AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_operons011_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944235292
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	nsd	277	nucleotide sugar dehydrogenase
#1	rodA	168	rod shape determining protein RodA
#2	aq_027	72	hypothetical protein
#3	aq_028	46	putative protein
#4	rpmB	44	ribosomal protein L28
#5	kdsA	264	3-deoxy-d-manno-octulosonic acid 8-phosphate synthase
#6	bioA	197	DAPA aminotransferase
#7	thiE2	37	thiamine phosphate synthase
#8	recN	163	recombination protein RecN
#9	mrcA	34	penicillin binding protein 1A
#10	gsa	24	glutamate-1-semialdehyde aminotransferase
#11	nifU	186	NifU protein
#12	aq_900	119	putative protein
#13	aroE	266	shikimate 5-dehydrogenase
#14	aq_972_secD	25	aq_972: hypothetical protein, secD: protein export membrane protein SecD
#15	cphA2	42	beta lactamase precursor
#16	aq_1137	29	putative protein
#17	aroA	37	5-enolpyruvylshikimate-3-phosphate synthetase
#18	aq_1873	300	putative protein
#19	rplM	45	ribosomal protein L13
#20	aq_2066	39	hypothetical protein
#21	argB	73	acetylglutamate kinase

Motif 1
CTCCTTCAAAGGAAAGGTAAACGGTGTCTTC	13	115	0
TTCCATTTCTGGAAAGGATAAC         	5	1	0
TGAGTTAATAGAAAAGGCTAAGTTCTTCAGG	21	11	1
AAGGAGACGAGGTAAGGGTAATTA       	1	154	1
AGAACCTGAGGGAAAAGGAAAGAATGATTAA	15	12	0
CGGATATTTTGGGAAGGATAAGGGTGTACAG	6	66	0
TTCAGGTGTTGAAAAGGAAATTATGAATGTT	8	44	1
GAATAATAATGAAAAAGGAAATCGTCTTAAG	0	17	1
GGTGTACAGGGATGAGGCAAACTTCCTTATA	6	44	0
CAGAAAAGCCGAAAAGGAACATTCTTTTGAC	18	136	1
TAGAATTCCTGGTAAGGATTACTCCGCCCGC	0	164	1
CAAGAACGCTGAGGAGGAAAAACCTCACGGG	5	131	0
AAAAGTAAACGATAAAGAAAACAAGAACGCT	5	152	0
CCGCCAAACAGATAAAGGAAATGGAAATAGG	12	75	1
GGAATTTCACGGAAAGGTTTTC         	21	61	1
ACGAGAAGCTGGAAAGGATTTGTTCCGTAAT	6	111	0
CGTTAAGAACGGTGAGGTTATATCCGAGGAC	1	110	1
TACACCCCAAGGACAGGGAAAAAGCTCTGAA	2	20	1
TGAGAAAATAGATGAGGAATACAAGAATGCA	0	51	1
GGAAAGTGTGGAGAAAGCTAAATCCATCCTT	18	235	1
AGAAGAGCCAAAAAAGGGAAAAATCCCATAG	5	92	1
CCGTAAAGTAGAAGAAGGATATATAAAGAAT	18	77	0
TTTAAACTCGGAAGAGGTGAATGGG      	19	30	1
AAAACCTCACGGGAAAGGTTACTATGGGATT	5	113	0
AAGAGCTCAAGGAAAAGAACTTC        	2	59	1
TCTTTTTTAGAGTAAGGTTAAATTAGTAGTT	5	243	1
GAAAAGTTCGGAAAAAGCTTTCCCTGAGAGG	0	204	0
TCTTTCCCCCGGTAAAGCACTT         	1	1	0
GAACGAACTGAGGGAGGTTAAAGTAATCAGA	18	109	1
CTTAACGACTAAAGAGGAAATAGGGGAAAGA	1	86	0
AATTTCCCGAAAAGAAGTTAAAGGCTAAAGA	1	37	1
          ******* ***
MAP Score: 26.7735

