AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_profile006_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251508
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB1968	32	PAB1968
#1	PAB1967	51	hypothetical protein
#2	PAB1784	103	PAB1784
#3	PAB7309	48	hypothetical protein
#4	PAB0810	22	hypothetical protein
#5	bchP-like	90	PAB1059
#6	PAB1240	94	hypothetical protein

Motif 1
 CGCTCGGCCAAGTCCCTCCCAATCATCGCGAT 	0	9	0
TACATTTAAAAGGATACCCGTAAACTCTCGAGC 	1	9	0
ATCCTTTTAAATGTAATCCTGAGAGTTTAAATC 	1	28	1
AAACTATTATAAATCATCCTCAAACTTCCTACC 	3	25	1
         TATGAGCCCCTGAATTACTGTAACG	5	75	0
AGGAATAATTAGGCCACTCTAAAATTTAAAGGTT	6	20	1
TTAAAGGTTTAAGAAATTCTTAAATAACCTCTGC	6	45	1
          * *  ***** ***
MAP Score: 2.90108

Motif 2
          GCTCGAGAGTTTACGGGTATCC	1	0	1
TTAAATGTAATCCTGAGAGTTTAAATC     	1	34	1
ACAGCGAGATAAAAAAGCGTTTTTAAACCCGA	2	13	0
         TTACTCAACATTTATGTCTAAAT	5	1	1
TGCAAAGCTCAATAGAACATTTTATATTCTTG	5	39	1
CCCCTGAATTACTGTAACGTTGCCAAGAATAT	5	62	0
TAATTAGGCCACTCTAAAATTTAAAGGTTTAA	6	25	1
TTTAAGAATTTCTTAAACCTTTAAATTTTAGA	6	37	0
AGCAGAGGTTATTTAAGAATTTCTTAAACCTT	6	48	0
ACCTCTGCTCACTAAAGCATTTGGTGATTTCT	6	71	1
          ***  *******
MAP Score: 2.8594

Motif 3
CTTTTAAATGTAATCCTGAGAGTTTAAATC 	1	31	1
AAAGCGTTTTTAAACCCGAAAA         	2	1	0
GTGAACATAATCATCCGGGATGCTCATCTTT	2	65	0
CTATTATAAATCATCCTCAAACTTCCTACC 	3	28	1
      CACTTCACCCAGGAATAATTAGGCC	6	4	1
          ****** ****
MAP Score: 1.59315