AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_sum_all067_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944254375
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB7092	97	PAB7092
#1	PAB0401	51	hypothetical protein
#2	PAB0965	52	hypothetical protein
#3	PAB1273	41	hypothetical protein
#4	PAB1271	142	PAB1271

Motif 1
      CCTCTCACCCGTTTTACTTTCTCCGAGGCATTTCTTA	0	4	1
CTAGCTTAGATCACTTTTTATACCTTAACGTCGAAAATTATTA	2	11	0
         GTTACCACCAATACCTTAAGGAGGAGAGAAGAAT	3	17	0
CATATTTATATTACAAAATGTATCTTTAATCAGGTGAGCGAG 	4	9	0
TTTCATCCGATGAACTTATTTGACATAAATTTGTAAACGAAAA	4	67	1
CCCTTAATATTCAAAAATTTTGACTTAAACATGGTGAAAACT 	4	110	1
          * **    * *  *** *    *
MAP Score: 4.10525

Motif 2
TCACCCGTTTTACTTTCTCCGAGGCATTTCT	0	14	1
      GATTTAAACTCTCAGGATTACATTT	1	4	1
AGGATACCCGTAAACTCTCGAGC        	1	38	1
TGATCTAAGCTAGATTCTCCG          	2	41	1
 ACTTTTTATTCTTCTCTCCTCCTTAAGGTA	3	9	1
          ** ********
MAP Score: 2.38076

Motif 3
 GTAATAATTTTCGACGTTAAGGTATAAAAA	2	9	1
GATGAACTTATTTGACATAAATTTGTAAACG	4	75	1
ATTCAAAAATTTTGACTTAAACATGGTGAAA	4	118	1
          ****** ****
MAP Score: 0.988106

Motif 4
TTCTCCGAGGCATTTCTTAACTGTTATCCC	0	28	1
ATCCCTGGGATAATTTTTAAAAGTCCCCTG	0	53	1
GGATACCCGTAAACTCTCGAGC        	1	39	1
      GTAATAATTTTCGACGTTAAGGTA	2	4	1
ATTAAAGATACATTTTGTAATATAAATATG	4	22	1
TATTTGACATAAATTTGTAAACGAAAACCC	4	83	1
TTGTAAACGAAAACCCTTAATATTCAAAAA	4	97	1
GTTTAAGTCAAAATTTTTGAATATTAAGGG	4	110	0
          **********
MAP Score: 0.771376