AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_sum_all061_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236465
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0458	300	129aa long hypothetical protein
#1	PH0459	32	232aa long hypothetical protein
#2	PH0935	40	246aa long hypothetical protein
#3	PH1743	55	218aa long hypothetical protein

Motif 1
TGTTTCTAAACTTCGCCATTTTTGAGAGAT	0	169	0
TAGAAACATTCTTCTCCATCAATACCGGAG	0	191	1
TCATACACCACTTCATCATCAATTCTCCGG	0	215	0
CAACGTATTCCATCACCTCTCTCAAAGTCC	0	277	0
ATTATTAGAGCTTCACCTTTC         	2	29	1
          **********
MAP Score: 4.4219

Motif 2
GAAGTGGAAAGATACCTGGAAGTTATTCAGAGTG	0	85	1
GTGCTTTTTAGAGCTCTCAAAGATCGGTGTAATA	0	116	1
GCTAGCAGATGATCTCTCAAAAATGGCGAAGTTT	0	158	1
GATGGAGAAGAATGTTTCTAAACTTCGCCATTTT	0	177	0
CTTCTCCATCAATACCGGAGAATTGATGATGAAG	0	201	1
TAATGAAGGATATACCTCTGACCTTGAGGACTTT	0	250	1
AAGCTCTAATAATTACTGGAATAGCATTGATA  	2	8	0
AAATCGTTTAAATGCCTCAAATTTTTAATAATTA	3	20	0
GCATTTAAACGATTTCGGGGAGGGTA        	3	39	1
          *** **** **  *
MAP Score: 2.77586

Motif 3
AAATACCTGTTTCTCGATATGTAATCACATAGTCGTTAGAAGTGGA	0	47	1
AGTGGAAAGATACCTGGAAGTTATTCAGAGTGCTTTTTAGAGCTCT	0	87	1
AACTTCGCCATTTTTGAGAGATCATCTGCTAGCTCTCTTGATATTA	0	145	0
TCTCCATCAATACCGGAGAATTGATGATGAAGTGGTGTATGAGATT	0	203	1
CCTTGAGGACTTTGAGAGAGGTGATGGAATACGTTGAGA       	0	271	1
       TATTCCTTGACATTTCTGCACTTGGTGGTGCT       	1	3	1
TTATTAAAAATTTGAGGCATTTAAACGATTTCGGGGAGGGTA    	3	23	1
          * *  ** *  * * *     *   *
MAP Score: 0.919044