AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_operons019_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944235715
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	rpmH	43	ribosomal protein L34
#1	atpB	49	ATP synthase F0 subunit a
#2	dnaA	90	chromosome replication initiator protein DnaA
#3	aq_323	91	putative protein
#4	gyrA	117	DNA gyrase A subunit
#5	aq_1029	268	putative protein
#6	recR	258	recombination protein RecR
#7	icd	113	isocitrate dehydrogenase
#8	aq_1515	25	putative protein
#9	aq_1516	58	putative protein
#10	pycA	23	pyruvate carboxylase c-terminal domain
#11	aq_1525	40	putative protein
#12	aq_1526	50	hypothetical protein
#13	aq_1527	70	hypothetical protein
#14	dnaX	178	DNA polymerase III gamma subunit
#15	aq_1873	300	putative protein
#16	rplM	45	ribosomal protein L13
#17	dnaN	24	DNA polymerase III beta chain
#18	aq_2060	284	hypothetical protein

Motif 1
AGCCAATTGCAAAAGAGGTAAGGGAA     	1	33	1
AGTGAAAGGGAAAAGAGGAAAGAACTTAAA 	2	9	0
ACGGGAAAGTGAAGGAGGTAAACTCAAAAAA	2	49	0
TGAGATTTATCAAGGAAGAAAAATAACGATT	4	49	1
GGGACAGATTGAAGGCGGAAAGCGTTTTCCT	5	104	1
ATTCTGAAAAGGAGGAGGAAAGAGA      	5	253	1
AGGAGACTATGGAGGAGGTAAAAAGGGAACT	6	46	1
TATTCCCTAACAAGGAGGTCATAA       	8	11	1
AAAGAGTCCGAAAGAAAGACACGAGCACCTC	9	11	0
   AAACTTTAAAGGAGGTAATATAG     	10	7	1
AAAAAGAAGGGAAAAAGGAAAGC        	11	2	0
GAGAGCCTTTGAAGGAGGTCTGGT       	13	56	1
CCGTAAAGTAGAAGAAGGATATATAAAGAAT	15	77	0
TGAACGAACTGAGGGAGGTTAAAGTAATCAG	15	108	1
CTTTTGACGCAAAGGAAGTAATAAACTCTCT	15	159	1
AAAAAATACTCAAAGAGGAAAGTGTGGAGAA	15	219	1
CTTTAAACTCGGAAGAGGTGAATGGG     	16	29	1
          ********* *
MAP Score: 29.0981

Motif 2
TATTTCCACTCCGTCCTTTTCAAGGATATCC	6	89	0
     TTATGACCTCCTTGTTAGGGAATAA 	8	9	0
 TCTCTTTCCTCCTCCTTTTCAGAATATACC	5	248	0
   CTATATTACCTCCTTTAAAGTTT     	10	5	0
     ACCAGACCTCCTTCAAAGGCTCTCAT	13	54	0
AACTGAGCTACCCGCCTTGTTTATAAATAAA	18	171	0
TTTTGAGTTTACCTCCTTCACTTTCCCGTGG	2	51	1
     TTCTCCACTCCTTATAAAGATTTACT	3	5	1
  GCCCTTCTCTCTCCTTTAAATTTTTATTT	0	8	1
TTCCCTTTCACTCTCCTTGACTTTTTTGAGT	2	28	1
TTTCCTTTTTCCCTTCTTTTTCTTTTAAAAT	11	12	1
AAAGCTAAATCCATCCTTGATGAAACCATTA	15	248	1
ACCCGCGACCTCCGCCTTGTAAGGGCGGCGC	18	208	0
AAGTTAAAGCCCGTCCTGATAGAACTTATAA	6	183	1
    TCAAGCCCCTCCTATTTATTTTCTAAC	15	283	0
TCAAAAATTCCCGTTCTTATATTATTAATCC	18	262	1
     TTTACACCTCCTGGTTAGTAAATTCT	14	5	1
TAACTTCTCGCAGTCCTTTTCTTCTCCCTTA	6	158	0
GAAAACGCTTTCCGCCTTCAATCTGTCCCCA	5	102	0
TCTTTATATATCCTTCTTCTACTTTACGGTG	15	79	1
AAGTATTAGGCTATCCTTAAAAGATTTGTGT	4	19	1
TAACTTGACACACTTCTTCAAAATGAATAAA	7	65	1
          ******** **
MAP Score: 22.4996

