AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_operons024_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944235904
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	kdsA	264	3-deoxy-d-manno-octulosonic acid 8-phosphate synthase
#1	argS	26	arginyl-tRNA synthetase
#2	aq_928	45	putative protein
#3	oadA	43	oxaloacetate decarboxylase alpha chain
#4	pstS	300	phosphate-binding periplasmic protein

Motif 1
TAACCTTTCCCGTGAGGTTTTTCCTCCTCAG	0	123	1
TTTTAAAGCTGGTGAGGTGATAGC       	3	29	1
 CATTCGTTTCGTGAAGGTTAGGTGTCTAAT	4	9	1
TAGGCACAGGCGTGCAGGGTTCCTAATGTAC	4	65	1
CCTAATGTACCGTGTGGAGTTGAAACCATAA	4	86	1
CCTAATGTACCGTGTGGAGTTGAAACTTGTC	4	151	1
AGAATTACATCGTCAGGAGTTTCTACTTCAA	4	183	1
CCTAATGTACCGTGTGGAGTTGAAACAACTT	4	218	1
          ******* ***
MAP Score: 18.0556

Motif 2
AGAACGCTGAGGAGGAAAAACCTCACGGGAA	0	129	0
TTAAAGCTGGTGAGGTGATAGC         	3	31	1
TGTACCGTGTGGAGTTGAAACCATAATAGGA	4	91	1
CTGATATGCGGGAGTTCCTAATGTACCGTGT	4	135	1
TGTACCGTGTGGAGTTGAAACTTGTCGAGAA	4	156	1
TACATCGTCAGGAGTTTCTACTTCAAGGTTC	4	188	1
TGTACCGTGTGGAGTTGAAACAACTTAACAA	4	223	1
TAACATTTACGGAGTACAAAACATAATAAGC	4	259	1
GCAAACTCAGGGAGGTAAAAGG         	4	288	1
          ****** ****
MAP Score: 18.0399

Motif 3
ATGGGATTTTTCCCTTTTTTGGCTCTTCTGTATA	0	87	0
AAGGGAAAAATCCCATAGTAACCTTTCCCGTGAG	0	105	1
CTTTACGATTTCCCACCTTCTCGGGCGTTTCTTC	0	205	1
       AACTACTAATTTAACCTTACTCTAAAA	0	247	0
GTTTAACCGTTCCTACCTTCAAGTATTATTAAGA	2	12	0
CGTGCAGGGTTCCTAATGTACCGTGTGGAGTTGA	4	75	1
ATATCAGCATTCCTAAATTCTCCTATTATGGTTT	4	108	0
ATGCGGGAGTTCCTAATGTACCGTGTGGAGTTGA	4	140	1
ACTTCAAGGTTCCTAATGTACCGTGTGGAGTTGA	4	207	1
 CCTTTTACCTCCCTGAGTTTGCTTATTATGTTT	4	277	0
          *****  **  ***
MAP Score: 17.4089

Motif 4
AAAGGGAAAAATCCCATAGTAACCTTTCCCGTGAGGTTTTT	0	104	1
TCGTTTACTTTTACAAGGCTGAAGGGGCTATTCTCTTTACG	0	171	1
TCTTTACGATTTCCCACCTTCTCGGGCGTTTCTTCCAGCTC	0	204	1
        AACTACTAATTTAACCTTACTCTAAAAAAGAGC	0	241	0
AGTTTAACCGTTCCTACCTTCAAGTATTATTAAGAAA    	2	6	0
GCGTGCAGGGTTCCTAATGTACCGTGTGGAGTTGAAACCAT	4	74	1
CATATCAGCATTCCTAAATTCTCCTATTATGGTTTCAACTC	4	102	0
TATGCGGGAGTTCCTAATGTACCGTGTGGAGTTGAAACTTG	4	139	1
TACTTCAAGGTTCCTAATGTACCGTGTGGAGTTGAAACAAC	4	206	1
          **** *   *  ***     *
MAP Score: 10.9378

Motif 5
GTATTATAGGCTTTTTAAGCGGTTTCCTTT	0	45	1
GGATTTTTCCCTTTTTTGGCTCTTCTGTAT	0	88	0
ATCGTTTACTTTTACAAGGCTGAAGGGGCT	0	170	1
ATATTATTAGTTTTTAAAGCTGGTGAGGTG	3	18	1
TTATCAATAACTTATTAGACACCTAACCTT	4	23	0
TAATAAGTTATTGATAAAGCGTTATTTTTT	4	36	1
TAAAGCGTTATTTTTTAGGCACAGGCGTGC	4	50	1
          **********
MAP Score: 2.59105

Motif 6
GTTCCATTTCTGGAAAGGATAAC        	0	2	0
TTCCTTTACAACGAAAGCATATACAGAAGAG	0	68	1
AAAACCTCACGGGAAAGGTTACTATGGGATT	0	113	0
TAAACGATAAAGAAAACAAGAACGCTGAGGA	0	147	0
ACTTGAAGGTAGGAACGGTTAAACTAATTTT	2	22	1
TAAGTTATTGATAAAGCGTTATTTTTTAGGC	4	39	1
ACGGTACATTAGGAACCCTGCACGCCTGTGC	4	68	0
CCGTGTGGAGTTGAAACCATAATAGGAGAAT	4	95	1
AGGAGAATTTAGGAATGCTGATATGCGGGAG	4	118	1
ACGGTACATTAGGAACCTTGAAGTAGAAACT	4	200	0
AAACAACTTAACAAATCCTTAACATTTACGG	4	240	1
          ***** *****
MAP Score: 1.43856