AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_fusions010_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944234540
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	aq_1328	60	hypothetical protein
#1	aq_1625	300	hypothetical protein
#2	aq_1691	32	hypothetical protein
#3	dplF	68	N-terminus of phage SPO1 DNA polymerase

Motif 1
AATTAATATTAACCCTGACATGGAAACTCTCTTCCT	0	30	0
GATTTATGAAAAAGAGGGGAAGGAAAAGATTA    	1	6	0
TTCAAAGGAGGTCTGAGCCATGGCAAAATTAAAGAC	1	52	1
ATTAAAGACCATGGTTGACCAGGAAACCTGTACGGC	1	79	1
CAAGTGTGACATAAAAGACGAGGAAGATCACTGCTG	1	184	1
TCACTGCTGGATGATAGTCCCGGAAGGACTGGAAGA	1	211	1
AGGACTGGAAGACGAAGTCAGAGAAGTAGAAGAAGA	1	235	1
TTCTATTATCGTTGAAGAACTCGAAGA         	1	283	1
GAAGGAAACGATAAAAGCCCTGGAAAGCATAGGGAT	3	17	1
CCTGGAAAGCATAGGGATAACGGAAATATACTTAAA	3	35	1
TAACGGAAATATACTTAAACAGGAAA          	3	52	1
          **    * ** *****
MAP Score: 12.8634

Motif 2
       TAATCTTTTCCTTCCCCTCTTTTT	1	3	1
AGGGCTTTTATCGTTTCCTTCAGTCCCA   	3	7	0
GACTTCGTCTTCCAGTCCTTCCGGGACTATC	1	223	0
       TCTTCGAGTTCTTCAACGATAATA	1	286	0
ACATGGAAACTCTCTTCCTTTTGTCTATAAT	0	18	0
ATTCCGTCTCCCCTGTTCTTGTAAACCTCGG	1	141	0
TCCTGGTCAACCATGGTCTTTAATTTTGCCA	1	72	0
CTTTTCCTTCCCCTCTTTTTCATAAATCTTT	1	14	1
GGGGCACTCTTCTTCTACTTCTCTGACTTCG	1	247	0
CAGTGATCTTCCTCGTCTTTTATGTCACACT	1	186	0
TTCCGTTATCCCTATGCTTTCCAGGGCTTTT	3	29	0
TTTCATAAATCTTTTTTCTTTTTCAAAGGAG	1	31	1
          ** ********
MAP Score: 10.3692

Motif 3
AGAGAGTTTCCATGTCAGGGTTAATATTAATTTAGA	0	34	1
TAATCTTTTCCTTCCCCTCTTTTTCATAAATCTTTT	1	10	1
TTTCAAAGGAGGTCTGAGCCATGGCAAAATTAAAGA	1	51	1
AGCCGTACAGGTTTCCTGGTCAACCATGGTCTTTAA	1	80	0
ACCTGTACGGCTTGCGAGCTGTGTTACGATAGAGTT	1	104	1
TTACGATAGAGTTCCCGAGGTTTACAAGAACAGGGG	1	127	1
AATAGCGGATGTTGTCAAGTGTGACATAAAAGACGA	1	169	1
CCAGCAGTGATCTTCCTCGTCTTTTATGTCACACTT	1	185	0
GTCTTCCAGTCCTTCCGGGACTATCATCCAGCAGTG	1	212	0
GGCTTTTATCGTTTCCTTCAGTCCCA          	3	0	0
TATCCCTATGCTTTCCAGGGCTTTTATCGTTTCCTT	3	18	0
          * **** **  *  **
MAP Score: 5.88628