AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID003_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943390910
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yhbE	126	orf, hypothetical protein
#1	rplU	258	50S ribosomal subunit protein L21

Motif 1
ATGAAAGCCCCGCAACACGTTGCGGGGCTT	0	32	1
TTATCGAATGTAAAAAGCCCCGCAACGTGT	0	46	0
ATTAACGTCGCACCATGCGCATTTTTACCG	0	77	0
CCGTATTCCCTGCAAAGCGCATTTGCGGAT	0	105	0
          CGCAAAAGCCGGGCTTTTCG	1	0	1
GTAATCGGGGCGAAAAGCCCGGCTTTTGCG	1	10	0
GCGAATATTACGCAAAACGCACGCCTTTGA	1	170	0
TATAAATATTCACAATAGGGCGCGAATATT	1	191	0
TTCAATGATTCAGAGTGCGCTATAAATATT	1	211	0
          **********
MAP Score: 4.44249

Motif 2
TTTCGCGTCCCGGTAACGGATGAAAGCCCCG	0	13	1
ATTCGATAACCGGTAAAAATGCGCATGGTGC	0	67	1
GGTGATTGTACTGAAAAAATGGCACAGATAA	1	86	1
ACAACTTGTACGGTAACGTTTATCTGTGCCA	1	105	0
CGTGTATTGACTGTAGCACTTGTCAAAGGCG	1	148	1
ATAGCGCACTCTGAATCATTGAAAAGGTGTG	1	218	1
AAGGTGTGCGCGGAAGCGGAGTTTTAT    	1	241	1
          ******** **
MAP Score: 4.41259

Motif 3
AAATGCGCTTTGCAGGGAATACGGT      	0	111	1
CCGATTACCTTACTGTGAACAAAGGCAACTT	1	32	1
ATAGGGTGATTGTACTGAAAAAATGGCACAG	1	82	1
TGACAAGTGCTACAGTCAATACACGAAGAAA	1	142	0
ATTCGCGCCCTATTGTGAATATTTATAGCGC	1	194	1
          ********* *
MAP Score: 0.913146

Motif 4
GTTACCGGGACGCGAAAAAC          	0	0	0
CCCGGTAACGGATGAAAGCCCCGCAACACG	0	21	1
GTTATCGAATGTAAAAAGCCCCGCAACGTG	0	47	0
GACGTTAATCCGCAAATGCGCTTTGCAGGG	0	98	1
          CGCAAAAGCCGGGCTTTTCG	1	0	1
GTAATCGGGGCGAAAAGCCCGGCTTTTGCG	1	10	0
TGCCTTTGTTCACAGTAAGGTAATCGGGGC	1	29	0
TGTAGCACTTGTCAAAGGCGTGCGTTTTGC	1	159	1
GCGAATATTACGCAAAACGCACGCCTTTGA	1	170	0
TATAAATATTCACAATAGGGCGCGAATATT	1	191	0
AAAAGGTGTGCGCGGAAGCGGAGTTTTAT 	1	239	1
          **********
MAP Score: 0.862429