AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_operons017_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249853
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB2243	54	hypothetical protein
#1	PAB2234	62	PAB2234
#2	PAB2233	60	PAB2233
#3	PAB2439	105	PAB2439
#4	PAB2227	288	PAB2227
#5	PAB3055	115	hypothetical protein
#6	PAB2026	106	PAB2026
#7	obg-like	95	PAB0558
#8	PAB0707	46	hypothetical protein
#9	PAB3260	94	hypothetical protein
#10	PAB0711	300	hypothetical protein
#11	PAB0713	22	hypothetical protein
#12	PAB0714	42	PAB0714
#13	PAB0720	62	hypothetical protein
#14	hflX-like	24	PAB0722
#15	PAB0921	81	hypothetical protein
#16	PAB1357	43	PAB1357
#17	PAB1356	51	PAB1356
#18	PAB1355	78	hypothetical protein
#19	PAB1354	70	PAB1354
#20	PAB1065	49	PAB1065

Motif 1
ACCCTAACTCATTTAGGTGAGGG         	2	47	1
ACTTCTTAGTTCTTTGGGGGTGATAGC     	3	88	1
ATCGACTCCGCCTTCGGCGGTGCTCCCCGGGC	4	61	0
CATATATGTTCATTCGGAGGGGTAGAA     	4	271	1
ATGAACCATACTTAAGGAGGGGTATAAAA   	5	96	1
TTTGGACGTTATATCGGAGGTGAGAGT     	7	78	1
CGTTAAATCGGTTTTGGTGGTGAAG       	8	31	1
CCTCGGTTGGCCTTCGTAGGGGAACAGAGACT	10	78	1
ACTTTTTAAAGTTTTGGGGGTTCAGTAGGAAG	10	259	0
   AGTGGTGGCTTGGGTGAGGACTTTTTAAA	10	281	0
AAACCTTTTTCCTTTGGTGTTGACG       	13	3	0
CCTTTTAAATCCTTTGGAGGGAAAAGACC   	15	62	1
GGTGAACCTAACTTCGGTGGTGTAAT      	17	35	1
CTTGGAACTACATTCGGTGGTATC        	19	56	1
GCTGACAAGTATTTAGGGGTTGAGATC     	20	5	0
          **** ** ****
MAP Score: 24.1402

Motif 2
   CTTTAATCCCAACATATTTAAGCAGGCGAAG	0	7	1
  GTTCTCTCCCGCTATCTTTTAAACTTCGCCTG	0	32	0
ACCGAAAAACCCTAACTCATTTAGGTGAGGG   	2	39	1
TTTTCCAAACCGAAACACTTTTTAGAATTCAATG	3	23	1
TATTTTCAGGCTAAAATTATTTAATTATCCTTTA	4	13	1
TCGAGAAATGCCGAAACATTTATATTCAATCAGC	4	203	1
ATAAGATCGGCCCAAGACTTTTAAGCTAGTTGAT	5	64	1
AAGATATGGGCCAAAAAGGTTTAAGTAAGATTTT	6	33	0
ACCTTTTTGGCCCATATCTTTTAAATAGCCAACC	6	47	1
GATATAACGTCCAAACCCAGTTTATAAAGGCTAT	7	59	0
 CTTCACCACCAAAACCGATTTAACGAGGTACTT	8	23	0
AAATGGAGAACGAAACGAATTTAAAGGTATTCTG	9	30	1
CCTACTGAACCCCCAAAACTTTAAAAAGTCCTCA	10	262	1
GATTTATTTTCCAAACCTTTTAAATCCTTTGGAG	15	47	1
   GACTTCTCCCCAGGGAGTTAAGATTGGAGAA	16	22	0
AATCTCATTACCAAAATACTTTTAAATTCTTGGT	18	39	1
          ** ***   *****
MAP Score: 16.0912

