AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_operons016_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249809
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	rps13P	100	PAB0360
#1	rpoD	32	PAB2410
#2	rpl18E	166	PAB0364
#3	rpoN	44	PAB7131
#4	rpoK	120	PAB7132
#5	thrC-like	39	PAB0369
#6	PAB0370	34	hypothetical protein

Motif 1
GGCTCTCAAGGCCCGCGCCCTACCAGG      	0	4	0
ACCCCGGCGGGCAAACGCCCACGGGCTCTCAAG	0	27	0
GGACGGGGATTTGAACCCCGGCGGGCAAACGCC	0	41	0
GGGTTCAAATCCCCGTCCCGGCGCCAGAATCCC	0	56	1
          TTTATCCCCCTCCAAATGAATGG	0	87	0
          TCTCACGCCTCCAAATTAAAAAG	1	19	0
GCCAGGCTCGGCAACCCCCGCTCGG        	2	2	0
GGACCCTAAATCCCGCGCCTTTGGCCAGGCTCG	2	25	0
GGATTTAGGGTCCCGTCCCGTAGGGGTTCCGGG	2	45	1
GTTCCGGGGTTCAAATCCCCGCCCCCGCACCAT	2	70	1
CACCATTTATTCACGCTCACCCCGCCCTTGTCG	2	97	1
AGAGTTTAATTCTCGCGCCGCAGGGAAACCGAC	2	126	0
CCAAGCTACCCCACGGCCCCGCCTAAATAAAGA	4	20	0
GTAGCTTGGCTATCCTCCCGGCCTGGGGCGCCG	4	44	1
TGAACCCGGGTCACCGGCGCCCCAGGCCGGGAG	4	58	0
TGACCCGGGTTCAAATCCCGGCGGCCCCACCAA	4	78	1
          TCTAGCCCACCCCTAAAGCTATA	6	21	0
          ** * ***** **
MAP Score: 26.7258

Motif 2
GTCCCGTCCCGTAGGGGTTCCGGGGTTCAAATCCCCGCCCCCGC	2	54	1
CTGGCCAAAGGCGCGGGATTTAGGGTCCCGTCCCGTAGGGGTTC	2	30	1
TCAATATTTTGGTGGGGCCGCCGGGATTTGAACCCGGGTCACCG	4	75	0
TCTTTATTTAGGCGGGGCCGTGGGGTAGCTTGGCTATCCTCCCG	4	20	1
GCCCGTGGGCGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGGC	0	34	1
        CCGAGCGGGGGTTGCCGAGCCTGGCCAAAGGCGCGG	2	2	1
       CCTGGTAGGGCGCGGGCCTTGAGAGCCCGTGGGCGTT	0	3	1
TTGGCTATCCTCCCGGCCTGGGGCGCCGGTGACCCGGGTTCAAA	4	49	1
AGAGTTTAATTCTCGCGCCGCAGGGAAACCGACAAGGGCGGGGT	2	115	0
CCCTCCAAATGAATGGGATTCTGGCGCCGGGACGGGGATTTGAA	0	59	0
AACCGACAAGGGCGGGGTGAGCGTGAATAAATGGTGCGGGGGCG	2	89	0
          *   ***    ****       **
MAP Score: 23.2362

Motif 3
CAAACGCCCACGGGCTCTCAAGGCCCGCGCCCTACCAG	0	11	0
CTTGAGAGCCCGTGGGCGTTTGCCCGCCGGGGTTCAAA	0	27	1
CGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGGCGCC	0	43	1
TCCAAATGAATGGGATTCTGGCGCCGGGACGGGGATTT	0	62	0
TTGGCCAGGCTCGGCAACCCCCGCTCGG          	2	0	0
CCCTACGGGACGGGACCCTAAATCCCGCGCCTTTGGCC	2	32	0
GGTGCGGGGGCGGGGATTTGAACCCCGGAACCCCTACG	2	63	0
ACCCGGGTCACCGGCGCCCCAGGCCGGGAGGATAGCCA	4	50	0
GGTGGGGCCGCCGGGATTTGAACCCGGGTCACCGGCGC	4	71	0
          ****    *    *****
MAP Score: 23.159

Motif 4
CGGGCTCTCAAGGCCCGCGCCCTACCAGG       	0	3	0
GAGAGCCCGTGGGCGTTTGCCCGCCGGGGTTCAAAT	0	30	1
GCCCGCCGGGGTTCAAATCCCCGTCCCGGCGCCAGA	0	48	1
TGGCCAGGCTCGGCAACCCCCGCTCGG         	2	1	0
TTGCCGAGCCTGGCCAAAGGCGCGGGATTTAGGGTC	2	21	1
GCGGGATTTAGGGTCCCGTCCCGTAGGGGTTCCGGG	2	42	1
GGGGTTCCGGGGTTCAAATCCCCGCCCCCGCACCAT	2	67	1
CACCATTTATTCACGCTCACCCCGCCCTTGTCGGTT	2	97	1
ACCCCGCCCTTGTCGGTTTCCCTGCGGCGCGAGAAT	2	115	1
TAGCCAAGCTACCCCACGGCCCCGCCTAAATAAAGA	4	20	0
GGGGTAGCTTGGCTATCCTCCCGGCCTGGGGCGCCG	4	41	1
ATTTGAACCCGGGTCACCGGCGCCCCAGGCCGGGAG	4	58	0
CGGTGACCCGGGTTCAAATCCCGGCGGCCCCACCAA	4	75	1
          ** **    **** **
MAP Score: 17.4488

