AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_operons016_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249819
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB0359	43	hypothetical protein
#1	rps13P	100	PAB0360
#2	rpoD	32	PAB2410
#3	rpl18E	166	PAB0364
#4	rpoN	44	PAB7131
#5	rpoK	120	PAB7132
#6	thrC-like	39	PAB0369
#7	PAB0370	34	hypothetical protein

Motif 1
CTTTATTTAGGCGGGGCCGTGGGGTAGCTTGGC	5	21	1
CCGAGCCTGGCCAAAGGCGCGGGATTTAGGGTC	3	24	1
       CCTGGTAGGGCGCGGGCCTTGAGAGC	1	3	1
ATCCTCCCGGCCTGGGGCGCCGGTGACCCGGGT	5	55	1
CAATATTTTGGTGGGGCCGCCGGGATTTGAACC	5	85	0
AATAAATGGTGCGGGGGCGGGGATTTGAACCCC	3	75	0
TGTCGGTTTCCCTGCGGCGCGAGAATTAAACTC	3	125	1
GAATCCCATTCATTTGGAGGGGGATAAA     	1	82	1
CGCGGGCCTTGAGAGCCCGTGGGCGTTTGCCCG	1	20	1
GGATTCTGGCGCCGGGACGGGGATTTGAACCCC	1	55	0
TTGGATATAGCTTTAGGGGTGGGCTAGA     	7	16	1
TTTATAATTCGAAGACAAGTGGGGGTCAAGCC 	4	22	1
GGGAAACCGACAAGGGCGGGGTGAGCGTGAATA	3	104	0
GCCCGTGGGCGTTTGCCCGCCGGGGTTCAAATC	1	34	1
GAGAATTAAACTCTAGAAGGGGGAATTTCGC  	3	145	1
GATTTAGGGTCCCGTCCCGTAGGGGTTCCGGGG	3	46	1
CCAAAATATTGAGGTGAGGCGGC          	5	107	1
CCGAGCGGGGGTTGCCGAGCCTGGCCAAAGGCG	3	10	1
TCTTTTTAATTTGGAGGCGTGAGA         	2	18	1
          *  * ********
MAP Score: 34.8719

Motif 2
CGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGGCGCC	1	43	1
CGTAGGGGTTCCGGGGTTCAAATCCCCGCCCCCGCACC	3	63	1
CTGGTAGGGCGCGGGCCTTGAGAGCCCGTGGGCGTTTG	1	11	1
TGGCTATCCTCCCGGCCTGGGGCGCCGGTGACCCGGGT	5	50	1
GGCCAAAGGCGCGGGATTTAGGGTCCCGTCCCGTAGGG	3	32	1
GCGCCGGTGACCCGGGTTCAAATCCCGGCGGCCCCACC	5	71	1
     CCGAGCGGGGGTTGCCGAGCCTGGCCAAAGGCG	3	5	1
CTCCAAATGAATGGGATTCTGGCGCCGGGACGGGGATT	1	63	0
TCCCTGCGGCGCGAGAATTAAACTCTAGAAGGGGGAAT	3	133	1
          *****  *   *  ** *
MAP Score: 28.862

Motif 3
GTTCAAATCCCCGCCCCCGCACCATTTATT	3	78	1
GGTTCAAATCCCGGCGGCCCCACCAAAATA	5	85	1
AAGCTACCCCACGGCCCCGCCTAAATAAAG	5	21	0
ACCCGGGTCACCGGCGCCCCAGGCCGGGAG	5	58	0
TGTCGGTTTCCCTGCGGCGCGAGAATTAAA	3	125	1
TATTCACGCTCACCCCGCCCTTGTCGGTTT	3	104	1
GCTTGGCTATCCTCCCGGCCTGGGGCGCCG	5	47	1
CGGGCTCTCAAGGCCCGCGCCCTACCAGG 	1	9	0
GGGGATTTGAACCCCGGCGGGCAAACGCCC	1	40	0
CGGGACCCTAAATCCCGCGCCTTTGGCCAG	3	30	0
CCAGGCTCGGCAACCCCCGCTCGG      	3	4	0
GTTCAAATCCCCGTCCCGGCGCCAGAATCC	1	58	1
CGGCGGGCAAACGCCCACGGGCTCTCAAGG	1	26	0
         GCCGCCTCACCTCAATATTTT	5	109	0
GAACCCCGGAACCCCTACGGGACGGGACCC	3	52	0
        TCTAGCCCACCCCTAAAGCTAT	7	22	0
          **********
MAP Score: 28.0842

