AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_operons026_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944235988
 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	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
          **********
MAP Score: 13.9329

Motif 2
      CAAGTTTATTTTAACTTCCTAACC	2	4	1
TAACCTTTAATTAACTTTATGTATATATAA	2	29	1
TAAACCAAACTATATTTTACTACTCGGCGG	2	82	0
TACCACCTCCTGAAATTTAAGTAAACCAAA	2	103	0
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          	10	0	0
          **********
MAP Score: 10.3976

Motif 3
      TTCCCTTACCTCTTTTGCAATTGG	3	4	1
CAGGCGGCTTCTGTCCCCGTATCATAGATA	4	51	1
ATGTATTTGGTTTTCCTCGTAATACTTCCC	6	117	1
GGTGAAAAGGCTTACTCCGTTTACGACAGG	6	195	1
AATTACGTCGCTTTTCCCGTTGTTGTAATC	6	228	1
ATCGTTTCTCTTTTCCTCGTTTACCTTGCA	6	255	1
       TCTCCTTCCTCCTGAAACTTAAT	7	3	1
TGGGTCCTGCTTTTCTTCTTCTTGCCATAA	9	21	0
GGAAGGTTACCCTTTCCCTTCCAAAGAGCA	9	57	1
GCACTTACTACATACTCCTTGGTATAGCTC	9	84	1
TATCCTCTATTATTCCCCTTATTAATTTAT	9	135	0
TTCCTCAGTTTCTTCCGCTTCTTCCTTGTG	9	224	0
          **********
MAP Score: 9.5794

Motif 4
TACGTTCCAAAGAGAGGTGAAAAGGCTTACTCCG	6	180	1
AAACGATTACAACAACGGGAAAAGCGACGTAATT	6	228	0
CTGCAAGGTAAACGAGGAAAAGAGAAACGATTAC	6	252	0
GTATTATGGCAAGAAGAAGAAAAGCAGGACCCAA	9	18	1
GGTATAGCTCAGGGAGATGAAAAGAAGTTGAATA	9	104	1
TGAATAAATTAATAAGGGGAATAATAGAGGATAA	9	132	1
GAACACAAGGAAGAAGCGGAAGAAACTGAGGAAA	9	221	1
GAAGAAACTGAGGAAACCGAACAACCTGCAACGG	9	239	1
          ** ***  *** **
MAP Score: 7.05957

Motif 5
AAGTTAATTAAAGGTTAGGAAGTTAAAATAA	2	15	0
GAGCCAATTGCAAAAGAGGTAAGGGAA    	3	6	0
ATTTACTATAAAATACAAGTA          	4	99	1
TTTACCATGTAAAGTCCAGAAATCAGTGCTG	6	49	0
AACCTGTCGTAAACGGAGTAAGCCTTTTCAC	6	196	0
ATTTTAATTAAAATACAATAAAATGTTGTTT	7	37	0
GTATTATGGCAAGAAGAAGAAAAGCAGGACC	9	18	1
AGCAGGACCCAAGTACAGGAAGGTTACCCTT	9	40	1
AGATGAAAAGAAGTTGAATAAATTAATAAGG	9	118	1
ATAAATTAATAAGGGGAATAATAGAGGATAA	9	135	1
GCAGAATCTACAGTAGAAGAACTCCAGATGT	9	170	1
GAACACAAGGAAGAAGCGGAAGAAACTGAGG	9	221	1
GAAGCGGAAGAAACTGAGGAAACCGAACAAC	9	233	1
          *** *******
MAP Score: 5.36884

Motif 6
TATCTATGATACGGGGACAGAAGCCGCCTGTGTAAG	4	45	0
TGCAAGGTAAACGAGGAAAAGAGAAACGATTACAAC	6	249	0
TATTATGGCAAGAAGAAGAAAAGCAGGACCCAAGTA	9	19	1
TAGCTCAGGGAGATGAAAAGAAGTTGAATAAATTAA	9	108	1
TAAATTAATAAGGGGAATAATAGAGGATAAGTTCGC	9	136	1
AATCTACAGTAGAAGAACTCCAGATGTACCTGACCA	9	174	1
CCAAACCCGAAAGGGAACACAAGGAAGAAGCGGAAG	9	207	1
          *** *** *  **  *
MAP Score: 3.50108

Motif 7
 TCCGCCCCTTTGGGGCTTTTTAAAAACTTTTT        	1	9	1
AATTAAAGGTTAGGAAGTTAAAATAAACTTG          	2	0	0
TATTTTAACTTCCTAACCTTTAATTAACTTTATGTATATAT	2	16	1
TAATTAACTTTATGTATATATAACGAAATTTTTATAAAAAT	2	36	1
GTATATATAACGAAATTTTTATAAAAATTTTCACCGCCGAG	2	49	1
ATTTTCACCGCCGAGTAGTAAAATATAGTTTGGTTTACTTA	2	75	1
TAGTAAAATATAGTTTGGTTTACTTAAATTTCAGGAGGTGG	2	90	1
CCTGTGTAAGCAGTTTTTTAAAATGAATCTTGTGAGGTCAC	4	14	0
         TCCGATAAATATAAATACTTTTATAGATATTT	5	13	0
      TCTCCTTCCTCCTGAAACTTAATTTTAAAACAACA	7	4	1
CCTCCTGAAACTTAATTTTAAAACAACATTTTATTGTATTT	7	17	1
TGGTATAGCTCAGGGAGATGAAAAGAAGTTGAATAAATTAA	9	103	1
          *       * ***  ** ***
MAP Score: 3.22554

Motif 8
CCTTTGGGGCTTTTTAAAAACTTTTT    	1	16	1
GGTGAAAATTTTTATAAAAATTTCGTTATA	2	54	0
TGTAAGCAGTTTTTTAAAATGAATCTTGTG	4	21	0
ATACTTGGCTTTTTTACAGCACTGATTTCT	6	33	1
CTGAAACTTAATTTTAAAACAACATTTTAT	7	21	1
ATATTATTAGTTTTTAAAGCTGGTGAGGTG	8	18	1
          **********
MAP Score: 0.776703