Motif 3
CAGGAAAACGCTTTCCGCCTTCAATCTGTCC	5	105	0
    TCTCTTTCCTCCTCCTTTTCAGAATAT	5	251	0
  TTTAAGTTCTTTCCTCTTTTCCCTTTCAC	2	8	1
TTTCTCCACACTTTCCTCTTTGAGTATTTTT	15	220	0
GCAGTCCTTTTCTTCTCCCTTAAACTCTATG	6	149	0
TCCTCTTTTCCCTTTCACTCTCCTTGACTTT	2	21	1
TTCAATGAGACTCTTCACTTTTGTTAAAAAG	5	203	0
AAATCGTTATTTTTCTTCCTTGATAAATCTC	4	50	0
    GCTTTCCTTTTTCCCTTCTTTTTCTTT	11	6	1
TGAGTTTACCTCCTTCACTTTCCCGTGGATA	2	54	1
TATATATCCTTCTTCTACTTTACGGTGAACG	15	83	1
         GCCCTTCTCTCTCCTTTAAATT	0	1	1
ACTGAAGGCTTCCTTTACCTTGTCCCTCGCT	6	230	0
TTCCCCACTCTCCTCACCCTTAACTTGGCGT	5	25	1
CGAACCCGCGACCTCCGCCTTGTAAGGGCGG	18	211	0
AAGAATGTTCCTTTTCGGCTTTTCTGATTAC	15	131	0
CTTCGGCGGACTTTTAGCCTTTGTATTTATT	15	49	1
GCGGGCTTACCCTTGCTCCCTTTCGGGCCTG	14	110	0
      TTCCCTTACCTCTTTTGCAATTGGC	1	34	0
AAGGATATCCTTTTCATCCCTCAGTTCCCTT	6	68	0
GGGGCTACCACTCTTCCGTTTTTCTTATCAC	18	60	0
          ****** ****
MAP Score: 16.7673

Motif 4
AATATCCTCCTAAATAAAAATTTAAAGGAG	0	20	0
TCAGAAAATTATAACATAAATTTG      	1	4	0
AAAGATTTACTAAATAAATATTATATTCCC	3	25	1
CTCAGTTGTGAAAATAAAAAAGAGTGCAAA	5	57	1
AGGCCGTAAATTAAGAAAAACACCATAACG	5	154	1
CTAGAGATTTATAACAAAAATCAAAAAGTG	7	27	1
CCGAGCTTATAAAACAAAAAGAGTCCGAAA	9	29	0
TAAAAATTTTAAAAGAAAAAGAAGGGAAAA	11	18	0
GGCTAATTAATAAATATAAACCTCGTGAAA	14	54	0
GCAGGGTCCTAAAACAAATACCCTCCAGAG	14	151	1
TTACTTACTAAAAACATAAAAAAATCGTCA	15	13	0
AAAAAGTTAGAAAATAAATAGGAGGGGCTT	15	278	1
CAGGTGGGTGATAAGAAAAACGGAAGAGTG	18	53	1
GCCTTGTTTATAAATAAAAAAAGAGTGGCA	18	159	0
          **********
MAP Score: 13.8762

