AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_sum_all002_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238148
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	mtfB	300	mannosyltransferase B
#1	spsK	63	spore coat polysaccharide biosynthesis protein SpsK
#2	frdB2_topA	39	frdB2: fumarate reductase iron-sulfur subunit, topA: topoisomerase I
#3	lpdA	85	dihydrolipoamide dehydrogenase
#4	aq_737	63	hypothetical protein
#5	aq_796	41	putative protein
#6	flgG2	43	flagellar hook basal-body protein FlgG
#7	thdF	145	thiophene and furan oxidation protein
#8	minC	23	septum site-determining protein MinC
#9	topG2	130	reverse gyrase
#10	motA	42	flagellar motor protein MotA
#11	topG1	276	reverse gyrase
#12	aq_1187	48	putative protein
#13	aq_1191	74	hypothetical protein
#14	aq_1211	37	putative protein
#15	aq_1400	300	hypothetical protein
#16	aq_1858	216	flagellar hook assembly protein
#17	fliP	231	flagellar biosynthetic protein FliP
#18	fliQ	300	flagellar biosynthesis protein FliQ
#19	aq_2013	74	hypothetical protein
#20	vacB	29	VacB protein (ribonuclease II family)

Motif 1
TCGTCCACATCAACTCCACCACAGCCATCTCT	0	179	0
GGACTTAGATCAGTTACACCACTGCAAGTCCA	1	38	0
CGACTCCCTCCACCCCCACCACCCAACC    	7	6	0
CCGCGTCTGCCAATTCCGCCACACCCCCTAAC	7	77	1
CGTCCTCGTAAACTTCCACAACTTTAGAAGGT	11	205	1
TGGATTTAACCTCCTCCACCACGAATTTTGCA	16	178	0
CATTACGTTTCAACTCCACTACGG        	18	2	0
TTCTACGTTTCAACTCCACTACGGTACATTAG	18	68	0
AATACAGTTTCAACTCCACTACGGTACATTAG	18	134	0
AAGTCAGTTTCAACTCCACTACGGTACATTAG	18	201	0
          ** ****** **
MAP Score: 29.8941

Motif 2
AGAAGAAATGGAAAAAGAGGAAGGTATGT   	11	7	0
TCCGAAGTAGGTTTATGAGGAAATTCATAAAT	16	62	1
TAATTTGCCTTAAAAGGAGGAAGCGA      	3	4	0
ACAAAAGCTGGATGAAGAGGAAGCCCTCAAGA	11	64	0
CTTCCACACGGTACATTAGGAACAAAGAAAAT	18	256	0
CTCCACTACGGTACATTAGGAACTGCTGGATT	18	55	0
CTCCACTACGGTACATTAGGAACAAGTGAGGA	18	121	0
CTCCACTACGGTACATTAGGAACTTATTTAGC	18	188	0
GAAGTGCAAAGTAAAGGAGGACGAGAACTACG	17	53	0
AAAGGCTTGGTAACATAAGGAATGAGCATGTG	0	102	1
 AATTTAAATTTTAAAAAGGAAATCCGATAAA	10	9	1
TAATGAACATTAAAATAAGGAAGGGAAATCCA	18	29	1
TGAAAAAGAAGTACAAGAAGAAGGTTTGTAAA	15	139	1
AGTTGTGGAAGTTTACGAGGACGGAACAGCCC	11	196	0
TAAAACCCCTTTTCAGGAGGAGCTTC      	3	69	1
 CTTAACTATTATTATAAGGAAGT        	8	2	0
          TAAAAGAAGGAGACTAAGTACT	15	288	0
TATATTATACTTATAGAAAGAACTTTTCTCAA	7	117	1
CACAAACTCTTTTCTGGAGGAAGAGGTA    	13	6	0
AAATTAAACTTTAAAGGAGGTAGGAGTT    	16	6	0
TCTCCAGAAAGAAGTTAAGGAAGGAAATAAAC	15	14	0
AATTTAAAAGTTAAATGAAGAGAAAAAAGAAG	16	120	1
TAGCTCTGGCTTTGAAAAAGAAGTACAAGAAG	15	127	1
AATTGGGACTTATCAAAAGGTAAAACTTCTTC	17	194	0
TAATGATCATGATGATGAGGTCAGGTGGTATG	0	147	1
          *** * ******
MAP Score: 27.9196

