AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_operons009_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249467
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB0081	157	hypothetical protein
#1	PAB0083	135	hypothetical protein
#2	napA-1	53	PAB0084
#3	PAB0085	251	hypothetical protein
#4	leuA-2	257	PAB0286
#5	rimK	206	PAB0290
#6	tkt1	300	PAB0295
#7	tmpC-like	43	PAB0302
#8	rbsA	44	PAB0303
#9	aroA	28	PAB0306
#10	PAB1921	106	PAB1921
#11	PAB1897	101	PAB1897
#12	trxB	180	PAB0500
#13	gabT	95	PAB0501
#14	PAB2386	39	PAB2386
#15	PAB1527	134	PAB1527
#16	PAB1244	165	PAB1244

Motif 1
AAAGGAAGGGAAAAGTTTTTAATTGAAAATGG	0	65	1
GTGCTGTTCTAAAAGTGGAAAAGGGGAAGGAG	0	134	1
GAGATCTGAGAAAAGTGGGAAAAGAAA     	3	5	0
TATAAGCAATAAAATTGAAGGAAGAAGAAAGG	3	36	0
ATTACTACTTAAAGTTTTATAATAATCTAGCC	3	91	0
GTAATGCTAAAAAGTTATGGAAAAATGTCTCT	3	118	1
CAAAGCTGGTAAAGTTTTATAAGCTGAATAGT	4	24	0
GCACATTGAGAAAAGTTGAGGACATTAATAAA	4	83	0
AAATATAGAAAAAATTTTCGCACATTGAGAAA	4	102	0
TATTTTCGACAAAATTCGAGAAATATAGAAAA	4	122	0
AATTTTGTCGAAAATAATTCCAAAACTGATAA	4	138	1
AATTATTCTTAAAATTTTATCAGTTTTGGAAT	4	154	0
TACCCTATATAAAATTTTCGGAATATTAGATG	4	195	0
     CCACTAAACGTTGTCCAAACCCCTTAT	10	5	1
ACATTTATCAAAAATTCTTTGAAAAAATTATT	10	48	1
ATTCTTTGAAAAAATTATTGAAGGTGTTTGAT	10	61	1
TCGAAACCTGAAACTTAGCGAAATCCGTATAA	11	35	0
GTTTCAAACCAAAGGTTGAGGAGGTTTGGAG 	12	9	0
AATTGAAAATAAAAGTGTTCAACCTTTGGTTT	12	118	1
TTCTTCCTTGAAAATTTTTCGATCAAGGATGT	13	16	1
CATAAAAGGGAAAAGAAGAGAAAAGGCG    	14	6	0
CAAGGCATTAAAAAGTTTTACAATTGACAAAA	15	22	1
CATTGATATCAAAATTAGTTCAAGTAAGTCTT	15	59	1
GGAATAGATAAAAATTTTTGCATTGAGACAAT	16	34	1
ATTGAGGTATAAAAGATTTGCACTTTGACAAA	16	128	0
          ****** * ***
MAP Score: 18.8001

Motif 2
TCAATTAAAAACTTTTCCCTTCCTTTCCAAGAAC	0	57	0
       ACTCCTTCCCCTTTTCCACTTTTAGAA	0	140	0
TCTCAGATCTCCTTTCTTCTTCCTTCAATTTTAT	3	26	1
CAGCTTTGGGCCTTTGTCCTATGTAAACCTCAGC	4	48	1
CCTATGTAAACCTCAGCGTTTATTAATGTCCTCA	4	65	1
TTATTAATGTCCTCAACTTTTCTCAATGTGCGAA	4	84	1
GGGCATTCTACCTTAACCATACTTCA        	5	2	0
GCGAGTAGCCCCTCCACTTTAATTTTTTGGAGGG	5	176	1
TAGGAGCTTCCCTTGTTCCATATTCTATTAGACC	6	225	0
GCTCCTAAACCCGTAACCCTAACTAGGGAAGGCA	6	252	1
 AGTTTTTAACCTTCTCTCTTTTTCTACTCTCCA	8	9	1
   GCTCCCACCTCTATTCTATTTCCATGAGAGC	11	80	0
CTCCAAACCTCCTCAACCTTTGGTTTGAAACGGC	12	10	1
CATTTTACTTCCTTATTTTTTTCTCTCCAAAGAT	12	43	1
          CCTCTCTTCTTCCTTGAAAATTTT	13	0	1
        CGCCTTTTCTCTTCTTTTCCCTTTTA	14	2	1
 CTCACATCCCCTCTTCCTATCCTGGGAATAGAT	16	9	1
          ****  *****  *
MAP Score: 14.5486