Motif 5
  GCCCTTCTCTCTCCTTTAAATTTTTATTTAGG	0	8	1
      TCCAATATCCTCCTAAATAAAAATTTAA	0	25	0
     TTCTCCACTCCTTATAAAGATTTACTAAA	3	5	1
AAGTATTAGGCTATCCTTAAAAGATTTGTGTGAG	4	19	1
TCATTGAATTAACTTCTTGAGAGGTATATTCTGA	5	226	1
CTTGAGAGGTATATTCTGAAAAGGAGGAGGAAAG	5	241	1
TTCCCTTTTTACCTCCTCCATAGTCTCCTGAAAG	6	41	0
GATGAAAAGGATATCCTTGAAAAGGACGGAGTGG	6	81	1
TAACTTGACACACTTCTTCAAAATGAATAAAATT	7	65	1
        CGCTCTCCTCCGAAAGTAGAGTGTAA	7	97	0
        TTATTCCCTAACAAGGAGGTCATAA 	8	2	1
   CTATATTACCTCCTTTAAAGTTT        	10	2	0
     ACCAGACCTCCTTCAAAGGCTCTCATAAT	13	51	0
     TTTACACCTCCTGGTTAGTAAATTCTAAT	14	5	1
ACCTCGTGAAATTTCCTGTAAAGTGGATTAGAAT	14	31	0
CCTAAAACAAATACCCTCCAGAGGTAATAA    	14	158	1
AGGAAGTAATAAACTCTCTCAAAGCCCTAAAGGT	15	171	1
    CCCATTCACCTCTTCCGAGTTTAAAGCAAG	16	25	0
TGGGAGAGCGCCGCCCTTACAAGGCGGAGGTCGC	18	201	1
          * *****   ****
MAP Score: 13.4726

Motif 6
TCCAATATCCTCCTAAATAAAAATTTAAAGGA	0	21	0
GCTCAGAAAATTATAACATAAATTTG      	1	4	0
CAAGCTGTGTTCCTAACTTAAAATTAACTACA	3	67	1
TATGAATAACTTATAAAACCAAGCTCTTCTGT	4	80	1
CTCTAGAGATTTATAACAAAAATCAAAAAGTG	7	25	1
GTCTCCGAGCTTATAAAACAAAAAGAGTCCGA	9	31	0
  TTTAAAAATTTTAAAAGAAAAAGAAGGGAA	11	20	0
GTTGCAAAGGTTATAAACGAAACCTGTTTAAA	12	18	1
GTGCGCAGGGTCCTAAAACAAATACCCTCCAG	14	147	1
CATTAAAAAGTTAGAAAATAAATAGGAGGGGC	15	274	1
CCCGCCTTGTTTATAAATAAAAAAAGAGTGGC	18	160	0
          *******  ***
MAP Score: 10.9012

Motif 7
ATTTATGAATAACTTATAAAACCAAGCTCTT	4	77	1
ACTTCTTCAAAATGAATAAAATTACACTCTA	7	76	1
GTCCTGATAGAACTTATAAATCAGGCTCAGG	6	195	1
     AATTAAAAGTATAAATTCCCCACTCT	5	5	1
CCGCAGGGCTAATTAATAAATATAAACCTCG	14	59	0
AAGGATATATAAAGAATAAATACAAAGGCTA	15	63	0
AACCATTAAAAAGTTAGAAAATAAATAGGAG	15	271	1
TGAGGCCGTAAATTAAGAAAAACACCATAAC	5	152	1
GAGATTTATCAAGGAAGAAAAATAACGATTT	4	50	1
GACGCAAAGGAAGTAATAAACTCTCTCAAAG	15	164	1
CAGGTCTCCGAGCTTATAAAACAAAAAGAGT	9	35	0
     TTTAAAAATTTTAAAAGAAAAAGAAG	11	24	0
          AACGATTAAAAGTATTAGGCT	4	0	1
TTGGCTCAGAAAATTATAACATAAATTTG  	1	8	0
AATTTAGATTAAGGTTTAAATGTTACGGAAT	13	23	0
CCTTGTTTATAAATAAAAAAAGAGTGGCACC	18	157	0
GAAGTTGCAAAGGTTATAAACGAAACCTGTT	12	15	1
AAGGGAACTGAGGGATGAAAAGGATATCCTT	6	68	1
GGTCTTGGAGAGATATTAAACATAGAGTTTA	6	129	1
          ** ********
MAP Score: 9.9583

