AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID191_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943393313
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yrbG	209	orf, hypothetical protein
#1	rpoN	47	RNA polymerase, sigma(54 or 60) factor; nitrogen and fermentation regulation

Motif 1
   AATTCACCCTTCGTCTTGCGTTGATTTTCTAAGC	0	7	1
TAAGCATGGCGCTCAATTTAACCTTGAACCCAACATA	0	39	1
AACCTTGAACCCAACATATTTACAGAATATTACCCGC	0	58	1
AGAATATTACCCGCCGTGGTTAGCGAAAGCTGGCATT	0	81	1
CGTAACGGATGCTTAATTTTGACTTTATGCGGCTAAA	0	128	0
TCGCCGGTCCGCTGAAGATTTTCAGAAAGCCGTAACG	0	158	0
CTTCAGCGGACCGGCGAGTATACCTGAAGAAAGGACG	0	178	1
GTAGAAGTTTGCGACGTTTTAGCAGGAGAGTACGATT	1	14	1
          **  *** **  * * *
MAP Score: 4.93473

Motif 2
          AATTCACCCTTCGTCTTGCG	0	0	1
CATGCTTAGAAAATCAACGCAAGACGAAGG	0	17	0
CATGGCGCTCAATTTAACCTTGAACCCAAC	0	43	1
ATATTTACAGAATATTACCCGCCGTGGTTA	0	73	1
AACGTCGCAAACTTCTACCCTA        	1	2	0
          **********
MAP Score: 0.932528