AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_operons022_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944250091
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB2233	60	PAB2233
#1	PAB2439	105	PAB2439
#2	PAB2203	300	PAB2203
#3	PAB2086	99	PAB2086
#4	PAB2083	90	hypothetical protein
#5	PAB1789	195	PAB1789
#6	PAB0588	101	hypothetical protein
#7	PAB0645	300	PAB0645
#8	aspS	61	PAB0646
#9	PAB0842	92	hypothetical protein
#10	PAB1477	30	hypothetical protein
#11	PAB1474	28	PAB1474
#12	PAB1471	28	PAB1471
#13	PAB1470	226	PAB1470
#14	hisS	165	PAB1100

Motif 1
AACTCTAAAGATCATCCATAAGTATCATTGA	1	51	0
       GCTATCACCCCCAAAGAACTAAGA	1	91	0
CTTTCCCTTCTTCACCGATAACGTTATAACC	2	10	1
CTGATACTCTCTCGTCCATAAATTTCAAAAT	2	170	1
TATACATCCATTCATCCAAAAAATTCTTAGA	2	200	1
TAATCAAAAGTTCATCGACAATGAACCATTA	2	235	1
ATTTAATTCCAACACCCAGAACCTTCAATCA	5	73	1
  ATCCTACCACCGCCCAAAGGTATTAGCGG	6	82	0
ATTTCTTGTATTCCTCCCTAAGTGACATGAA	7	193	1
GTTCGCTTTCATCATCGCAAACCGTAGGCTT	9	45	1
     ATCACACCACCCCAAAATAATTAATA	11	12	0
     GGATATCCCTCCAAAAAGTTAAGAAG	12	12	0
GCATTATACTTTCACCGAAAGTCTTTTATAA	13	57	0
ACAATCGACTATCGTCGATAACGCATTATAC	13	79	0
CTTTGAGCTTAGCACCGAAAACTACATAAAT	13	146	1
          ******** **
MAP Score: 12.5218

Motif 2
CGTTTTCAAACAAACCTTTATAAGACCGAAAAA	0	15	1
ATCAGCAAAGCAAAAGTTCATCATAACTGTAGG	2	115	0
GATATTTAATCAAAAGTTCATCGACAATGAACC	2	229	1
ACCACACCTTCAAAGCTTTTCTAACGGTGAATT	2	274	0
CATTTAAGTCGAAAACTTTATAAACCCTTTTTA	3	35	1
ATGCTGGATCCAAAATTTTTATATAGTGATTGA	5	97	0
TTCACTTTCCGAAAGCTTGATTAGTTCCTTTAA	7	113	1
CTCCAAGGAGGAAAAGTTGACAATCGCCAAGAG	7	150	0
TTTCCTCTCAGAAATCTTATAAAGGGAAAACTT	7	254	1
CTTATAAAGGGAAAACTTTAGAATAAAATCAGG	7	269	1
GATATCCCTCCAAAAAGTTAAGAAGAA      	12	4	0
TAGGTAATGCCAAAATTTGACAATTGTCGTAAC	13	112	1
GTGCTAAGCTCAAAGCGTTACGACAATTGTCAA	13	128	0
GCTTAGCACCGAAAACTACATAAATCAAATTCA	13	152	1
AAATCAAATTCAAAAATTCAAGATTGAACTCGG	13	173	1
CGGATTAATTGAAAGCTTAAGGGGGCAGAAAAG	13	203	1
TGTCAAAGTGCAAATCTTTTATACCTCAATGCC	14	22	0
          ******** *  *
MAP Score: 12.3062

Motif 3
      CTTTCCCTTCTTCACCGATAACGTTATAA	2	4	1
GATGAGCACGCCCTTCGCTGATACTCTCTCGTCCA	2	153	1
        GTCCCTTTTCTTTTAGCTATATTACCA	3	2	1
ACTTTATAAACCCTTTTTATTTTAGTAACCATTGG	3	49	1
GGTTTAAATACCCTTCTCCTTCATTGTGATTTGAT	4	47	1
    TTCTTTCCCTCCTTCCCTCGTGGTTCCCCCA	5	6	1
          CCCTTCTCAGGCCTCCTTGGGAAAT	5	180	0
CTTCGCTTCGCCCTCCTTTATCCCTAATTTCCTAT	7	59	1
          CCTTTCTTCATTTATAGTAAATTTA	8	0	1
ATTTAATAATCCTTCCTCGGTTCTTCATCTGGGGA	8	30	1
TTTTTAATCCCCCTTTACCTCTTCTTTT       	10	12	1
  CTCACATCCCCTCTTCCTATCCTGGGAATAGAT	14	142	0
          ********   *  *
MAP Score: 11.7899

