AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_operons026_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236005
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	aq_040	56	putative protein
#1	aq_041	32	putative protein
#2	petA	125	Rieske-I iron sulfur protein
#3	hisF	49	HisF (cyclase)
#4	glgP	110	glycogen phosphorylase
#5	speC	35	ornithine decarboxylase
#6	hisD	300	histidinol dehydrogenase
#7	pyrDB	67	dihydroorotate dehydrogenase electron transfer subunit
#8	oadA	43	oxaloacetate decarboxylase alpha chain
#9	hisC	264	histidinol-phosphate aminotransferase
#10	aq_2087	28	putative protein
#11	pepA	26	leucine aminopeptidase

Motif 1
TTAAAGGTTAGGAAGTTAAAATAAACTTG 	2	9	0
TTTACTACTCGGCGGTGAAAATTTTTATAA	2	67	0
TTAAATTTCAGGAGGTGGTATT        	2	113	1
TACTTCCCTTAGAGGTTATAAACTTCTACT	6	139	1
CGTTCCAAAGAGAGGTGAAAAGGCTTACTC	6	182	1
TTAAAGCTGGTGAGGTGATAGC        	8	31	1
         AGGAGGTGGTATTATGGCAAG	9	1	1
AGTGCTCTTTGGAAGGGAAAGGGTAACCTT	9	59	0
TATAGCTCAGGGAGATGAAAAGAAGTTGAA	9	106	1
GGAGATGAAAAGAAGTTGAATAAATTAATA	9	116	1
AACACAAGGAAGAAGCGGAAGAAACTGAGG	9	222	1
AACTTATTTTAGCGGTTATAATTAA     	10	5	0
          **********
MAP Score: 15.5927

Motif 2
AATCGTTTCTCTTTTCCTCGTTTACCTTGC	6	254	1
       TTCCCTTACCTCTTTTGCAATTG	3	3	1
CGGAGTAAGCCTTTTCACCTCTCTTTGGAA	6	184	0
ATTCTGCGAACTTATCCTCTATTATTCCCC	9	147	0
TTGGGTCCTGCTTTTCTTCTTCTTGCCATA	9	22	0
TATTCAACTTCTTTTCATCTCCCTGAGCTA	9	108	0
GGAAGGTTACCCTTTCCCTTCCAAAGAGCA	9	57	1
AATTACGTCGCTTTTCCCGTTGTTGTAATC	6	228	1
GATGTATTTGGTTTTCCTCGTAATACTTCC	6	116	1
       TCTCCTTCCTCCTGAAACTTAAT	7	3	1
          GCTATCACCTCACCAGCTTT	8	33	0
AGGTGAAAAGGCTTACTCCGTTTACGACAG	6	194	1
ATTTTAACTTCCTAACCTTTAATTAACTTT	2	17	1
GATTTCTGGACTTTACATGGTAAAGCTTTT	6	56	1
          **********
MAP Score: 10.8981

Motif 3
      CAAGTTTATTTTAACTTCCTAACC	2	4	1
TAACCTTTAATTAACTTTATGTATATATAA	2	29	1
TAAACCAAACTATATTTTACTACTCGGCGG	2	82	0
TATAGTTTGGTTTACTTAAATTTCAGGAGG	2	98	1
CCTCACAAGATTCATTTTAAAAAACTGCTT	4	18	1
      TACTTGTATTTTATAGTAAATCCG	4	96	0
CACTGATTTCTGGACTTTACATGGTAAAGC	6	52	1
      AATATGGATTTTAAGGTTTAATTA	6	286	0
CTCCTGAAACTTAATTTTAAAACAACATTT	7	18	1
AACATTTTATTGTATTTTAATTAAAATAAA	7	41	1
    ACTTGATTTATTTTAATTAAAATACA	7	51	0
GTTTATACTATATACTTTAA          	11	0	0
          **********
MAP Score: 10.1475

Motif 4
ATTAAGTTTCAGGAGGAAGGAGA          	7	0	0
CTTAAATTTCAGGAGGTGGTATT          	2	112	1
          AGGAGGTGGTATTATGGCAAGAA	9	0	1
GAAGAAACTGAGGAAACCGAACAACCTGCAACG	9	239	1
GAACACAAGGAAGAAGCGGAAGAAACTGAGGAA	9	221	1
GTATTATGGCAAGAAGAAGAAAAGCAGGACCCA	9	18	1
GGGAGATGAAAAGAAGTTGAATAAATTAATAAG	9	115	1
ATTAAAGGTTAGGAAGTTAAAATAAACTTG   	2	7	0
AGCTATACCAAGGAGTATGTAGTAAGTGCTCTT	9	80	0
AAGTATTACGAGGAAAACCAAATACATCTTAAG	6	111	0
AAGGTAAACGAGGAAAAGAGAAACGATTACAAC	6	249	0
TGAATAAATTAATAAGGGGAATAATAGAGGATA	9	132	1
          ******  *** *
MAP Score: 8.06033

