AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_sum_all032_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944253571
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB0562	300	hypothetical protein
#1	PAB0563	41	PAB0563
#2	PAB1455	81	hypothetical protein
#3	PAB1379	67	PAB1379
#4	PAB1378	115	PAB1378

Motif 1
AGTTTTAACACTTTTCTTGCAAGAACCCT   	0	7	0
TGTTTATAAGCTTTTCGGTCGAGAAAATTAAG	0	151	0
CCGCCAGACTCTTCTCAGGGGAGAAAA     	0	283	1
GTCACCCAATGTTTAATTGCCAACTTAATTTA	1	16	0
       GGTCTTTTCCCTCCAAAGGATTTAA	2	3	1
TTTTCCAAACCTTTTAAATCCTTTGGAGGGAA	2	16	0
TGCCTTTTTACCTCTCTTTCGATTTTAACATT	3	23	1
TGTAGTTCAACTTTTACAGGCACTTCCACACA	4	55	1
ACAAAAAATGGTTTTATATCCAGCCATTTTTA	4	86	1
          ******  ****
MAP Score: 4.06582

Motif 2
GCGCTAGTTCTGGAACCTTTGGAGCCTGTAGA	0	52	1
TCCCCTCCCATCAAACATCGGGCTGTGGGCCG	0	185	1
CGGCGGACTCTTAATCCGCAGGTCGGGGGTTC	0	237	1
AAGTTGGCAATTAAACATTGGGTGACGGG   	1	22	1
CCAAACCTTTTAAATCCTTTGGAGGGAAAAGA	2	12	0
          * ******* **
MAP Score: 2.50673

Motif 3
GGAACCTTTGGAGCCTGTAGACATTAAGATT	0	63	1
AGTCCGTGAAGAGGCAGAGGATACGCTCTAT	0	98	1
CATCAAACATCGGGCTGTGGGCCGGTAGCTT	0	193	1
TAGCCTGGTTAGAGCGGCGGACTCTTAATCC	0	223	1
TTTGAACCCCCGACCTGCGGATTAAGAGTCC	0	241	0
AGAGTCTGGCGGGCCGGGGGGGATTTGAACC	0	264	0
          ******* ***
MAP Score: 2.42617

Motif 4
TAAAACTTGACTTCGTTGAGGCGCTAGTTCT	0	32	1
AGAGGATACGCTCTATCGATGATATCATTGT	0	113	1
GAGTCCGCCGCTCTAACCAGGCTAAGCTACC	0	216	0
GCCCGCCAGACTCTTCTCAGGGGAGAAAA  	0	281	1
CTTTTTACCTCTCTTTCGATTTTAACATTAA	3	26	1
TTAACATTAATTTCTTTGAGGGGTGATACT 	3	47	1
   TTTTATTCTTTTTTGATGTCGATAACCT	4	7	1
          **** ******
MAP Score: 1.06691