AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons057_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944256958
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0226	61	227aa long hypothetical protein
#1	PH1135	86	134aa long hypothetical protein
#2	PH1304	119	276aa long hypothetical protein

Motif 1
TATAGCTTAATCCTGAACAATTTTAAATATTTAGAGGACACCT	0	25	0
ACCCTTTATATAGCAAAAAATCTTTTCCATTCACG        	1	2	0
        TCTAAGTCACCAAATTTAACAATTTCAAATAGTAC	2	2	1
TTTCAAATAGTACTTAAAAACATTATCCAATAAAAATCAAACA	2	32	1
ATAAATATATTTTTAGATTAGTTTTGTCATTGTGTTTGATTTT	2	64	0
ACAAAACTAATCTAAAAATATATTTATCTTTGACATTATTTTT	2	80	1
          *     *  *  **   **** *
MAP Score: 4.20198

Motif 2
AATCCTGAACAATTTTAAATATTTAGAGGACAC	0	27	0
      CGTGAATGGAAAAGATTTTTTGCTATA	1	4	1
CTAAGTCACCAAATTTAACAATTTCAAATAGTA	2	11	1
TTCAAATAGTACTTAAAAACATTATCCAATAAA	2	33	1
AATCAAACACAATGACAAAACTAATCTAAAAAT	2	66	1
TTATAAAAATAATGTCAAAGATAAATATATTTT	2	94	0
          ****  *** ***
MAP Score: 3.49016

Motif 3
AAATTGTTCAGGATTAAGCTATAAAC     	0	45	1
   CGTGAATGGAAAAGATTTTTTGCTATAT	1	7	1
TTTCCTATGGGGATGATACTTGAGTAAGTAT	1	47	1
CTCAAGCAGAGGCTTATACTTACTCAAGTAT	1	62	0
AAGTACTATTTGAAATTGTTAAATTTGGTGA	2	16	0
GATTTTTATTGGATAATGTTTTTAAGTACTA	2	39	0
TCAAACACAATGACAAAACTAATCTAAAAAT	2	68	1
TATTTATCTTTGACATTATTTTTATAAAC  	2	100	1
          *** *******
MAP Score: 1.73936