Motif 3
TTTCAATTAAAAACTTTTCCCTTCCTTTCCAA	0	61	0
TTCCCCTTTTCCACTTTTAGAACAGCACTCTC	0	130	0
 TTTCTTTTCCCACTTTTCTCAGATCTCCTTT	3	9	1
TAATCTAGCCAAATATTTCCCAAATTTATAAG	3	69	0
ATTACTACTTAAAGTTTTATAATAATCTAGCC	3	91	0
ATTTTTCCATAACTTTTTAGCATTACTACTTA	3	112	0
ATAAAAAGAGACATTTTTCCATAACTTTTTAG	3	124	0
AGGAAATCTTAATATATTAGCATGGTAACTCT	3	223	1
CAAAGCTGGTAAAGTTTTATAAGCTGAATAGT	4	24	0
TTAATGTCCTCAACTTTTCTCAATGTGCGAAA	4	87	1
AAATATAGAAAAAATTTTCGCACATTGAGAAA	4	102	0
ATATTTCTCGAATTTTGTCGAAAATAATTCCA	4	128	1
AATTATTCTTAAAATTTTATCAGTTTTGGAAT	4	154	0
TAATATTCCGAAAATTTTATATAGGGTATGTT	4	199	1
TGACCAAAATCCTATTTTACCAAGGTGAACGC	7	20	1
    CCACTAAACGTTGTCCAAACCCCTTATA	10	6	1
CACCTTCAATAATTTTTTCAAAGAATTTTTGA	10	55	0
TCTTCCTTGAAAATTTTTCGATCAAGGATGTT	13	17	1
AAGGCATTAAAAAGTTTTACAATTGACAAAAA	15	23	1
CTCAATGCAAAAATTTTTATCTATTCCCAGGA	16	29	0
AGTTATATGTCAATTTGTCAAAGTGCAAATCT	16	115	1
          *** ***** **
MAP Score: 12.2276

Motif 4
CTTATCATTTGGAAGTTTAAATGCTTCACCAT	0	18	1
TTCTTGGAAAGGAAGGGAAAAGTTTTTAATTG	0	58	1
CTAGATGTGCGGTGGGAAAAAGTATAATACGA	2	11	1
TAAAATTGAAGGAAGAAGAAAGGAGATCTGAG	3	27	0
GATCGAGCTTGAAAGTGTAGAGCTGCACCAGA	5	51	1
CTGAGGTAGAGGAGGACTGGGGCGAGTAGCCC	5	155	1
TTAATTTTTTGGAGGGATAGAG          	5	194	1
ACGCTCTACTGGAAGAGTTAAGCCGCAAGGAG	6	142	1
CCCTAACTAGGGAAGGCAAGTTCATTCTCAGC	6	268	1
CAAAGGTTGAGGAGGTTTGGAG          	12	0	0
AAAAAAATAAGGAAGTAAAATGCCGTTTCAAA	12	33	0
AAATTTTCAAGGAAGAAGAGAGG         	13	1	0
AAAAGGGAAAAGAAGAGAAAAGGCG       	14	3	0
TCCCAGGATAGGAAGAGGGGATGTGAG     	16	5	0
          ******  ****
MAP Score: 8.9673

Motif 5
     TCTAGATGTGCGGTGGGAAAAAGTAT	2	5	1
GTATGTTGATGGTTGATGTGGGTGGTGCCTA	4	224	1
AGAATGCCCCGTGTGCGGAGCTGAGATCGAG	5	27	1
TGAATGTCCTGTTTGCGGTGCCGAGCTTGAG	5	87	1
GCGGTGCCGAGCTTGAGGTAGTCAGCTTGAA	5	101	1
ATCCGCTAGTGCTCGAGGAGGTTCCTGAGGT	5	131	1
AGGTTCCTGAGGTAGAGGAGGACTGGGGCGA	5	149	1
TAGGGTTACGGGTTTAGGAGCTTCCCTTGTT	6	242	0
TGATAATTAGATGTTAGGTGGAACGTT    	10	89	1
ATGGAAATAGAATAGAGGTGGGAGC      	11	86	1
TCAAACCAAAGGTTGAGGAGGTTTGGAG   	12	7	0
AACTGGTCAAAACTGAGGTGCATGCAACTAC	16	88	0
          * *********
MAP Score: 8.89895

Motif 6
AATTATACATGAAAACTTAAAAATAAAAAGAG	3	146	0
AGATAGCGTAGAAATCTTAAAAGAGTTTTTTA	12	78	1
ATTAGCATGGTAACTCTTAGAAT         	3	238	1
AAGAGTTTTTTAAAGCTTAGAATTGAAAATAA	12	98	1
    CCTCCAGAATGCTGAGAATGAACTTGCC	6	282	0
GTTTATGTAGGAAATCTTAATATATTAGCATG	3	215	1
TAAGAAAATCGAAACCTGAAACTTAGCGAAAT	11	43	0
CTTTAAGTAGTAATGCTAAAAAGTTATGGAAA	3	109	1
TTAGTTCAAGTAAGTCTTAAATAGTTCACTAA	15	73	1
ATCATCGAAATTATTCTTAAAATTTTATCAGT	4	162	0
AAGAAGAAAGGAGATCTGAGAAAAGTGGGAAA	3	15	0
          ***  *******
MAP Score: 3.89655

