAAGAAGTTAAGGAAGGAAATAAACA	9	13	0
TGGCTTTGAAAAAGAAGTACAAGAAGAAGGTTTGTAAAT	9	133	1
TAAAGAGATACAGTGTCTTGCAGAGGAGGGGCAGCGTGA	9	230	1
ATCTTTAGTAAATTAAACTTTAAAGGAGGTAGGAGTT  	11	8	0
ACAACTTCCGAAGTAGGTTTATGAGGAAATTCATAAATG	11	56	1
TTAAAAGTTAAATGAAGAGAAAAAAGAAGCTAAAAAAGA	11	123	1
TGACTTTGCAAAATTCGTGGTGGAGGAGGTTAAATCCAA	11	172	1
GGATTACGGGAAGTGCAAAGTAAAGGAGGACGAGAACTA	12	55	0
CAAAGCTAAAAACCTAAAACTTGAGGAAGTTCTTCCCCT	12	116	1
TCGTGTGTGTAAGGATAAAGGAGAAGAAGTTTTACCTTT	12	172	1
GAAACGTAATGAACATTAAAATAAGGAAGGGAAATCCAG	13	23	1
          **         ********
MAP Score: 21.4139

Motif 6
GAAGGTTGAAAAGAAGCTCTCAATAAGCCA	0	41	0
          AAGAAATTATTGTATACACG	4	31	0
      AGGCAAGAAATTATAAGGGGCTTA	8	4	1
TCTCTCCAGAAAGAAGTTAAGGAAGGAAAT	9	18	0
AATCGCAACGACGAACTTTTTGTTCGAAAG	9	84	0
TGTAAATTCTACGAAACTCTACTTTCCGAG	9	165	1
TAGGTTTATGAGGAAATTCATAAATGCTTT	11	69	1
GAAGAGAAAAAAGAAGCTAAAAAAGAGAGT	11	136	1
          ACGAAGTTCTTGAATACCTG	12	0	1
CTAAAACTTGAGGAAGTTCTTCCCCTCGGG	12	129	1
GATAAAGGAGAAGAAGTTTTACCTTTTGAT	12	185	1
GAAAGACATGAGGAAATTCTACGTTTCAAC	13	86	0
GCATTCAAAAAAGGAGTTCTTGTAAATACA	13	160	0
ACGGTACATTAGGAACTTATTTAGCATTCA	13	183	0
TACCGTGTGGAAGAAGCTATGGTAAAAATC	13	275	1
          **********
MAP Score: 16.7725

Motif 7
ATACACCACTTTCTCCTTCCAC        	0	2	0
TTTAAACACATGCTCATTCCTTATGTTACC	0	110	0
GACCTGATTATTTTCTCGTCCACATCAACT	0	196	0
GCCCCTTATAATTTCTTGCCT         	8	1	0
  GACTGTTTATTTCCTTCCTTAACTTCTT	9	8	1
TTCCGAGATTTTCTCTCTCCAGAAAGAAGT	9	31	0
TTAAACTTTATGTCCACTCCGATCAAATCG	9	203	0
TCTTTTCACGCTGCCCCTCCTCTGCAAGAC	9	244	0
TTAGCTTCTTTTTTCTCTTCATTTAACTTT	11	126	0
CCAGTTTGGATTTAACCTCCTCCACCACGA	11	186	0
AAAGGTTGGCATTTCTCTCCTCGTAGTTCT	12	32	1
CCTCCTTTACTTTGCACTTCCCGTAATCCT	12	65	1
AAAGGTAAAACTTCTTCTCCTTTATCCTTA	12	181	0
GTTCATTACGTTTCAACTCCACTACGG   	13	7	0
AACTGCTGGATTTCCCTTCCTTATTTTAAT	13	37	0
GAATTTCCTCATGTCTTTCCCATCTCCTCA	13	97	1
GTAAATACAGTTTCAACTCCACTACGGTAC	13	139	0
CCGAAGTCAGTTTCAACTCCACTACGGTAC	13	206	0
ATCCAAGAAATGTCCACGCCCTCCGAAGTC	13	228	0
          **********
MAP Score: 3.03626