AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_sum_all061_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236458
 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
GAAGTGGAAAGATACCTGGAAGTTATTCAGAGTG	0	85	1
ATATTACACCGATCTTTGAGAGCTCTAAAAAGCA	0	117	0
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: 3.85226

Motif 2
AAATACCTGTTTCTCGATATGTAATCACATAGTCGTTAGAAGTGG	0	47	1
TCTGAATAACTTCCAGGTATCTTTCCACTTCTAACGACTATGTGA	0	71	0
TGGAAGTTATTCAGAGTGCTTTTTAGAGCTCTCAAAGATCGGTGT	0	101	1
CTCTCAAAGATCGGTGTAATATCAAGAGAGCTAGCAGATGATCTC	0	129	1
CATCATCAATTCTCCGGTATTGATGGAGAAGAATGTTTCTAAACT	0	187	0
ACCTCTGACCTTGAGGACTTTGAGAGAGGTGATGGAATACGTTGA	0	263	1
       TATTCCTTGACATTTCTGCACTTGGTGGTGCT      	1	3	1
ATCAATGCTATTCCAGTAATTATTAGAGCTTCACCTTTC      	2	11	1
TATTAAAAATTTGAGGCATTTAAACGATTTCGGGGAGGGTA    	3	24	1
          **   *  **     *** *    *
MAP Score: 2.41781

Motif 3
TGACCTTGAGGACTTTGAGAGAGGTGATGG	0	268	1
ATAGTCGTTAGAAGTGGAAAGATACCTGGA	0	75	1
AATTGATGATGAAGTGGTGTATGAGATTAT	0	221	1
CAAAAATGGCGAAGTTTAGAAACATTCTTC	0	175	1
GGTGATGGAATACGTTGAGA          	0	290	1
CAATACCGGAGAATTGATGATGAAGTGGTG	0	210	1
CACTTCTAACGACTATGTGATTACATATCG	0	61	0
          **********
MAP Score: 2.27359