AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_operons013_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944235402
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	rpsP	81	ribosomal protein S16
#1	aq_142	300	putative protein
#2	xcpC	253	chromosome assembly protein homolog
#3	prfA	260	peptide chain release factor RF-1
#4	ftsY	33	cell division protein FtsY
#5	aq_922	26	putative protein
#6	aq_1057	52	hypothetical protein
#7	htrA	28	periplasmic serine protease
#8	rpoD	38	RNA polymerase sigma factor RpoD
#9	dnaG	66	DNA primase
#10	ffh	40	signal recognition particle receptor protein
#11	aq_1723	24	hypothetical protein
#12	prfB	255	peptide chain release factor RF-2

Motif 1
TTACTCTATAGAAGGGGAAGGTTTAGTAATA	1	145	1
AGCATTGAGTGAAGTTGAAGGAGTATCGGAG	12	90	1
TTTATCTTGCGAGGAGGTAGGTAAATGAAGA	3	36	1
TCAAGAATAAGGAGTGGAAGATGGAGCTGTT	1	15	1
TTATGATCCGGAAGTGGCAAGAAAAATTAAG	1	211	1
GGAACTGGAAGAAGAGGTAAAGAAAAATCCC	2	74	1
AGGAGTATCGGAGGTGGAAGTTTCCCTGGAA	12	108	1
TGGAAGAAGGGAAGGCGAAAGTAAAACTCGA	12	134	1
TTTGTGGAGAGAAGCGTAAAGGTGTTTCCGC	3	112	0
AACCCTAAAGGAAGCTGTAGAAACTTGGGGA	12	183	1
AATACCTCTCGAAAAGGAAAAGTATGAGATA	1	52	1
AGGTAAGAAAGAAGAGTAAAAA         	3	248	1
AGTAAAACTCGAAAAGGAAGTGCCCTTTGAA	12	153	1
AATGCTTGCGGAATTTGAAGGAGGTAAGAAA	3	227	1
TGATCTGTGTCAAGCTGAAGAAATACCTGTA	9	20	0
TTTACGCGGGCAAACTGAAGATAAAGCCCGC	3	187	1
          **** ******
MAP Score: 17.7811

Motif 2
GAAAATTTACGGAGGTACGGGAAA      	0	67	1
AATAAGGAGTGGAAGATGGAGCTGTTATTA	1	20	1
ATTCCCTATGGGAGGTAAGGC         	1	289	1
TCAGCAAAATGGCGGAAGGGCTAGTTGAGA	2	34	1
CCCAGGAACTGGAAGAAGAGGTAAAGAAAA	2	70	1
TATCTTGCGAGGAGGTAGGTAAATGAAGAA	3	38	1
GGTAGGTAAATGAAGAAGGGTATTCACCCC	3	51	1
CTCCACAAAAGGAGGAACTGTTTACTTAGA	3	134	1
GGAATTTGAAGGAGGTAAGAAAGAAGAGTA	3	236	1
TTTAGAGTTAGGAGGTAAGAGA        	8	26	1
ATTCTTTATGGGCGAAAAGGAGTTAAAAAT	12	18	1
AAGTTTCCCTGGAAGAAGGGAAGGCGAAAG	12	125	1
          **********
MAP Score: 17.4047

Motif 3
TTACAGGTATTTCTTCAGCTTGACACAGATC	9	19	1
CCTCCGATACTCCTTCAACTTCACTCAATGC	12	91	0
CCTCCCTCGCTTTTTCAACTTTTCCCGCCCT	2	147	0
TTTGGGATTTTTCTTTACCTCTTCTTCCAGT	2	77	0
TTCAGGATATTCCTTTATCTCATACTTTTCC	1	67	0
TTATAATAACTTTTTTATCTTGCGAGGAGGT	3	23	1
CCTGAACTACTTTTTAAGCTCGGAATTGCTT	2	111	1
CATGCCCTGAATTTTTAACTCCTTTTCGCCC	12	27	0
TAACAGCTCCATCTTCCACTCCTTATTCTTG	1	16	0
ATCCCCAAGTTTCTACAGCTTCCTTTAGGGT	12	184	0
CTATTACTAAACCTTCCCCTTCTATAGAGTA	1	146	0
TTTACTCTTCTTTCTTACCTCCTTCAAATTC	3	237	0
 AAAAAAGGTATTTTAATCTTAGTG      	11	9	1
          TCTCTTACCTCCTAACTCTAA	8	27	0
          TTTTTACTCTTCTTTCTTACC	3	249	0
TTGTTCTAGTACTTTAAACTTTCCTTTATAC	1	249	1
   TTTGTAATTTTATCCCTTAAATAACATA	6	34	0
          ******* ***
MAP Score: 14.6953