Motif 5
  CCTGGTAGGGCGCGGGCCTTGAGAGCCCGTGGGCGTTTGCC	0	8	1
ATTCTGGCGCCGGGACGGGGATTTGAACCCCGGCGGGCAAACG	0	43	0
         CCGAGCGGGGGTTGCCGAGCCTGGCCAAAGGCGC	2	1	1
CCTGGCCAAAGGCGCGGGATTTAGGGTCCCGTCCCGTAGGGGT	2	29	1
TAAATGGTGCGGGGGCGGGGATTTGAACCCCGGAACCCCTACG	2	63	0
GTTTAATTCTCGCGCCGCAGGGAAACCGACAAGGGCGGGGTGA	2	113	0
TCTTTATTTAGGCGGGGCCGTGGGGTAGCTTGGCTATCCTCCC	4	20	1
CCGGGTCACCGGCGCCCCAGGCCGGGAGGATAGCCAAGCTACC	4	43	0
ATTTTGGTGGGGCCGCCGGGATTTGAACCCGGGTCACCGGCGC	4	71	0
          ** * ***      *   **  *
MAP Score: 14.2907

Motif 6
GGGCTCTCAAGGCCCGCGCCCTACCAGG      	0	4	0
AACCCCGGCGGGCAAACGCCCACGGGCTCTCAAG	0	27	0
TTCAAATCCCCGTCCCGGCGCCAGAATCCCATTC	0	59	1
    CCGAGCGGGGGTTGCCGAGCCTGGCCAAAG	2	6	1
GCCGAGCCTGGCCAAAGGCGCGGGATTTAGGGTC	2	23	1
GCGGGATTTAGGGTCCCGTCCCGTAGGGGTTCCG	2	42	1
GGTTCAAATCCCCGCCCCCGCACCATTTATTCAC	2	77	1
CATTTATTCACGCTCACCCCGCCCTTGTCGGTTT	2	100	1
TTGTCGGTTTCCCTGCGGCGCGAGAATTAAACTC	2	124	1
GCCAAGCTACCCCACGGCCCCGCCTAAATAAAGA	4	20	0
GGGGTAGCTTGGCTATCCTCCCGGCCTGGGGCGC	4	41	1
AACCCGGGTCACCGGCGCCCCAGGCCGGGAGGAT	4	55	0
GGTTCAAATCCCGGCGGCCCCACCAAAATATTGA	4	85	1
          *** * *****  *
MAP Score: 12.7073

Motif 7
       CCTGGTAGGGCGCGGGCCTTGAGAGCCC	0	3	1
CCTTGAGAGCCCGTGGGCGTTTGCCCGCCGGGGTT	0	26	1
ATGGGATTCTGGCGCCGGGACGGGGATTTGAACCC	0	56	0
         CCGAGCGGGGGTTGCCGAGCCTGGCC	2	1	1
CTGGCCAAAGGCGCGGGATTTAGGGTCCCGTCCCG	2	30	1
GGTCCCGTCCCGTAGGGGTTCCGGGGTTCAAATCC	2	53	1
GTGAATAAATGGTGCGGGGGCGGGGATTTGAACCC	2	76	0
AGAGTTTAATTCTCGCGCCGCAGGGAAACCGACAA	2	124	0
TCTTTATTTAGGCGGGGCCGTGGGGTAGCTTGGCT	4	20	1
CTTGGCTATCCTCCCGGCCTGGGGCGCCGGTGACC	4	48	1
GGTTCAAATCCCGGCGGCCCCACCAAAATATTGAG	4	85	1
          **  *****   ***
MAP Score: 10.7375

Motif 8
GCTCTCAAGGCCCGCGCCCTACCAGG    	0	6	0
ACCCCGGCGGGCAAACGCCCACGGGCTCTC	0	30	0
GGGGTTCAAATCCCCGTCCCGGCGCCAGAA	0	55	1
GGCGCCAGAATCCCATTCATTTGGAGGGGG	0	75	1
     TTTATCCCCCTCCAAATGAATGGGA	0	85	0
GCTCGGCAACCCCCGCTCGG          	2	0	0
CGCGCCTTTGGCCAGGCTCGGCAACCCCCG	2	15	0
GGACCCTAAATCCCGCGCCTTTGGCCAGGC	2	28	0
GGATTTAGGGTCCCGTCCCGTAGGGGTTCC	2	45	1
GTTCCGGGGTTCAAATCCCCGCCCCCGCAC	2	70	1
TCAAATCCCCGCCCCCGCACCATTTATTCA	2	80	1
ATTTATTCACGCTCACCCCGCCCTTGTCGG	2	101	1
TGTCGGTTTCCCTGCGGCGCGAGAATTAAA	2	125	1
CTACCCCACGGCCCCGCCTAAATAAAGAAA	4	18	0
GGATAGCCAAGCTACCCCACGGCCCCGCCT	4	29	0
TTGGCTATCCTCCCGGCCTGGGGCGCCGGT	4	49	1
AACCCGGGTCACCGGCGCCCCAGGCCGGGA	4	59	0
TTCAAATCCCGGCGGCCCCACCAAAATATT	4	87	1
          GCCGCCTCACCTCAATATTT	4	110	0
      TCTAGCCCACCCCTAAAGCTATAT	6	20	0
          **********
MAP Score: 4.38679