Motif 3
AATCTTACTTAAACCTTTTTGGCCCATATC	6	35	1
TTTATATCAAAAACCTTTTTCCTTTGGTGT	13	15	0
GTTTTCAAACAAACCTTTATAAGACCGAAA	2	16	1
TTTATTTTCCAAACCTTTTAAATCCTTTGG	15	49	1
AGTTCCAAGGAAACCTTTTATACTTCTTTT	19	35	0
CCTTCTTTTTCAAACTTTTTCAAAAATTTA	1	16	1
      AAACCAAACTTTTTACGTTAAAAT	9	4	1
CTGAACCCCCAAAACTTTAAAAAGTCCTCA	10	266	1
AGAAATGCCGAAACATTTATATTCAATCAG	4	206	1
  CTTCTCACCTACCTTTATTTTAGCTGAC	20	31	0
TTTTTTCAGAATACCTTTAAATTCGTTTCG	9	40	0
AAACTTTTTCAAAAATTTATAAACTATACA	1	27	1
AAGGCTATGCAAAACTATTTATGGTTAAAG	7	37	0
TCCAAACCGAAACACTTTTTAGAATTCAAT	3	26	1
          **********
MAP Score: 15.8533

Motif 4
TCTCTATATTTTTCCAAACCGAAACACTTTTTAGAATTCAATG	3	14	1
        GCTATCACCCCCAAAGAACTAAGAAGTAAATAAAA	3	80	0
CAGCGAAAGATATCAATGCCTGAAAACGTTCAACCGAACATAT	4	233	1
        TTCTACCCCTCCGAATGAACATATATGTTCGGTTG	4	263	0
        GCTCTCACCACATACAAAGGGGGTATTTAAGGTCG	5	2	1
     TTTTATACCCCTCCTTAAGTATGGTTCATCAACTAGCT	5	87	0
ATCTTTTAAATAGCCAACCTTAAGTTAGGATGAGAGAGGTCAG	6	62	1
        ACTCTCACCTCCGATATAACGTCCAAACCCAGTTT	7	70	0
CCCATTTTATTAGGCCAACCTAATTTTTTCAGAATACCTTTAA	9	50	0
GACTCCCCACTTCCTTAGCCTAAGCAGTCTTCATTCGGGCTTA	10	106	1
TCATTCGGGCTTACAAACCCCACATACCTAGAACTGCCTACCA	10	136	1
CACTTCGAGATTCTACTTCCTACTGAACCCCCAAAACTTTAAA	10	244	1
      GGTCTTTTCCCTCCAAAGGATTTAAAAGGTTTGGAAA	15	54	0
         ATTACACCACCGAAGTTAGGTTCACCTAAACGTA	17	27	0
ACTTTGGTAATCTCATTACCAAAATACTTTTAAATTCTTGGTA	18	31	1
        GATCTCAACCCCTAAATACTTGTCAGCTAAAATAA	20	2	1
          *  ***  ** **  *      *
MAP Score: 12.5763

Motif 5
TCTCTCCCGCTATCTTTTAAACTTCGCCTGC	0	31	0
ATAGTTTATAAATTTTTGAAAAAGTTTGAAA	1	23	0
GTTTTCAAACAAACCTTTATAAGACCGAAAA	2	16	1
ATTATTTAATTATCCTTTAAGTTATTATCAT	4	28	1
GATCTTATGCAAATTTTTATAAATTACCGAC	5	41	0
TTTTGGCCCATATCTTTTAAATAGCCAACCT	6	51	1
TAGTTTTGCATAGCCTTTATAAACTGGGTTT	7	50	1
CTGAACCCCCAAAACTTTAAAAAGTCCTCAC	10	266	1
TTATTTTCCAAACCTTTTAAATCCTTTGGAG	15	50	1
          ACGCTTTTAAACTTCTCCAAT	16	0	1
CATTACCAAAATACTTTTAAATTCTTGGTAG	18	44	1
GTTCCAAGGAAACCTTTTATACTTCTTTTCG	19	33	0
          ** ********
MAP Score: 5.85195