Motif 5
     ATCGTAAGAAACGGTAGGGACGCTGAT	0	39	0
AAGTTAATTAAAGGTTAGGAAGTTAAAATAAA	2	14	0
CCTGAAATTTAAGTAAACCAAACTATATTTTA	2	93	0
AAGTATTACGAGGAAAACCAAATACATCTTAA	6	112	0
TGGAACGTAAAAGTTGACCAAGTAGAAGTTTA	6	157	0
AATTACTGCAAGGTAAACGAGGAAAAGAGAAA	6	259	0
ATTTTAATTAAAATAAATCAAGT         	7	54	1
GTATTATGGCAAGAAGAAGAAAAGCAGGACCC	9	18	1
AGCAGGACCCAAGTACAGGAAGGTTACCCTTT	9	40	1
CATCTCCCTGAGCTATACCAAGGAGTATGTAG	9	91	0
GGTATAGCTCAGGGAGATGAAAAGAAGTTGAA	9	104	1
GGGTTTGGTCAGGTACATCTGGAGTTCTTCTA	9	183	0
CAAACCCGAAAGGGAACACAAGGAAGAAGCGG	9	208	1
GAACACAAGGAAGAAGCGGAAGAAACTGAGGA	9	221	1
GAAGAAACTGAGGAAACCGAACAACCTGCAAC	9	239	1
          ***** * ****
MAP Score: 7.69444

Motif 6
    AGGAGTCATTTGATCTAGGTAGTATTTGTATCAGCG	0	6	1
ACCGCCGAGTAGTAAAATATAGTTTGGTTTACTTAAATTT	2	81	1
 AGCAAATATCTATAAAAGTATTTATATTTATCGGA    	5	9	1
ATACTCACAAACTTGGAAATACTTGGCTTTTTTACAGCAC	6	15	1
ATGGTTAAGGCTTAAGATGTATTTGGTTTTCCTCGTAATA	6	101	1
CGTTTACGACAGGTTTAATTACGTCGCTTTTCCCGTTGTT	6	212	1
TTAATTTTAAAACAACATTTTATTGTATTTTAATTAAAAT	7	28	1
        CTCGTATTATATTATTAGTTTTTAAAGCTGGT	8	2	1
        TCCGTTGCAGGTTGTTCGGTTTCCTCAGTTTC	9	242	0
          *     *  ** ** * ***
MAP Score: 6.19677

Motif 7
      AAAAAGTTTTTAAAAAGCCCCAAA	1	18	0
      CAAGTTTATTTTAACTTCCTAACC	2	4	1
CTGTGTAAGCAGTTTTTTAAAATGAATCTT	4	24	0
      TACTTGTATTTTATAGTAAATCCG	4	96	0
TATCTATAAAAGTATTTATATTTATCGGA 	5	16	1
CTTCCCTTAGAGGTTATAAACTTCTACTTG	6	141	1
TTTACCTTGCAGTAATTAAACCTTAAAATC	6	274	1
      AATATGGATTTTAAGGTTTAATTA	6	286	0
AATAAAATGTTGTTTTAAAATTAAGTTTCA	7	22	0
AACATTTTATTGTATTTTAATTAAAATAAA	7	41	1
    ACTTGATTTATTTTAATTAAAATACA	7	51	0
TTATATTATTAGTTTTTAAAGCTGGTGAGG	8	16	1
          **********
MAP Score: 5.39527

Motif 8
GTATTATGGCAAGAAGAAGAAAAGCAGGACC	9	18	1
GGTATAGCTCAGGGAGATGAAAAGAAGTTGA	9	104	1
ATAAATTAATAAGGGGAATAATAGAGGATAA	9	135	1
GCAGAATCTACAGTAGAAGAACTCCAGATGT	9	170	1
CACAAGGAAGAAGCGGAAGAAACTGAGGAAA	9	224	1
          *** *******
MAP Score: 1.5699

Motif 9
TTAACTTCCTAACCTTTAATTAACTTTATGTAT	2	20	1
  AATACCACCTCCTGAAATTTAAGTAAACCAA	2	104	0
AATACTCACAAACTTGGAAATACTTGGCTTTTT	6	14	1
AGAAGTTTATAACCTCTAAGGGAAGTATTACGA	6	133	0
GCAGTAATTAAACCTTAAAATCCATATT     	6	282	1
  TCTCCTTCCTCCTGAAACTTAATTTTAAAAC	7	8	1
TACCTGACCAAACCCGAAAGGGAACACAAGGAA	9	200	1
GAAACCGAACAACCTGCAACGGA          	9	251	1
          ****** ** * *
MAP Score: 1.20794