Motif 2
TGAAATGAAGAAGGTTGAAGAAATTGAAAA	13	18	1
AGTTCTCTCGGAGGTAGAAGA         	4	33	1
GTTAGAACCTGAGGGAAAAGGAAAGAATGA	15	16	0
TTACTTTTACAAGGCTGAAGGGGCTATTCT	5	175	1
CTTCAAAGGAAAGGTAAACGGTGTCTTCCT	13	113	0
TACAGTAATTAAGGGAAACGTCAAGTGGGT	13	195	1
AAAGAAGTTAAAGGCTAAAGAGCTCTTAAA	1	47	1
CGAACTGAGGGAGGTTAAAGTAATCAGAAA	18	112	1
GTAGAACCCCAAGGTATAAGGAAGTTTGCC	6	30	1
   GAACATAAAGGCTGACGTAGTTCACGA	12	7	1
CTATTTTCTCAAGGCTTAAGACGATTTCCT	0	32	0
AGAGCCAAAAAAGGGAAAAATCCCATAGTA	5	95	1
CGTTCACCGTAAAGTAGAAGAAGGATATAT	18	84	0
ATTCATTTGCAAGGTTTACGTTATGACTGA	11	125	0
ATTTTTTCAGGAGGTAAAAAAATC      	3	4	0
GAACAAGAACGAGGGAAAAATTTAAGAGCG	0	125	1
AATAAATACAAAGGCTAAAAGTCCGCCGAA	18	50	0
TAAATACTTTACGGGAGAAG          	9	24	1
CAGCCTTGTAAAAGTAAACGATAAAGAAAA	5	162	0
CAAGGATTGAAAGGTTTAAAAAAGGCTACC	0	80	1
ATACGTGGAAGAAGGAGACGAGGTAAGGGT	1	143	1
GATATTTTGGGAAGGATAAGGGTGTACAGG	6	65	0
GTGGGTTAAGAAAGTAGAAATAACTCAGCA	13	219	1
          **********
MAP Score: 26.1497

Motif 3
CCTTGAGAAAATAGATGAGGAATACAAGAATGCAAGGATT	0	48	1
ATTAAGTTTAGAAGAACAAGAACGAGGGAAAAATTTAAGA	0	112	1
TTGAAAATCTACACCCCAAGGACAGGGAAAAAGCTCTGAA	2	11	1
TGTAAAAGTAAACGATAAAGAAAACAAGAACGCTGAGGAG	5	146	0
AGCTGGAAGAAACGCCCGAGAAGGTGGGAAATCGTAAAGA	5	204	0
TATTACAGTAGAACCCCAAGGTATAAGGAAGTTTGCCTCA	6	23	1
GAAGGATAAGGGTGTACAGGGATGAGGCAAACTTCCTTAT	6	45	0
AAATAGTAATGATGCACGAGAAGCTGGAAAGGATTTGTTC	6	117	0
TTTTTCAGGTGTTGAAAAGGAAATTATGAATGTTTAAATT	8	41	1
CAACCGGAACGGGGCAAAAGGTTCCCGTAACGTCGTGAAC	12	29	0
AAACCGCCAAACAGATAAAGGAAATGGAAATAGGCCAGGT	12	72	1
GTATGGCTGAAATGAAGAAGGTTGAAGAAATTGAAAAAGT	13	11	1
GAAACGTCAAGTGGGTTAAGAAAGTAGAAATAACTCAGCA	13	209	1
GGAAAAGTTAGAACCTGAGGGAAAAGGAAAGAATGATTAA	15	12	0
  AATTACTCGAAGTCGGAGAAAGAGTAAAATCTTTTCT 	17	8	1
TCACCGTAAAGTAGAAGAAGGATATATAAAGAATAAATAC	18	71	0
CGGTGAACGAACTGAGGGAGGTTAAAGTAATCAGAAAAGC	18	105	1
ACATTCTTTTGACGCAAAGGAAGTAATAAACTCTCTCAAA	18	154	1
          *  *   *****    * **
MAP Score: 24.0242