Motif 8
TGACTTTTTTGAGTTTACCTCCTTCACTTTCCCGTGGATAATGAGCT	2	45	1
TTCGGGCCTGGGGGAGTTCACCCTGTCCCGCCGCAGGGCTAATTAAT	14	73	0
AAGGGAGCAAGGGTAAGCCCGCCGTCCCGTGCGCAGGGTCCTAAAAC	14	119	1
AAACGGAAGAGTGGTAGCCCCCGTCGTCTAGCCTGGCCTAGGACGCC	18	70	1
GTCTAGCCTGGCCTAGGACGCCGGCCTTTCACGCCGGAAACGCGGGT	18	95	1
GCTCAGTTGGGAGAGCGCCGCCCTTACAAGGCGGAGGTCGCGGGTTC	18	194	1
          * *     * **    *    **  **
MAP Score: 4.35718

Motif 9
GTATTGGGGACAGATTGAAGGCGGAAAGCGTTTT	5	98	1
GAGAGGTATATTCTGAAAAGGAGGAGGAAAGAGA	5	244	1
GGATATCCTTGAAAAGGACGGAGTGGAAATAGTC	6	89	1
     TTATTCCCTAACAAGGAGGTCATAA    	8	5	1
AATTATGAGAGCCTTTGAAGGAGGTCTGGT    	13	50	1
ACAGGGTGAACTCCCCCAGGCCCGAAAGGGAGCA	14	94	1
AGGACCCTGCGCACGGGACGGCGGGCTTACCCTT	14	127	0
GTCTAGCCTGGCCTAGGACGCCGGCCTTTCACGC	18	95	1
TAGGACGCCGGCCTTTCACGCCGGAAACGCGGGT	18	108	1
AAAAAAGAGTGGCACCCCCGGCGGGATTTGAACC	18	139	0
GAGAGCGCCGCCCTTACAAGGCGGAGGTCGCGGG	18	204	1
CGGGAATTTTTGAATGGTAGGCGGGGCGGGACTC	18	241	0
          * *   ********
MAP Score: 1.33003

Motif 10
TTAAGTTCTTTCCTCTTTTCCCTTTCACTCTCCTTG	2	11	1
AAGTATAAATTCCCCACTCTCCTCACCCTTAACTTG	5	16	1
GCAAGGGTAAGCCCGCCGTCCCGTGCGCAGGGTCCT	14	125	1
AAGAGTGGTAGCCCCCGTCGTCTAGCCTGGCCTAGG	18	76	1
GGCCTAGGACGCCGGCCTTTCACGCCGGAAACGCGG	18	104	1
TTCAAATCCCGCCGGGGGTGCCACTCTTTTTTTATT	18	141	1
TTGGGAGAGCGCCGCCCTTACAAGGCGGAGGTCGCG	18	200	1
CGGGTTCGAGTCCCGCCCCGCCTACCATTCAAAAAT	18	234	1
          ***** * * **   *
MAP Score: 0.897355

Motif 11
         GCCCTTCTCTCTCCTTTAAATTTTTATT	0	1	1
TTTAAGTTCTTTCCTCTTTTCCCTTTCACTCTCCTTG	2	10	1
TTTTTGAGTTTACCTCCTTCACTTTCCCGTGGATAAT	2	50	1
AAAGTATAAATTCCCCACTCTCCTCACCCTTAACTTG	5	15	1
  TCTCTTTCCTCCTCCTTTTCAGAATATACCTCTCA	5	243	0
         GCTTTCCTTTTTCCCTTCTTTTTCTTTT	11	1	1
TCTTTATATATCCTTCTTCTACTTTACGGTGAACGAA	15	79	1
ATTTAGCTTTCTCCACACTTTCCTCTTTGAGTATTTT	15	221	0
TGGCCTAGGACGCCGGCCTTTCACGCCGGAAACGCGG	18	103	1
GTTGGGAGAGCGCCGCCCTTACAAGGCGGAGGTCGCG	18	199	1
GTTCGAGTCCCGCCCCGCCTACCATTCAAAAATTCCC	18	237	1
          * ** * *** **   *
MAP Score: 0.187987