AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_operons005_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944234918
 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	aq_1922	24	hypothetical protein
#14	fliQ	300	flagellar biosynthesis protein FliQ
#15	aq_2013	74	hypothetical protein
#16	vacB	29	VacB protein (ribonuclease II family)

Motif 1
GCTTATTGAGAGCTTCTTTTCAACCTTCGA	0	43	1
CGTCCACATCAACTCCACCACAGCCATCTC	0	180	0
TCCGATATCATGCTCCTTTGGGACTTGGAC	1	13	1
     TCGCTTCCTCCTTTTAAGGCAAATT	2	5	1
AGGCAATTAAAACCCCTTTTCAGGAGGAGC	2	62	1
        GAAGCTCCTCCTGAAAAGGGGT	2	73	0
    TTACTTACCTCCTTTAGGAAATATGA	3	47	0
      AACCACCTCCCTCTAGGTACTTAT	5	29	0
ACTGTTTATTTCCTTCCTTAACTTCTTTCT	9	11	1
CTTCTTCTTGTACTTCTTTTTCAAAGCCAG	9	132	0
GAATTTACAAACCTTCTTCTTGTACTTCTT	9	144	0
GTACTTAGTCTCCTTCTTTTA         	9	289	1
   AACTCCTACCTCCTTTAAAGTTTAATT	11	7	1
TCTCTTTTTTAGCTTCTTTTTTCTCTTCAT	11	134	0
TTTGGATTTAACCTCCTCCACCACGAATTT	11	182	0
GTAGTTCTCGTCCTCCTTTACTTTGCACTT	12	54	1
CGAGGGGAAGAACTTCCTCAAGTTTTAGGT	12	127	0
CAAAAGGTAAAACTTCTTCTCCTTTATCCT	12	183	0
ATTACGTTTCAACTCCACTACGG       	14	3	0
TCTACGTTTCAACTCCACTACGGTACATTA	14	69	0
ATACAGTTTCAACTCCACTACGGTACATTA	14	135	0
TATTTACAAGAACTCCTTTTTTGAATGCTA	14	162	1
AGTCAGTTTCAACTCCACTACGGTACATTA	14	202	0
          **********
MAP Score: 28.8111

Motif 2
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	14	0	1
TCCTAATGTACCGTAGTGGAGTTGAAACGTAGAA	14	66	1
TCCTAATGTACCGTAGTGGAGTTGAAACTGTATT	14	132	1
TCCTAATGTACCGTAGTGGAGTTGAAACTGACTT	14	199	1
          ***  ******  *
MAP Score: 27.2301

Motif 3
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	14	31	0
AATCCAGCAGTTCCTAATGTACCGTAGTGG	14	55	1
AACGTAGAATTTCCTCATGTCTTTCCCATC	14	91	1
TCTTTCCCATCTCCTCACTTGTTCCTAATG	14	110	1
TCCTCACTTGTTCCTAATGTACCGTAGTGG	14	121	1
TTTACAAGAACTCCTTTTTTGAATGCTAAA	14	164	1
GCTAAATAAGTTCCTAATGTACCGTAGTGG	14	188	1
ATTTTCTTTGTTCCTAATGTACCGTGTGGA	14	256	1
          **********
MAP Score: 25.9579

Motif 4
TGGCTTATTGAGAGCTTCTTTTCAACCTTC	0	41	1
CGTGTATACAATAATTTCTT          	4	31	1
TAAGCCCCTTATAATTTCTTGCCT      	8	4	0
ATTTCCTTCCTTAACTTCTTTCTGGAGAGA	9	18	1
CTTTCGAACAAAAAGTTCGTCGTTGCGATT	9	84	1
CTCGGAAAGTAGAGTTTCGTAGAATTTACA	9	165	0
AAAGCATTTATGAATTTCCTCATAAACCTA	11	69	0
ACTCTCTTTTTTAGCTTCTTTTTTCTCTTC	11	136	0
CAGGTATTCAAGAACTTCGT          	12	0	0
CCCGAGGGGAAGAACTTCCTCAAGTTTTAG	12	129	0
ATCAAAAGGTAAAACTTCTTCTCCTTTATC	12	185	0
GTTGAAACGTAGAATTTCCTCATGTCTTTC	14	86	1
TGTATTTACAAGAACTCCTTTTTTGAATGC	14	160	1
TGAATGCTAAATAAGTTCCTAATGTACCGT	14	183	1
GATTTTTACCATAGCTTCTTCCACACGGTA	14	275	0
          **********
MAP Score: 16.6447