Motif 4
AATAATAATGAAAAAGGAAATCGTCTTAAG	0	18	1
GAAGAACAAGAACGAGGGAAAAATTTAAGA	0	122	1
CTTAACGACTAAAGAGGAAATAGGGGAAAG	1	87	0
GGAAGAAGGAGACGAGGTAAGGGTAATTA 	1	149	1
ACACCCCAAGGACAGGGAAAAAGCTCTGAA	2	21	1
TGCTTTCGTTGTAAAGGAAACCGCTTAAAA	5	57	0
AGAAGAGCCAAAAAAGGGAAAAATCCCATA	5	92	1
CAAGAACGCTGAGGAGGAAAAACCTCACGG	5	132	0
TTCAGCCTTGTAAAAGTAAACGATAAAGAA	5	164	0
TTCAGGTGTTGAAAAGGAAATTATGAATGT	8	44	1
CGCCAAACAGATAAAGGAAATGGAAATAGG	12	76	1
TCCTTCAAAGGAAAGGTAAACGGTGTCTTC	13	115	0
GAACCTGAGGGAAAAGGAAAGAATGATTAA	15	12	0
GAAGTCGGAGAAAGAGTAAAATCTTTTCT 	17	18	1
CGTAAAGTAGAAGAAGGATATATAAAGAAT	18	77	0
AAAAATACTCAAAGAGGAAAGTGTGGAGAA	18	220	1
          **********
MAP Score: 15.1469

Motif 5
TCGGAAAAAGCTTTCCCTGAGAGGATATCTTCAG	0	194	0
TCAGGGAAAGCTTTTTCCGAACTTTTCAGAGAAA	0	208	1
AAAGAGTACGAATTTCCCGAAAAGAAGTTAAAGG	1	27	1
CTTTCAGAGCTTTTTCCCTGTCCTTGGGGTGTAG	2	19	0
    GAAGTTCTTTTCCTTGAGCTCTTCTACGGC	2	52	0
     GTTATCCTTTCCAGAAATGGAACGTCCAG	5	5	1
CCCATAGTAACCTTTCCCGTGAGGTTTTTCCTCC	5	116	1
CGGAACAAATCCTTTCCAGCTTCTCGTGCATCAT	6	115	1
TACTTTAAATTATTTCCCGAATTTTTCAGGTGTT	8	20	1
          CTTCTCCCGTAAAGTATTTAATAT	9	20	0
ACGGGGCAAAAGGTTCCCGTAACGTCGTGAACTA	12	27	0
GGCCTATTTCCATTTCCTTTATCTGTTTGGCGGT	12	74	0
   CCGCTATCAGTTCCAGAACCTGGCCTATTTC	12	98	0
ACACCGTTTACCTTTCCTTTGAAGGAGGTTGCTC	13	119	1
ACCCACTTGACGTTTCCCTTAATTACTGTATCAA	13	191	0
TCATTCTTTCCTTTTCCCTCAGGTTCTAACTTTT	15	16	1
CGTCAAAAGAATGTTCCTTTTCGGCTTTTCTGAT	18	134	0
          * ******* *  *
MAP Score: 10.2633

Motif 6
GGCGGAGTAATCCTTACCAGGAATTCTACTAA	0	160	0
GCTGAAGATATCCTCTCAGGGAAAGCTTTTTC	0	193	1
       AAGTGCTTTACCGGGGGAAAGAGTA	1	3	1
AGCCTTTAACTTCTTTTCGGGAAATTCGTACT	1	31	0
      GTTATCCTTTCCAGAAATGGAACGTC	5	4	1
TTAAGCGGTTTCCTTTACAACGAAAGCATATA	5	59	1
TCCCATAGTAACCTTTCCCGTGAGGTTTTTCC	5	115	1
GTGAGGTTTTTCCTCCTCAGCGTTCTTGTTTT	5	134	1
TACACCCTTATCCTTCCCAAAATATCCGAGAG	6	69	1
ACGGAACAAATCCTTTCCAGCTTCTCGTGCAT	6	114	1
ATTCATAATTTCCTTTTCAACACCTGAAAAAT	8	40	0
ATATATTAAATACTTTACGGGAGAAG      	9	18	1
GCCTTGATGTTCCTTAAGAGCAGGCCTTATTT	13	59	0
TGGAGCAACCTCCTTCAAAGGAAAGGTAAACG	13	123	0
ATCCTTCTTCTACTTTACGGTGAACGAACTGA	18	88	1
AAAAGAATGTTCCTTTTCGGCTTTTCTGATTA	18	132	0
GTTTATTACTTCCTTTGCGTCAAAAGAATGTT	18	153	0
          ****** *** *
MAP Score: 8.31165

