AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_operons024_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944235915
 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
ATGGTTTCAACTCCACACGGTACATTAGGAACCCTGCACGC	4	74	0
GAGTTGAAACCATAATAGGAGAATTTAGGAATGCTGATATG	4	102	1
GTTGTTTCAACTCCACACGGTACATTAGGAACCTTGAAGTA	4	206	0
CAAGTTTCAACTCCACACGGTACATTAGGAACTCCCGCATA	4	139	0
GAGTACAAAACATAATAAGCAAACTCAGGGAGGTAAAAGG 	4	270	1
AAAGCATATACAGAAGAGCCAAAAAAGGGAAAAATCCCATA	0	81	1
AAAAACCTCACGGGAAAGGTTACTATGGGATTTTTCCCTTT	0	104	0
TAACCTTACTCTAAAAAAGAGCTGGAAGAAACGCCCGAGAA	0	222	0
    TTTCTTAATAATACTTGAAGGTAGGAACGGTTAAACT	2	6	1
CGATAAAGAAAACAAGAACGCTGAGGAGGAAAAACCTCACG	0	133	0
          *   * * *  *    *****
MAP Score: 16.2266

Motif 4
AGTAACCTTTCCCGTGAGGTTTTTCCTCCTC	0	121	1
GAGGTTTTTCCTCCTCAGCGTTCTTGTTTTC	0	136	1
AGAGAATAGCCCCTTCAGCCTTGTAAAAGTA	0	176	0
AGGGGCTATTCTCTTTACGATTTCCCACCTT	0	193	1
GGAAGAAACGCCCGAGAAGGTGGGAAATCGT	0	209	0
TCTCGGGCGTTTCTTCCAGCTCTTTTTTAGA	0	223	1
TTCTTAATAATACTTGAAGGTAGGAACGGTT	2	11	1
     GCTATCACCTCACCAGCTTTAAAAAC	3	27	0
   CATTCGTTTCGTGAAGGTTAGGTGTCTA	4	7	1
ATGGTTTCAACTCCACACGGTACATTAGGAA	4	84	0
CAAGTTTCAACTCCACACGGTACATTAGGAA	4	149	0
CGATGTAATTCTCGACAAGTTTCAACTCCAC	4	164	0
GAAGTAGAAACTCCTGACGATGTAATTCTCG	4	181	0
CAGGAGTTTCTACTTCAAGGTTCCTAATGTA	4	196	1
GTTGTTTCAACTCCACACGGTACATTAGGAA	4	216	0
AACTTAACAAATCCTTAACATTTACGGAGTA	4	244	1
          ********* *
MAP Score: 12.7798

Motif 5
GTATTATAGGCTTTTTAAGCGGTTTCCTTTACAAC	0	45	1
GGGATTTTTCCCTTTTTTGGCTCTTCTGTATATGC	0	84	0
TGAGGTTTTTCCTCCTCAGCGTTCTTGTTTTCTTT	0	135	1
AAGAGAATAGCCCCTTCAGCCTTGTAAAAGTAAAC	0	173	0
CGATTTCCCACCTTCTCGGGCGTTTCTTCCAGCTC	0	210	1
GTGCAGGGTTCCTAATGTACCGTGTGGAGTTGAAA	4	76	1
TGCGGGAGTTCCTAATGTACCGTGTGGAGTTGAAA	4	141	1
TCGAGAATTACATCGTCAGGAGTTTCTACTTCAAG	4	180	1
CTTCAAGGTTCCTAATGTACCGTGTGGAGTTGAAA	4	208	1
          ***  *  ***** *
MAP Score: 11.6399

Motif 6
TTTTTAAGCGGTTTCCTTTACAACGAAAGCATATA	0	56	1
CCCGTGAGGTTTTTCCTCCTCAGCGTTCTTGTTTT	0	131	1
TTCTTTATCGTTTACTTTTACAAGGCTGAAGGGGC	0	164	1
CTCTTTACGATTTCCCACCTTCTCGGGCGTTTCTT	0	203	1
GGCGTGCAGGGTTCCTAATGTACCGTGTGGAGTTG	4	73	1
ATATGCGGGAGTTCCTAATGTACCGTGTGGAGTTG	4	138	1
ATCGTCAGGAGTTTCTACTTCAAGGTTCCTAATGT	4	191	1
CTACTTCAAGGTTCCTAATGTACCGTGTGGAGTTG	4	205	1
          *** **  * ** **
MAP Score: 11.1461