Motif 4
         TTTCCCGTACCTCCGTAAATT	0	70	0
CAGCTCCATCTTCCACTCCTTATTCTTGAA	1	14	0
TTACTAAACCTTCCCCTTCTATAGAGTAAT	1	144	0
TAATTTTTCTTGCCACTTCCGGATCATAAA	1	210	0
        GCCTTACCTCCCATAGGGAATT	1	288	0
TTACCTCTTCTTCCAGTTCCTGGGCTAACT	2	64	0
TTTTCAACTTTTCCCGCCCTTATGTAAGCA	2	137	0
CAGTTGTTTGTATACCTCCCTCGCTTTTTC	2	162	0
CCCTTCTTCATTTACCTACCTCCTCGCAAG	3	41	0
TTGCAACCAGTGTCACCCCTTTTACGCGGG	3	167	1
ACTCTTCTTTCTTACCTCCTTCAAATTCCG	3	235	0
       TCTCTTACCTCCTAACTCTAAAA	8	25	0
AGAAATAAAATATCACTTCTAAAGAGAAAG	10	19	0
GCCCTGAATTTTTAACTCCTTTTCGCCCAT	12	25	0
CCAGGGAAACTTCCACCTCCGATACTCCTT	12	107	0
TTACTTTCGCCTTCCCTTCTTCCAGGGAAA	12	128	0
TTTTCAATTATTCCACTACCTTGTATCCCC	12	209	0
          **********
MAP Score: 14.6085

Motif 5
AAAAATACCTCTCGAAAAGGAAAAGTATGAGA	1	49	1
AAAGGAATATCCTGAAACGGGAACGATGTTAA	1	82	1
CCAGATTACTCTATAGAAGGGGAAGGTTTAGT	1	140	1
CGTTTATGATCCGGAAGTGGCAAGAAAAATTA	1	208	1
 AGATGTTTGGCAAAAAAGGCGTTTTCAGCAA	2	9	1
AGCCCAGGAACTGGAAGAAGAGGTAAAGAAAA	2	68	1
GCAATTCCGAGCTTAAAAAGTAGTTCAGGATC	2	108	0
GGCGGGAAAAGTTGAAAAAGCGAGGGAGGTAT	2	149	1
ACGCTTCTCTCCACAAAAGGAGGAACTGTTTA	3	126	1
CAGTTTGCCCGCGTAAAAGGGGTGACACTGGT	3	172	0
ATTCTTTATGGGCGAAAAGGAGTTAAAAATTC	12	18	1
TGTGTAAACACCGTAAAAAGAGCATTGAGTGA	12	70	1
GGAAGTTTCCCTGGAAGAAGGGAAGGCGAAAG	12	123	1
GAAAGTAAAACTCGAAAAGGAAGTGCCCTTTG	12	150	1
          ** ******* *
MAP Score: 11.5299

Motif 6
TTCGAGAGGTATTTTTAATAACAGCTCCATCTTCCAC	1	28	0
TTCAGGATATTCCTTTATCTCATACTTTTCCTTTTCG	1	61	0
CGTTTTTAAATTCTATTACTAAACCTTCCCCTTCTAT	1	152	0
GCTCCTGCTTAATTTTTCTTGCCACTTCCGGATCATA	1	212	0
ATTAAGCAGGAGCTTGTTCTAGTACTTTAAACTTTCC	1	236	1
TAGTACTTTAAACTTTCCTTTATACTTAATAAAAATT	1	255	1
GATCTTTGGGATTTTTCTTTACCTCTTCTTCCAGTTC	2	75	0
  AAGCGAAGAACTTTTATAATAACTTTTTTATCTTG	3	8	1
TAAAACCCACAACTTTCGTATGCGGTTGCGGAAACAC	3	85	1
 TTTTTACTCTTCTTTCTTACCTCCTTCAAATTCCGC	3	234	0
       AGGAACTTTATTTTATACTTGTAGGT    	5	3	1
        TTAACTTTAATAAATTTTTAGAGTTAGGA	8	2	1
TTCCTTTTCGAGTTTTACTTTCGCCTTCCCTTCTTCC	12	135	0
ATTTATTTTCAATTATTCCACTACCTTGTATCCCCAA	12	207	0
          * ****  **    ***
MAP Score: 11.0216