Motif 4
GCCGAGCCTGGCCAAAGGCGCGGGATTTAGGGTC	3	23	1
TGAATAAATGGTGCGGGGGCGGGGATTTGAACCC	3	76	0
ATGGGATTCTGGCGCCGGGACGGGGATTTGAACC	1	57	0
CAGGGAAACCGACAAGGGCGGGGTGAGCGTGAAT	3	105	0
GGCCTGGGGCGCCGGTGACCCGGGTTCAAATCCC	5	63	1
        CCTGGTAGGGCGCGGGCCTTGAGAGC	1	2	1
GGTCACCGGCGCCCCAGGCCGGGAGGATAGCCAA	5	49	0
ACCCCGGAACCCCTACGGGACGGGACCCTAAATC	3	46	0
TCTTTATTTAGGCGGGGCCGTGGGGTAGCTTGGC	5	20	1
TTGTCGGTTTCCCTGCGGCGCGAGAATTAAACTC	3	124	1
CAATATTTTGGTGGGGCCGCCGGGATTTGAACCC	5	84	0
CCGTGGGCGTTTGCCCGCCGGGGTTCAAATCCCC	1	36	1
GGCGCGGGCCTTGAGAGCCCGTGGGCGTTTGCCC	1	18	1
ATTGGATATAGCTTTAGGGGTGGGCTAGA     	7	15	1
CAGAATCCCATTCATTTGGAGGGGGATAAA    	1	80	1
          * *   ********
MAP Score: 26.3249

Motif 5
GCTCTCAAGGCCCGCGCCCTACCAGG    	1	6	0
CGGGCAAACGCCCACGGGCTCTCAAGGCCC	1	23	0
CGTGGGCGTTTGCCCGCCGGGGTTCAAATC	1	37	1
GGGGTTCAAATCCCCGTCCCGGCGCCAGAA	1	55	1
GGCTCGGCAACCCCCGCTCGG         	3	1	0
GAGCGGGGGTTGCCGAGCCTGGCCAAAGGC	3	12	1
GACCCTAAATCCCGCGCCTTTGGCCAGGCT	3	27	0
GGATTTAGGGTCCCGTCCCGTAGGGGTTCC	3	45	1
GGATTTGAACCCCGGAACCCCTACGGGACG	3	58	0
GGGGTTCAAATCCCCGCCCCCGCACCATTT	3	75	1
CATTTATTCACGCTCACCCCGCCCTTGTCG	3	100	1
CTTGTCGGTTTCCCTGCGGCGCGAGAATTA	3	123	1
   GGCTTGACCCCCACTTGTCTTCGAATT	4	27	0
CCAAGCTACCCCACGGCCCCGCCTAAATAA	5	23	0
CTTGGCTATCCTCCCGGCCTGGGGCGCCGG	5	48	1
GAACCCGGGTCACCGGCGCCCCAGGCCGGG	5	60	0
CGGGTTCAAATCCCGGCGGCCCCACCAAAA	5	83	1
          **********
MAP Score: 18.4523

Motif 6
  CCTGGTAGGGCGCGGGCCTTGAGAGCCC	1	8	1
GGCGGGCAAACGCCCACGGGCTCTCAAGGC	1	25	0
GGATTTGAACCCCGGCGGGCAAACGCCCAC	1	38	0
GGGTTCAAATCCCCGTCCCGGCGCCAGAAT	1	56	1
TTTGGCCAGGCTCGGCAACCCCCGCTCGG 	3	9	0
GGATTTGAACCCCGGAACCCCTACGGGACG	3	58	0
GGGTTCAAATCCCCGCCCCCGCACCATTTA	3	76	1
TATTCACGCTCACCCCGCCCTTGTCGGTTT	3	104	1
TGTCGGTTTCCCTGCGGCGCGAGAATTAAA	3	125	1
AGCCAAGCTACCCCACGGCCCCGCCTAAAT	5	25	0
GCTTGGCTATCCTCCCGGCCTGGGGCGCCG	5	47	1
AACCCGGGTCACCGGCGCCCCAGGCCGGGA	5	59	0
GGGTTCAAATCCCGGCGGCCCCACCAAAAT	5	84	1
          **********
MAP Score: 16.242

Motif 7
GCTCTCAAGGCCCGCGCCCTACCAGG       	1	3	0
CCCGTGGGCGTTTGCCCGCCGGGGTTCAAATCC	1	35	1
GGGGTTCAAATCCCCGTCCCGGCGCCAGAATCC	1	55	1
          TTTATCCCCCTCCAAATGAATGG	1	87	0
GGCCAGGCTCGGCAACCCCCGCTCGG       	3	3	0
AATCCCGCGCCTTTGGCCAGGCTCGGCAACCCC	3	17	0
GGCGCGGGATTTAGGGTCCCGTCCCGTAGGGGT	3	39	1
GGGGCGGGGATTTGAACCCCGGAACCCCTACGG	3	62	0
GGGGTTCAAATCCCCGCCCCCGCACCATTTATT	3	75	1
CATTTATTCACGCTCACCCCGCCCTTGTCGGTT	3	100	1
AGTTTAATTCTCGCGCCGCAGGGAAACCGACAA	3	124	0
        GGCTTGACCCCCACTTGTCTTCGAA	4	29	0
CCAAGCTACCCCACGGCCCCGCCTAAATAAAGA	5	20	0
GGTAGCTTGGCTATCCTCCCGGCCTGGGGCGCC	5	43	1
CCCGGGTCACCGGCGCCCCAGGCCGGGAGGATA	5	54	0
GCCGCCGGGATTTGAACCCGGGTCACCGGCGCC	5	70	0
AATATTTTGGTGGGGCCGCCGGGATTTGAACCC	5	84	0
          **   ********
MAP Score: 11.5364

