AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_operons010_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249497
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB2199	72	PAB2199
#1	trub	112	PAB0356
#2	psmA	158	PAB0417
#3	PAB0418	27	hypothetical protein
#4	PAB0467	140	hypothetical protein
#5	PAB1867	78	PAB1867
#6	PAB1865	36	hypothetical protein
#7	PAB1864	60	PAB1864
#8	aif2A	65	PAB0568
#9	PAB1751	82	hypothetical protein
#10	PAB0751	105	hypothetical protein
#11	PAB0754	37	PAB0754
#12	infB	52	PAB0755

Motif 1
          CTCACCACCTATCTCGTGGA	0	0	1
    ATTCCTCTCACCACAAAGAGGTTTGC	0	56	0
       GGTTTCACCCCCAGGTTATTTAA	1	3	1
      CTCCAATCCCCCCACTAACTACCC	1	98	0
     GCTCTATCACCACCATTAAAGTTCA	2	5	1
TTTTATTTAAATTCCCACAAGGTATAGGTG	2	81	0
       CCTCTCACCTCCACCTTAAGTAA	2	145	0
   AAAACATCACCCCACAAAAATGAAAAA	3	10	0
       CCAAACACCCCCGCCGGCGGTCT	4	3	1
GCGGTCTGAGAACCCCCTCAATATAACTAC	4	26	1
     GCTTCCTCCCCATCGGCGTTTCGAA	7	45	0
       CTTCTCACCTCCAACGAATCCCT	8	52	0
CAAATTAATTATCCCCACAACCTTATAAAG	9	11	1
     AGTTGTTCCCCCTAAAAAAGAGGAA	11	22	0
       TTCCTCACCACCAAACTAAAGGC	12	39	0
          **********
MAP Score: 28.8608

Motif 2
GTGGAAATAGGAAGGTATTAAAAATAATACCGC	0	25	1
AGGTATAGGTGAAAGCATGGAAACATTTTAATA	2	59	0
TTCGCCCGCGGAAGGTATATAAAAGCCTCGGCT	2	113	1
ACGAATACCGAAAGGTATATAAACCTTTTGTGT	4	54	1
          AAACGCTCTTAAATCTATTTCTT	6	0	1
GAGTTCTTAAGAAAGCTTAAAAATCAACCTTCG	7	16	1
GTCTAATAATGAAGGTATATAAAAATTTATCGA	10	70	0
TCATTATTAGACAAGTACAAAAAA         	10	91	1
TACAGGTTTTAAAAGTTTGGAAAG         	12	1	0
          *** ****  ***
MAP Score: 12.9497

Motif 3
AAACGCTCGCCCAACTTATAAGTTTTTTCAAC	1	44	1
CTACCCTGACCCTCCTTATAAAGGAATAGTTG	1	72	0
 GCTCTATCACCACCATTAAAGTTCAACGTTC	2	9	1
GGTATAGGTGAAAGCATGGAAACATTTTAATA	2	59	0
CCTCTCACCTCCACCTTAAGTAAGCCGAGGCT	2	136	0
AAAGGTATATAAACCTTTTGTGTTACTTCGGC	4	64	1
ACGCTTAAACAATCCTTTAATACTACCTCCAA	4	109	1
AGTTCTTAAGAAAGCTTAAAAATCAACCTTCG	7	17	1
GCTTAAAAATCAACCTTCGAAACGCCGATGGG	7	30	1
GTTTGAGGGGCAACTTTAAAAGGCTCCCGATT	8	18	1
ATTATCCCCACAACCTTATAAAGCAAGTTCGG	9	18	1
   GTAAATTACACCATATGTAAATTACATGC	10	7	1
ATGTAATAAAAAACCTTCTGTAAGCACAAATC	10	40	1
     CTTTCCAAACTTTTAAAACCTGTAGGA	12	5	1
          *******  ***
MAP Score: 9.75535