Motif 3
        TACCTCTTCCTCCAGAAAAGAGTT	13	2	1
TTGGATTTAACCTCCTCCACCACGAATTTTGC	16	179	0
TCGACTCCCTCCACCCCCACCACCCAACC   	7	7	0
TTGAGGGCTTCCTCTTCATCCAGCTTTTGTAT	11	66	1
TCCTCGTAGTTCTCGTCCTCCTTTACTTTGCA	17	49	1
TTTAAGTCCCCCGCGTCTGCCAATTCCGCCAC	7	67	1
CAAGAAATGTCCACGCCCTCCGAAGTCAGTTT	18	223	0
TTGCCATACACCACTTTCTCCTTCCAC     	0	5	0
          TCGCTTCCTCCTTTTAAGGCAA	3	0	1
TCACGCTGCCCCTCCTCTGCAAGACACTGTAT	15	237	0
        AACCACCTCCCTCTAGGTACTTAT	6	29	0
TACCACCTGACCTCATCATCATGATCATTATC	0	145	0
GCCAATTCCGCCACACCCCCTAACTAAAGAAA	7	85	1
 ACATACCTTCCTCTTTTTCCATTTCTTCTAT	11	9	1
CTGATTATTTTCTCGTCCACATCAACTCCACC	0	191	0
CACATCAACTCCACCACAGCCATCTCTCATAC	0	174	0
TTATGAATTTCCTCATAAACCTACTTCGGAAG	16	60	0
TTAAGATATACCTCTTTCCCGAAGATGACAAG	9	54	1
          **** *** ***
MAP Score: 20.9585

Motif 4
GTTCATTACGTTTCAACTCCACTACGG    	18	6	0
AAATTCTACGTTTCAACTCCACTACGGTACA	18	72	0
GTAAATACAGTTTCAACTCCACTACGGTACA	18	138	0
CCGAAGTCAGTTTCAACTCCACTACGGTACA	18	205	0
CCCAGAGGGTTATAAATTCCATGCTCTGTCC	0	249	0
ACACGGGTAGTATAAAATCCATAAAA     	5	5	0
TCCTACCTCCTTTAAAGTTTAATTTACTAAA	16	13	1
AGGTACTTATTTTAAAATTTAAGCTTAAC  	6	8	0
        AATTTAAATTTTAAAAAGGAAAT	10	2	1
ACTGTATCTCTTTAAACTTTATGTCCACTCC	15	213	0
TGCTTTAAATTATAAACTCTATTCGCC    	20	6	0
TGTACTTCTTTTTCAAAGCCAGAGCTATGGC	15	123	0
GAAGAAGGTTTGTAAATTCTACGAAACTCTA	15	155	1
CCTTCCTTATTTTAATGTTCATTACGTTTCA	18	22	0
CGGGGATAAATTTAAAAGTTAAATGAAGAGA	16	112	1
TTCTCGTCCACATCAACTCCACCACAGCCAT	0	183	0
GTTGTATACTTTTAATCTTTAGTAAATTAAA	16	30	0
          ****** ****
MAP Score: 17.8227

Motif 5
AATCTGGATAATAAATTCTAAAGCTATAAAAT	2	10	1
   GTTAAGCTTAAATTTTAAAATAAGTACCT	6	7	1
TAAACTTAGTTTAAAAAATCAAACTCAAAGGA	9	11	0
GATTTCCTTTTTAAAATTTAAATT        	10	2	0
ACCCTCGGAGTCAAAAGGAAAATTTCCCTCGA	11	156	0
AGTTTGTGAATTAAAATATAAAAATTCCTTAA	13	30	1
AACTTTTTGTTCGAAAGGTCAACCTTTACGTA	15	69	0
CGGAGTGGACATAAAGTTTAAAGAGATACAGT	15	212	1
CTTTAGTAAATTAAACTTTAAAGGAGGTAGGA	16	13	0
TAAATGCTTTTCAAATGCTAAATCGGGGATAA	16	89	1
GGGGATAAATTTAAAAGTTAAATGAAGAGAAA	16	113	1
GGGGCAGACTTCAAAGGCTCAAAGCTAAAAAC	17	97	1
TTGGGACTTATCAAAAGGTAAAACTTCTTCTC	17	192	0
AACTCCTTTTTTGAATGCTAAATAAGTTCCTA	18	172	1
    TATGCTTTAAATTATAAACTCTATTCGC	20	11	0
          ***** * ****
MAP Score: 17.6608

Motif 6
     ACGAAGTTCTTGAATACCTGCTAAAGGTTG	17	5	1
AAATCCAGCAGTTCCTAATGTACCGTAGTGGAGTT	18	54	1
CTCCTCACTTGTTCCTAATGTACCGTAGTGGAGTT	18	120	1
TGCTAAATAAGTTCCTAATGTACCGTAGTGGAGTT	18	187	1
GATTTTCTTTGTTCCTAATGTACCGTGTGGAAGAA	18	255	1
          ****** *    ***
MAP Score: 5.76942

Motif 7
GTAATTGCCTGAGAAGATTTCCCCGCCTCG	9	93	1
AATGGAAAAAGAGGAAGGTATGT       	11	3	0
GCTGGATGAAGAGGAAGCCCTCAAGAGTCT	11	60	0
TTCTAAAGTTGTGGAAGTTTACGAGGACGG	11	204	0
GTAGGTTTATGAGGAAATTCATAAATGCTT	16	68	1
CCTAAAACTTGAGGAAGTTCTTCCCCTCGG	17	128	1
GGAAAGACATGAGGAAATTCTACGTTTCAA	18	87	0
TTCGGAGGGCGTGGACATTTCTTGGATTTT	18	231	1
ACGACTTTCTGAGGAATCTCATACTGAGTT	19	42	1
         AGTGGAAATTTTAACTCAGTA	19	63	0
          **********
MAP Score: 1.85662