Motif 8
  CCTGGTAGGGCGCGGGCCTTGAGAGCCCGTGGGCGTTTG	1	8	1
GGGGATTTGAACCCCGGCGGGCAAACGCCCACGGGCTCTCA	1	29	0
CCTTTGGCCAGGCTCGGCAACCCCCGCTCGG          	3	0	0
CCTGGCCAAAGGCGCGGGATTTAGGGTCCCGTCCCGTAGGG	3	29	1
TCCCGTAGGGGTTCCGGGGTTCAAATCCCCGCCCCCGCACC	3	60	1
CGGGAGGATAGCCAAGCTACCCCACGGCCCCGCCTAAATAA	5	23	0
TTGAACCCGGGTCACCGGCGCCCCAGGCCGGGAGGATAGCC	5	51	0
ATTTTGGTGGGGCCGCCGGGATTTGAACCCGGGTCACCGGC	5	73	0
          * * ***    *     ****
MAP Score: 10.1288

Motif 9
       TAACTTTAACCTTTAAATTTTTAA	0	3	1
AACCTTTAAATTTTTAACCCTCCAAATACCC	0	17	1
CCCGTGGGCGTTTGCCCGCCGGGGTTCAAAT	1	35	1
GGGACGGGGATTTGAACCCCGGCGGGCAAAC	1	44	0
          TTTATCCCCCTCCAAATGAAT	1	89	0
GGGGCGGGGATTTGAACCCCGGAACCCCTAC	3	64	0
        GGCTTGACCCCCACTTGTCTTCG	4	31	0
GCCGCCGGGATTTGAACCCGGGTCACCGGCG	5	72	0
          **** ******
MAP Score: 6.93435

Motif 10
TTTTAACCCTCCAAATACCCAAAGG      	0	28	1
CCACGGGCTCTCAAGGCCCGCGCCCTACCAG	1	11	0
ACCCCGGCGGGCAAACGCCCACGGGCTCTCA	1	29	0
CCGCCGGGGTTCAAATCCCCGTCCCGGCGCC	1	50	1
CGTCCCGGCGCCAGAATCCCATTCATTTGGA	1	69	1
GCCAGGCTCGGCAACCCCCGCTCGG      	3	4	0
CCGAGCCTGGCCAAAGGCGCGGGATTTAGGG	3	24	1
GGGACGGGACCCTAAATCCCGCGCCTTTGGC	3	33	0
ATTTGAACCCCGGAACCCCTACGGGACGGGA	3	55	0
GTTCCGGGGTTCAAATCCCCGCCCCCGCACC	3	70	1
CCCGCCCTTGTCGGTTTCCCTGCGGCGCGAG	3	117	1
         GCGAAATTCCCCCTTCTAGAGT	3	154	0
        GGCTTGACCCCCACTTGTCTTCG	4	31	0
GGATAGCCAAGCTACCCCACGGCCCCGCCTA	5	28	0
ACCCGGGTCACCGGCGCCCCAGGCCGGGAGG	5	57	0
TGACCCGGGTTCAAATCCCGGCGGCCCCACC	5	78	1
TCAAATCCCGGCGGCCCCACCAAAATATTGA	5	88	1
          TCTAGCCCACCCCTAAAGCTA	7	23	0
          ***** *****
MAP Score: 6.30304

Motif 11
GCTCTCAAGGCCCGCGCCCTACCAGG         	1	1	0
GCGCGGGCCTTGAGAGCCCGTGGGCGTTTGCCCGC	1	19	1
GACGGGGATTTGAACCCCGGCGGGCAAACGCCCAC	1	38	0
GGGTTCAAATCCCCGTCCCGGCGCCAGAATCCCAT	1	56	1
          TTTATCCCCCTCCAAATGAATGGGA	1	85	0
GCCAGGCTCGGCAACCCCCGCTCGG          	3	0	0
AAATCCCGCGCCTTTGGCCAGGCTCGGCAACCCCC	3	16	0
GCGCGGGATTTAGGGTCCCGTCCCGTAGGGGTTCC	3	40	1
GTTCCGGGGTTCAAATCCCCGCCCCCGCACCATTT	3	70	1
CCGCCCTTGTCGGTTTCCCTGCGGCGCGAGAATTA	3	118	1
      GGCTTGACCCCCACTTGTCTTCGAATTAT	4	25	0
CCAAGCTACCCCACGGCCCCGCCTAAATAAAGAAA	5	18	0
CAGGCCGGGAGGATAGCCAAGCTACCCCACGGCCC	5	34	0
TTGGCTATCCTCCCGGCCTGGGGCGCCGGTGACCC	5	49	1
TGACCCGGGTTCAAATCCCGGCGGCCCCACCAAAA	5	78	1
          TCTAGCCCACCCCTAAAGCTATATC	7	19	0
          **   **** *** *
MAP Score: 1.78768