Motif 7
TAAAGTATCGCTCTTAAATTTTTCCCTCGTTCTTGTTCTTC	0	122	0
TTTTCGGGAAATTCGTACTCTTTCCCCCGGTAAAGCACTT 	1	9	0
GCTCTTAAAGAAGCTCGGTCTTTCCCCTATTTCCTCTTTAG	1	68	1
GGAAAGGTTACTATGGGATTTTTCCCTTTTTTGGCTCTTCT	5	92	0
AGGGGCTATTCTCTTTACGATTTCCCACCTTCTCGGGCGTT	5	193	1
CATCCCTGTACACCCTTATCCTTCCCAAAATATCCGAGAGG	6	61	1
TAATTTAATACTTTAAATTATTTCCCGAATTTTTCAGGTGT	8	12	1
CTTTCTTAACCCACTTGACGTTTCCCTTAATTACTGTATCA	13	192	0
  AATTAATCATTCTTTCCTTTTCCCTCAGGTTCTAACTTT	15	8	1
         CCCATTCACCTCTTCCGAGTTTAAAGCAAGAT	19	23	0
          *  *    * ******    *
MAP Score: 7.27901

Motif 8
       ATTTTTAGAATAATAATGAAAAA	0	3	1
CCCCATTAAGTTTAGAAGAACAAGAACGAG	0	108	1
AGAGCGATACTTTAGTAGAATTCCTGGTAA	0	149	1
AGGTTTTAATTTTAACAGAAAGTATATTAA	0	255	0
          GTTAAAAGATTTTAATATAA	4	0	1
GTTAAAAGATTTTAATATAATAAAGTTCTC	4	10	1
CCAGCTCTTTTTTAGAGTAAGGTTAAATTA	5	238	1
CGGGAAATAATTTAAAGTATTAAATTATT 	8	9	0
        TATTTAGAATATATTAAATACT	9	2	1
 TAAGTTAAATTTAAAATAACAAGT     	10	9	1
AGCAACCTCCTTCAAAGGAAAGGTAAACGG	13	122	0
AAATTAATGATTTAATATATAAAACTCAC 	16	9	0
ACTGAGGGAGGTTAAAGTAATCAGAAAAGC	18	115	1
CTTCCTTTGCGTCAAAAGAATGTTCCTTTT	18	147	0
      ATGAGTTAATAGAAAAGGCTAAGT	21	4	1
          **********
MAP Score: 4.70938

Motif 9
AGGATATCTTCAGCGGGCGGAGTAATCCTTAC	0	175	0
AGTGCTTTACCGGGGGAAAGAGTACGAATTTC	1	11	1
TTAACGACTAAAGAGGAAATAGGGGAAAGACC	1	84	0
GAGGTTATATCCGAGGACGAATACGTGGAAGA	1	123	1
GAGGACGAATACGTGGAAGAAGGAGACGAGGT	1	135	1
GAAGAAGGAGACGAGGTAAGGGTAATTA    	1	150	1
AATCTACACCCCAAGGACAGGGAAAAAGCTCT	2	16	1
AAAGCCGTAGAAGAGCTCAAGGAAAAGAACTT	2	49	1
AAAGTTCTCTCGGAGGTAGAAGA         	4	31	1
AACAAGAACGCTGAGGAGGAAAAACCTCACGG	5	132	0
TACTCTAAAAAAGAGCTGGAAGAAACGCCCGA	5	225	0
CTTCGTAAGCCTGAGGTCGTGGGTTCGAATCC	8	120	1
GCTCCGGACCCCGGGGTCGCGGGTTCAAGTCC	11	38	0
CTCAGGTGGACAGAGCACGGGGCTCCGGACCC	11	59	0
CTCTGTCCACCTGAGCTACGGGCACTATTATA	11	76	1
GCAACCGGAACGGGGCAAAAGGTTCCCGTAAC	12	38	0
CAACCTCCTTCAAAGGAAAGGTAAACGGTGTC	13	118	0
AAGTTAGAACCTGAGGGAAAAGGAAAGAATGA	15	16	0
TACTCGAAGTCGGAGAAAGAGTAAAATCTTTT	17	13	1
AAAAGTCCGCCGAAGGTAGGATTACTTACTAA	18	32	0
GAATAAATACAAAGGCTAAAAGTCCGCCGAAG	18	49	0
TCTTTTGACGCAAAGGAAGTAATAAACTCTCT	18	158	1
          * ******* **
MAP Score: 1.78761