Motif 7
 TACATTCAAGAATAAGGAGTGGAAGATGGAGCTGTTATTAA	1	9	1
AATACCTCTCGAAAAGGAAAAGTATGAGATAAAGGAATATCC	1	52	1
GGAATATCCTGAAACGGGAACGATGTTAATAGTACATAAAGA	1	85	1
TTACTCTATAGAAGGGGAAGGTTTAGTAATAGAATTTAAAAA	1	145	1
AGACGTTTATGATCCGGAAGTGGCAAGAAAAATTAAGCAGGA	1	205	1
CAAAATGGCGGAAGGGCTAGTTGAGAAGTTAGCCCAGGAACT	2	38	1
GGAACTGGAAGAAGAGGTAAAGAAAAATCCCAAAGATCCTGA	2	74	1
GGAAAAGTTGAAAAAGCGAGGGAGGTATACAAACAACTGAGA	2	153	1
TTTATCTTGCGAGGAGGTAGGTAAATGAAGAAGGGTATTCAC	3	36	1
TCTCTCCACAAAAGGAGGAACTGTTTACTTAGAAGTTTGCAA	3	131	1
CGCTTACTACGAAATGCTTGCGGAATTTGAAGGAGGTAAGAA	3	215	1
GAGTGAAGTTGAAGGAGTATCGGAGGTGGAAGTTTCCCTGGA	12	96	1
GTTTCCCTGGAAGAAGGGAAGGCGAAAGTAAAACTCGAAAAG	12	127	1
AGTAAAACTCGAAAAGGAAGTGCCCTTTGAAACCCTAAAGGA	12	153	1
          ***  ** ** *        **
MAP Score: 8.9726

Motif 8
TGAATTTTTAACTCCTTTTCGCCCATAAAGA	12	20	0
TCAAAGGGCACTTCCTTTTCGAGTTTTACTT	12	152	0
ATCTCATACTTTTCCTTTTCGAGAGGTATTT	1	51	0
TTTGCTGAAAACGCCTTTTTTGCCAAACATC	2	11	0
ATTACTAAACCTTCCCCTTCTATAGAGTAAT	1	144	0
GTAAACAGTTCCTCCTTTTGTGGAGAGAAGC	3	128	0
GGATTTTTCTTTACCTCTTCTTCCAGTTCCT	2	73	0
GCAACCAGTGTCACCCCTTTTACGCGGGCAA	3	169	1
GGTTGCGGAAACACCTTTACGCTTCTCTCCA	3	108	1
ACTAGCCCTTCCGCCATTTTGCTGAAAACGC	2	28	0
TAAGATTAAAATACCTTTTTT          	11	0	0
TCAACTTTTCCCGCCCTTATGTAAGCAATTC	2	133	0
TGTGTAAATCTCCCCGTTTTTAAATTCTATT	1	172	0
AGTAGTTCGTTAGCCTTTTCTTTGTCTAAGT	2	196	0
TTTACTTTCGCCTTCCCTTCTTCCAGGGAAA	12	128	0
GTTTCTACAGCTTCCTTTAGGGTTTCAAAGG	12	176	0
CTTCATTTACCTACCTCCTCGCAAGATAAAA	3	35	0
          ** ********
MAP Score: 7.52072

Motif 9
  TACATTCAAGAATAAGGAGTGGAAGATGGAGCTGT	1	8	1
TATTAAAAATACCTCTCGAAAAGGAAAAGTATGAGAT	1	45	1
AGATAAAGGAATATCCTGAAACGGGAACGATGTTAAT	1	78	1
ATAGTACATAAAGACTTGAGAGGAGAGCCAGATTACT	1	113	1
GAGCCAGATTACTCTATAGAAGGGGAAGGTTTAGTAA	1	137	1
TTAGTAATAGAATTTAAAAACGGGGAGATTTACACAA	1	167	1
ACACAATAGACGTTTATGATCCGGAAGTGGCAAGAAA	1	198	1
TTGAGAAGTTAGCCCAGGAACTGGAAGAAGAGGTAAA	2	58	1
AAGGGCGGGAAAAGTTGAAAAAGCGAGGGAGGTATAC	2	146	1
TAACTTTTTTATCTTGCGAGGAGGTAGGTAAATGAAG	3	29	1
ACTTTAATAAATTTTTAGAGTTAGGAGGTAAGAGA  	8	13	1
AAGTTGAAGGAGTATCGGAGGTGGAAGTTTCCCTGGA	12	101	1
AGGCGAAAGTAAAACTCGAAAAGGAAGTGCCCTTTGA	12	146	1
          *   *  ***  *****
MAP Score: 6.61708

Motif 10
       AAAGATAAATATTAAAGGTTTTT	0	3	1
AACTTATTGTGTTAAAATTATTCGTCCGAA	0	40	1
TGGAGCTGTTATTAAAAATACCTCTCGAAA	1	36	1
CTTTATACTTAATAAAAATTCCCTATGGGA	1	272	1
  CAGATACGGATAAATTATACTTCGTAAA	2	235	0
TTATTTAAGGGATAAAATTACAAA      	6	38	1
  TTAACTTTAATAAATTTTTAGAGTTAGG	8	8	1
ACAGATCAGAAATAAAATAAATTCTTTTGA	9	43	1
      AAGAAATAAAATATCACTTCTAAA	10	26	0
   CACTAAGATTAAAATACCTTTTTT   	11	7	0
          GTTAAATTATTCTTTATGGG	12	0	1
GCGAAAAGGAGTTAAAAATTCAGGGCATGA	12	29	1
AATAATTGAAAATAAATTTCAATTGCAATA	12	227	1
TTTCAATTGCAATAAATTATAA        	12	243	1
          **********
MAP Score: 6.11882