Motif 4
TCGTTTTCAAACAAACCTTTATAAGACCGAAAAACCCTA	0	14	1
CGAAAAACCCTAACTCATTTAGGTGAGGG          	0	41	1
TTGAATTCTAAAAAGTGTTTCGGTTTGGAAAAATATAGA	1	16	0
AAAATGGGTTATAACGTTATCGGTGAAGAAGGGAAAG  	2	8	0
ATGTATATTTTGAAATTTATGGACGAGAGAGTATCAGCG	2	168	0
TAAATATCTAAGAATTTTTTGGATGAATGGATGTATATT	2	198	0
AAAAGGGTTTATAAAGTTTTCGACTTAAATGGTAATATA	3	27	0
ATATAGTGATTGAAGGTTCTGGGTGTTGGAATTAAATTG	5	71	0
CAATCACTATATAAAAATTTTGGATCCAGCATCGAAGTG	5	98	1
GCCTATCCGCTAATACCTTTGGGCGGTGGTAGGAT    	6	76	1
TAGTTCCTTTAAAATCCTCTTGGCGATTGTCAACTTTTC	7	134	1
     TTTATTAATTATTTTGGGGTGGTGTGAT      	11	5	1
    TTCTTCTTAACTTTTTGGAGGGATATCC       	12	6	1
TTATCTTTATAAAAGACTTTCGGTGAAAGTATAATGCGT	13	51	1
TCGGATTAATTGAAAGCTTAAGGGGGCAGAAAAG     	13	202	1
TGGGAATAGATAAAAATTTTTGCATTGAGACAATCCAAG	14	114	0
          * **   *** ** *   *
MAP Score: 10.8824

Motif 5
       TTCTTTCCCTCCTTCCCTCGTGGT	5	3	1
GATTGTCAACTTTTCCTCCTTGGAGGATACC	7	158	1
GAATTTCTTGTATTCCTCCCTAAGTGACATG	7	191	1
TTCCTTCGCTTCGCCCTCCTTTATCCCTAAT	7	56	1
      CTTTTCTGCCCCCTTAAGCTTTCAA	13	211	0
         CTTTCCCTTCTTCACCGATAAC	2	1	1
    GGTTTTTAATCCCCCTTTACCTCTTCT	10	6	1
GATGGGCCCGGCTCCCGCCCTCTCCGGGGAA	2	59	1
      CTCACATCCCCTCTTCCTATCCTGG	14	150	0
   CCCTTCTCAGGCCTCCTTGGGAAATCCT	5	177	0
CTTCCCTCGTGGTTCCCCCATTACGGGGACA	5	21	1
GTAAATTTAATAATCCTTCCTCGGTTCTTCA	8	26	1
       GGATATCCCTCCAAAAAGTTAAGA	12	14	0
          * *********
MAP Score: 8.62433

Motif 6
TATTTACTTCTTAGTTCTTTGGGGGTGATAGC   	1	83	1
ACTCCAACTTTTATATAATTGGTGGGGAGGATATT	6	32	1
ATTGTCAACTTTTCCTCCTTGGAGGATACCTTGAA	7	159	1
      TTTATTAATTATTTTGGGGTGGTGTGAT 	11	4	1
    TTCTTCTTAACTTTTTGGAGGGATATCC   	12	6	1
TGAATTTGATTTATGTAGTTTTCGGTGCTAAGCTC	13	150	0
          ***  *  **** **
MAP Score: 6.03077

Motif 7
AGTCGAAAACTTTATAAACCCTTTTTATTTT	3	41	1
GGAGGATATTTTCATAAACGCCTATCCGCTA	6	57	1
GATTAGTTCCTTTAAAATCCTCTTGGCGATT	7	131	1
GGAGGAAAAGTTGACAATCGCCAAGAGGATT	7	146	0
CTAAGTGACATGAATAATCCTTCGACTAATT	7	210	1
TATAGTAAATTTAATAATCCTTCCTCGGTTC	8	22	1
GCAGTTCGCTTTCATCATCGCAAACCGTAGG	9	42	1
CGTAGGCTTTTTAATAAACCTACTTAAAAGG	9	67	1
        GGTTTTTAATCCCCCTTTACCTC	10	2	1
          ** ********
MAP Score: 3.40267

Motif 8
TCTTAGTTCTTTGGGGGTGATAGC      	1	91	1
ATTCCCCGGAGAGGGCGGGAGCCGGGCCCA	2	61	0
CTAAGAATTTTTTGGATGAATGGATGTATA	2	200	0
AACCACGAGGGAAGGAGGGAAAGAA     	5	5	0
TTTTATATAATTGGTGGGGAGGATATTTTC	6	40	1
CCTTTGGGCGGTGGTAGGAT          	6	91	1
GTGAACCTTATTGGGAGGAAGTTGATAGGA	7	88	0
TCATGTCACTTAGGGAGGAATACAAGAAAT	7	193	0
ATTAATTATTTTGGGGTGGTGTGAT     	11	13	1
TTCTTAACTTTTTGGAGGGATATCC     	12	13	1
          **********
MAP Score: 1.52056

Motif 9
ATATAATTGGTGGGGAGGATATTTTCATAA	6	44	1
CCTTTGGGCGGTGGTAGGAT          	6	91	1
TGGGAGGAAGTTGATAGGAAATTAGGGATA	7	77	0
GTGAACCTTATTGGGAGGAAGTTGATAGGA	7	88	0
CCAAGAGGATTTTAAAGGAACTAATCAAGC	7	127	0
ACTTTTCCTCCTTGGAGGATACCTTGAATT	7	166	1
TCATGTCACTTAGGGAGGAATACAAGAAAT	7	193	0
ATAGTAATTAGTCGAAGGATTATTCATGTC	7	216	0
TATAAGATTTCTGAGAGGAAAGGAGTTAAA	7	245	0
ATGAAGAACCGAGGAAGGATTATTAAATTT	8	28	0
TTCTTAACTTTTTGGAGGGATATCC     	12	13	1
AAGACTTTCGGTGAAAGTATAATGCGTTAT	13	63	1
          **********
MAP Score: 0.824174