AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons024_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249740
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE1716	55	104aa long hypothetical protein
#1	APE2200	261	427aa long hypothetical L-asparaginase
#2	APE2202	153	642aa long hypothetical Glu-tRNA amidotransferase, subunit B

Motif 1
TTTGCTATGCCGGGGGGTCTCGAGACCCCA	1	10	0
TTAGGCTCTACTGGAGGTCTCTGGAGGTGG	1	147	1
CTGGAGGTCTCTGGAGGTGGGTTTACCCTG	1	157	1
ACCGGCTTTACTGAGGAGCTTGGCTACAAC	1	223	0
GGTGCTAAACCTGGCGATGTA         	1	250	1
AGCCAATATCCAGGAGAGCTTCGCATAGGC	2	23	0
AACCCGGGAGCTGGAGGTGGTTAGGAAGAT	2	55	1
AGAAATCTCGCTGGAGAGGTTAGCGAGAGG	2	92	1
TACCGCCATATAGGAGGTGTCTAACC    	2	137	1
          **********
MAP Score: 17.7726

Motif 2
GACAGTAATAGGTATAGCCA          	0	0	0
GAGACCCCCCGGCATAGCAAAACTGTTTTA	1	19	1
TAGCAAAACTGTTTTAGACAACAGCAGCTT	1	33	1
AGAGACCTCCAGTAGAGCCTAAAAGGGATA	1	139	0
TTTCAGCCAGGGTAAACCCACCTCCAGAGA	1	164	0
GTTAGACGAGGTTTCAGCCAGGGTAAACCC	1	175	0
ATACAAGGGTGTTGTAGCCAAGCTCCTCAG	1	213	1
TACATCGCCAGGTTTAGCACCGGCTTTACT	1	241	0
CAGCTCCCGGGTTCTAGCCAATATCCAGGA	2	38	0
CCTATATGGCGGTATAGCCTCAGTATGTGC	2	121	0
          **********
MAP Score: 11.4706

Motif 3
        TGGGGTCTCGAGACCCCCCGGC	1	2	1
AGACAACAGCAGCTTTCTAGCTATAAGGGA	1	48	1
ATCCCTTTTAGGCTCTACTGGAGGTCTCTG	1	140	1
GCTCTACTGGAGGTCTCTGGAGGTGGGTTT	1	151	1
GTTGTAGCCAAGCTCCTCAGTAAAGCCGGT	1	223	1
         TACATCGCCAGGTTTAGCACC	1	250	0
CGCATAGGCAGCCTCGCTGGTC        	2	2	0
GCCTATGCGAAGCTCTCCTGGATATTGGCT	2	23	1
AACCACCTCCAGCTCCCGGGTTCTAGCCAA	2	47	0
CCTCTCGCTAACCTCTCCAGCGAGATTTCT	2	92	0
          **********
MAP Score: 10.7809

Motif 4
ACTGTCACAGGGGGATAAGCTAGATTTGGGCGGA	0	24	1
TTGCTATGCCGGGGGGTCTCGAGACCCCA     	1	5	0
TTATCCCTTTTAGGCTCTACTGGAGGTCTCTGGA	1	138	1
GGAGGTCTCTGGAGGTGGGTTTACCCTGGCTGAA	1	159	1
GCTTTACTGAGGAGCTTGGCTACAACACCCTTGT	1	215	0
   GACCAGCGAGGCTGCCTATGCGAAGCTCTCC	2	7	1
CTGCCTATGCGAAGCTCTCCTGGATATTGGCTAG	2	21	1
CCCGGGAGCTGGAGGTGGTTAGGAAGATGTTCCA	2	57	1
ATCTCGCTGGAGAGGTTAGCGAGAGGCACATACT	2	96	1
GGCACATACTGAGGCTATACCGCCATATAGGAGG	2	120	1
CCGCCATATAGGAGGTGTCTAACC          	2	139	1
          ******   * ***
MAP Score: 4.3657