AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_operons048_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944250846
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB2311	91	hypothetical protein
#1	PAB1968	32	PAB1968
#2	PAB1967	51	hypothetical protein
#3	PAB1465	150	PAB1465
#4	PAB1464	77	PAB1464

Motif 1
CTAATTACATACCCAAATTAGGGTAAAGAAC	0	49	0
ATAAAAGAATACCCGAAGTAGACAACGGAAA	3	61	1
   TCTCTCACCCCCGATTAGCCAAGGTCAA	4	59	0
CTTCTCAGCTAGCCTAATAAGGACTT     	3	5	0
CACCTACGAAACTCTAATTACATACCCAAAT	0	62	0
          **** ******
MAP Score: 3.05086

Motif 2
ATTTAGTTTTGAAAAACCTTTTAACGTTCTTTAC	0	24	1
AACTCTAATTACATACCCAAATTAGGGTAAAGAA	0	50	0
GAGAGTTTACGGGTATCCTTTTAAATGTAATCCT	2	14	1
AGGCCTTCTCAGCTAGCCTAATAAGGACTT    	3	6	0
TGTCTACTTCGGGTATTCTTTTATAAGCTTCTTC	3	51	0
AGTAGACAACGGAAAAACTTATTTATTTAGAGGT	3	77	1
TTAAGCATGAGCCTAACCCTCTCTTTACCTCTAA	3	103	0
TTAGGCTCATGCTTAACATTCTGAGGGAGGTGCA	3	121	1
GCCAAGGTCAAGGTAACCTAATTTAAAATAAAAA	4	36	0
          ** ** **** * *
MAP Score: 2.81414

Motif 3
CAAAACTAAATAAATAGAAAAGAAA       	0	3	0
TCTATTTATTTAGTTTTGAAAAACCTTTTAAC	0	17	1
TTAGGGTAAAGAACGTTAAAAGGTTTTTCAAA	0	31	0
TAGAGTTTCGTAGGTGGGAAAATA        	0	77	1
CTCTCAGGATTACATTTAAAAGGATACCCGTA	2	21	0
CTTATTAGGCTAGCTGAGAAGGCCTTGAAAGA	3	15	1
GGCCTTGAAAGAATTGGAAGAAGCTTATAAAA	3	35	1
CTTATTTATTTAGAGGTAAAGAGAGGGTTAGG	3	94	1
CATTCTGAGGGAGGTGCAAAAGG         	3	137	1
CAAGGTAACCTAATTTAAAATAAAAACTTTTA	4	30	0
          *** ** *****
MAP Score: 1.12499