Motif 6
TCCCAACATATTTAAGCAGGCGAAGTTTAAAAGA	0	16	1
CCGGGGAGCACCGCCGAAGGCGGAGTCGATGAAC	4	63	1
CATATATGTTCATTCGGAGGGGTAGAA       	4	271	1
GCTCTCACCACATACAAAGGGGGTATTTAAGGTC	5	10	1
ATGAACCATACTTAAGGAGGGGTATAAAA     	5	96	1
CCTCGGTTGGCCTTCGTAGGGGAACAGAGACTCC	10	78	1
CCTTTTAAATCCTTTGGAGGGAAAAGACC     	15	62	1
          * * ** ***** *
MAP Score: 4.03515

Motif 7
GTTTTATTTACTTCTTAGTTCTTTGGGGGTGATAGC    	3	79	1
AAAAGTACCTCGTTAAATCGGTTTTGGTGGTGAAG     	8	21	1
  ATTAGGGCCCTCCCATTTTATTAGGCCAACCTAATTTT	9	66	0
TGGGTGAGGACTTTTTAAAGTTTTGGGGGTTCAGTAGGAA	10	260	0
ATTTTCCAAACCTTTTAAATCCTTTGGAGGGAAAAGACC 	15	52	1
CATTCGCAAATCTCATATACGTTTAGGTGAACCTAACTTC	17	10	1
AAAAGGTTTCCTTGGAACTACATTCGGTGGTATC      	19	46	1
CTTTATTTTAGCTGACAAGTATTTAGGGGTTGAGATC   	20	7	0
          ***   *     ** ** **
MAP Score: 3.68805

Motif 8
AAGGCGGAGTCGATGAACCTGGGCGGGTTA	4	79	1
TGAAAAAATTAGGTTGGCCTAATAAAATGG	9	62	1
CTTTTGGAGCAGGTGAAACTTTCAGTAGCG	10	24	1
CTTTCAGTAGCGGATAACCTTCCAGCCTTC	10	42	1
CTATATTCCTCGGTTGGCCTTCGTAGGGGA	10	71	1
CCCCCGAGTTAGATTAACCTAAAGGGAATT	12	16	0
ATATACGTTTAGGTGAACCTAACTTCGGTG	17	24	1
          **********
MAP Score: 3.40975

Motif 9
ACTTCGCCTGCTTAAATATGTTGGGATTAAAG      	0	4	0
GACCGAAAAACCCTAACTCATTTAGGTGAGGG      	2	38	1
  GCTATCACCCCCAAAGAACTAAGAAGTAAATAAAAC	3	79	0
CGAAGGCGGAGTCGATGAACCTGGGCGGGTTATTACCC	4	77	1
CATCAACTAGCTTAAAAGTCTTGGGCCGATCTTATGCA	5	61	0
CAAAATCTTACTTAAACCTTTTTGGCCCATATCTTTTA	6	32	1
TTTTGCATAGCCTTTATAAACTGGGTTTGGACGTTATA	7	53	1
TTAAAGGTATTCTGAAAAAATTAGGTTGGCCTAATAAA	9	50	1
CCTTCCAGCCTTCTATATTCCTCGGTTGGCCTTCGTAG	10	59	1
GGTGAGGACTTTTTAAAGTTTTGGGGGTTCAGTAGGAA	10	260	0
TTCCCTTTAGGTTAATCTAACTCGGGGGAGAGTT    	12	18	1
TTTTCCAAACCTTTTAAATCCTTTGGAGGGAAAAGACC	15	53	1
ACTTCTCCAATCTTAACTCCCTGGGGAGAAGTC     	16	20	1
ATTCGCAAATCTCATATACGTTTAGGTGAACCTAACTT	17	11	1
TACCAAAATACTTTTAAATTCTTGGTAGTGCAAATACC	18	47	1
  GATCTCAACCCCTAAATACTTGTCAGCTAAAATAAA	20	8	1
          *** **    ** **  *
MAP Score: 2.37097