AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons035_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944234326
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE0510	53	352aa long hypothetical protein
#1	APE1958	199	246aa long hypothetical NH(3)-dependent NAD(+) synthetase

Motif 1
ACTAATGTATAGTGTTGGAGG          	0	0	0
CACCAATTGGAGTGTTGTAGAGCGGAGGCAG	1	51	0
CAACACTCCAATTGGTGTGGGGGTTTGGCTG	1	65	1
TAGTTTAGACGATGTTGTTGACATAGATTAT	1	109	1
CATAGATTATAATGGTGTAAGACAGGCAATA	1	130	1
          * *********
MAP Score: 3.99826

Motif 2
          CCTCCAACACTATACATTAGTGG	0	0	1
GCCTTCTCATCCGCCTGAACACGTATAACCCAC	0	29	0
GGATACGTGGCAGCCTTCTCTTTTACCTGCCTC	1	25	1
TCTCTTTTACCTGCCTCCGCTCTACAACACTCC	1	41	1
AACAGCCAAACCCCCACACCAATTGGAGTGTTG	1	65	0
          ****** * ** *
MAP Score: 1.35562

Motif 3
          CCTCCAACACTATACATTAGTGGG	0	0	1
CGCCTGAACACGTATAACCCACTAATGTATAGTG	0	17	0
GGATACGTGGCAGCCTTCTCTTTTACCTGCCTCC	1	25	1
TCTCTTTTACCTGCCTCCGCTCTACAACACTCCA	1	41	1
TATTGCCTGTCTTACACCATTATAATCTATGTCA	1	127	0
          * **** * ** **
MAP Score: 0.218436