Motif 7
GAAAGGAAGGGAAAAGTTTTTAATTGAAAATGGTTG	0	64	1
AGTGCTGTTCTAAAAGTGGAAAAGGGGAAGGAGT  	0	133	1
TCAACTTTTCTCAATGTGCGAAAATTTTTTCTATAT	4	96	1
AGATCGAGCTTGAAAGTGTAGAGCTGCACCAGATAG	5	50	1
CTCCAAAAAATTAAAGTGGAGGGGCTACTCGCCCCA	5	172	0
AATCCTGGAGTGAAAGTTCTTAAGAGACTTCTTCTT	6	42	1
GCGTTGAGCTTTAATGTTGATAGTGGTTTTCTCTCC	6	170	0
      GGTTTATAAGTGACCAAAATCCTATTTTAC	7	4	1
AAAGAGTTTTTTAAAGCTTAGAATTGAAAATAAAAG	12	97	1
GAATTGAAAATAAAAGTGTTCAACCTTTGGTTTACT	12	117	1
ACTATTTAACTTTAAGTTCGAAAATGAACATCCTTG	13	39	0
ATCACCTCCATAAAAGGGAAAAGAAGAGAAAAGGCG	14	10	0
TGTCAATTTGTCAAAGTGCAAATCTTTTATACCTCA	16	122	1
          * ******   **  *
MAP Score: 2.76719

Motif 8
   CAGGGGAACTTATCATTTGGAAGTTTAAATGCTTCACCATT	0	7	1
TGGATGAGAGAGTGCTGTTCTAAAAGTGGAAAAGGGGAAGGAGT	0	123	1
TGGCTAGATTATTATAAAACTTTAAGTAGTAATGCTAAAAAGTT	3	90	1
GAAAAATGTCTCTTTTTATTTTTAAGTTTTCATGTATAATTTGC	3	137	1
TCAAGATACTATTCAGCTTATAAAACTTTACCAGCTTTGGGCCT	4	17	1
ACCAATGGAAAATCCTGGAGTGAAAGTTCTTAAGAGACTTCTTC	6	32	1
AAACACCTTCAATAATTTTTTCAAAGAATTTTTGATAAATGTCA	10	46	0
AAGGATGTTCATTTTCGAACTTAAAGTTAAATAGTAATCCCCCG	13	40	1
AAATTTTTGCATTGAGACAATCCAAGTTATGCTGAGCTTGAATG	16	45	1
          * *       *  ****  *  **
MAP Score: 2.4217

Motif 9
 CAGGGGAACTTATCATTTGGAAGTTTAAATGCTTCAC	0	9	1
      ATTGGAATGCGTTGATGGGTGATATTCAATAA	1	4	1
ATTTTATATAGGGTATGTTGATGGTTGATGTGGGTGGT	4	212	1
CCCTCCACTTTAATTTTTTGGAGGGATAGAG       	5	185	1
CACTCCAGGATTTTCCATTGGTAGGGCATCACCTTGAA	6	16	0
GATAGTGGTTTTCTCTCCTTGCGGCTTAACTCTTCCAG	6	150	0
    CCACTCGAGTTATCTGAGGGATTATTTATACGGA	11	6	1
ATCCCCCGAGTTTTTTCTTGGTGGTTGAT         	13	76	1
AATGGTGAATTAATCCCTTGGGGGATCAACA       	15	113	1
          *  *   **** ** * *
MAP Score: 2.3342

Motif 10
TTGTTCCCAAATTAGCGGGGCCTGAATGGAT	0	97	1
TTCTAAAAGTGGAAAAGGGGAAGGAGT    	0	140	1
TCTCAGCTCCGCACACGGGGCATTCTACCTT	5	22	0
ATCCGCTAGTGCTCGAGGAGGTTCCTGAGGT	5	131	1
AGGTTCCTGAGGTAGAGGAGGACTGGGGCGA	5	149	1
AAAAAATTAAAGTGGAGGGGCTACTCGCCCC	5	173	0
ACGCTAGGATCCTAAAGGAGCTGGGTCTAAT	6	202	1
TAGGGTTACGGGTTTAGGAGCTTCCCTTGTT	6	242	0
TCAAACCAAAGGTTGAGGAGGTTTGGAG   	12	7	0
TCCCAGGATAGGAAGAGGGGATGTGAG    	16	6	0
          *** *******
MAP Score: 1.57915