Motif 5
TACCACCTGACCTCATCATCATGATCATTATCCCAACTT	0	138	0
CTGTTATGATCTCCCTGACCTGATTATTTTCTCGTCCAC	0	203	0
    TCGCTTCCTCCTTTTAAGGCAAATTATTAGTATAT	2	6	1
    GAAGCTCCTCCTGAAAAGGGGTTTTAATTGCCTTT	2	60	0
   TTACTTACCTCCTTTAGGAAATATGAGTATTCCCTT	3	37	0
    AACCACCTCCCTCTAGGTACTTATTTTAAAATTTA	5	18	0
         ACTTCCTTATAATAATAGTTAAG       	6	1	1
ATTATTTTAAGCCCCTTATAATTTCTTGCCT        	8	2	0
TGTTTATTTCCTTCCTTAACTTCTTTCTGGAGAGAGAAA	9	13	1
TCACGCTGCCCCTCCTCTGCAAGACACTGTATCTCTTTA	9	230	0
  AACTCCTACCTCCTTTAAAGTTTAATTTACTAAAGAT	11	8	1
TTATGAATTTCCTCATAAACCTACTTCGGAAGTTGTATA	11	53	0
TTGGATTTAACCTCCTCCACCACGAATTTTGCAAAGTCA	11	172	0
TTCTTGAATACCTGCTAAAGGTTGGCATTTCTCTCCTCG	12	16	1
TAGTTCTCGTCCTCCTTTACTTTGCACTTCCCGTAATCC	12	55	1
AGGGGAAGAACTTCCTCAAGTTTTAGGTTTTTAGCTTTG	12	116	0
CTGGATTTCCCTTCCTTATTTTAATGTTCATTACGTTTC	14	23	0
AAATCCAGCAGTTCCTAATGTACCGTAGTGGAGTTGAAA	14	54	1
CTCCTCACTTGTTCCTAATGTACCGTAGTGGAGTTGAAA	14	120	1
TGCTAAATAAGTTCCTAATGTACCGTAGTGGAGTTGAAA	14	187	1
GATTTTCTTTGTTCCTAATGTACCGTGTGGAAGAAGCTA	14	255	1
TCAGTATGAGATTCCTCAGAAAGTCGTGCACCTTTAAGT	15	30	0
          ****** *   *     **
MAP Score: 12.0348

Motif 6
GATGGCTGTGGTGGAGTTGATGTGGACGAGAA	0	182	1
          GTTAAGCTTAAATTTTAAAATA	5	0	1
AAGAAATTATAAGGGGCTTAAAATAATCCTTG	8	14	1
CGGAGTGGACATAAAGTTTAAAGAGATACAGT	9	212	1
CTTTAGTAAATTAAACTTTAAAGGAGGTAGGA	11	13	0
GAAGAGAAAAAAGAAGCTAAAAAAGAGAGTGA	11	136	1
ATTCGTGGTGGAGGAGGTTAAATCCAAACTGG	11	184	1
ATCCTGAGGGGCAGACTTCAAAGGCTCAAAGC	12	90	1
CTTCAAAGGCTCAAAGCTAAAAACCTAAAACT	12	105	1
     CCGTAGTGGAGTTGAAACGTAATGAAC	14	5	1
ATGTACCGTAGTGGAGTTGAAACGTAGAATTT	14	71	1
ATGTACCGTAGTGGAGTTGAAACTGTATTTAC	14	137	1
ATGTACCGTAGTGGAGTTGAAACTGACTTCGG	14	204	1
GGAATCTCATACTGAGTTAAAATTTCCACT  	15	54	1
     GGCGAATAGAGTTTATAATTTAAAGCA	16	5	1
          * ****** ***
MAP Score: 9.01316

Motif 7
CCGATATCATGCTCCTTTGGGACTTGGACTTGC	1	14	1
AATACTCATATTTCCTAAAGGAGGTAAGTAA  	3	42	1
AAATCCAGCAGTTCCTAATGTACCGTAGTGGAG	14	54	1
CTCCTCACTTGTTCCTAATGTACCGTAGTGGAG	14	120	1
TGCTAAATAAGTTCCTAATGTACCGTAGTGGAG	14	187	1
GATTTTCTTTGTTCCTAATGTACCGTGTGGAAG	14	255	1
          * ****** * **
MAP Score: 8.90773