AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID003_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943390913
 numcols =     	10
 undersample = 	1
 oversample = 	1

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

Motif 1
AATGTAAAAAGCCCCGCAACGTGTTGCGGGG	0	39	0
GTTTTTCGCGTCCCGGTAACGGATGAAAGCC	0	10	1
ACGGATGAAAGCCCCGCAACACGTTGCGGGG	0	28	1
AACACAACTTGTACGGTAACGTTTATCTGTG	1	108	0
GAAAAGGTGTGCGCGGAAGCGGAGTTTTAT 	1	238	1
   ACCGTATTCCCTGCAAAGCGCATTTGCG	0	108	0
TAGGGTGATTGTACTGAAAAAATGGCACAGA	1	83	1
GCACTCTGAATCATTGAAAAGGTGTGCGCGG	1	223	1
          ****** ****
MAP Score: 8.72809

Motif 2
GTAACGGATGAAAGCCCCGCAACACGTTGCGGGGCT	0	25	1
TCGAATGTAAAAAGCCCCGCAACGTGTTGCGGGGCT	0	37	0
TAACCGGTAAAAATGCGCATGGTGCGACGTTAATCC	0	73	1
TTTGCGGATTAACGTCGCACCATGCGCATTTTTACC	0	78	0
      CGCAAAAGCCGGGCTTTTCGCCCCGATTAC	1	4	1
AGCACTTGTCAAAGGCGTGCGTTTTGCGTAATATTC	1	162	1
GAATCATTGAAAAGGTGTGCGCGGAAGCGGAGTTTT	1	230	1
          **** *****     *
MAP Score: 6.99359

Motif 3
GGCTTTCATCCGTTACCGGGACGCGAAAAAC   	0	7	0
CGCAAATGCGCTTTGCAGGGAATACGGT      	0	108	1
GCCCCGATTACCTTACTGTGAACAAAGGCAACTT	1	29	1
AATATAGGGTGATTGTACTGAAAAAATGGCACAG	1	79	1
AATATTCGCGCCCTATTGTGAATATTTATAGCGC	1	191	1
AATATTTATAGCGCACTCTGAATCATTGAAAAGG	1	211	1
CATTGAAAAGGTGTGCGCGGAAGCGGAGTTTTAT	1	234	1
          *  *** ***** *
MAP Score: 1.16377