AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID212_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943392895
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ycaI	129	orf, hypothetical protein
#1	msbA	36	ATP-binding transport protein; multicopy suppressor of htrB
#2	ycaQ	36	orf, hypothetical protein
#3	ycaR	51	orf, hypothetical protein
#4	b2253	274	putative enzyme

Motif 1
      GTTTTTTACTCAAACTTGAACGAGAGAAAAGCACC	0	4	1
CAGATTAGAGAAATGAAAAAAGCACCCGACAGGTGCTTTTC	0	35	0
AATTTAACGAAAGGGTGAAAACTGTTCAAAACTCTGCGAGG	0	89	0
TCGGGTTATGAATGCATAAATCTTATCATAATCAT      	3	4	0
AACCAGACAATTACCGTGAAATTGAGCTACATTTCTGGCGA	4	35	1
ATATTACACCAACTGCGAATTATCGCCAGAAATGTAGCTCA	4	57	0
TGTCGGCAAAATGCCTCAAAATTTTGCCAAATGCAAAGCCT	4	112	1
GTTAATATTCTATCCTTAAAATTTCGCTCCAAATGGCAAAA	4	213	1
TTTCGCTCCAAATGGCAAAATATACACAACACTCTTTATAG	4	234	1
          **  *  ***  *   *  **
MAP Score: 3.98128

Motif 2
   GTTTTTTACTCAAACTTGAACGAGAGAAAAGCACC	0	7	1
       ATTCAGAAGAATTTAACGAAAGGGTGAAAAC	0	108	0
CAGACAATTACCGTGAAATTGAGCTACATTTCTGGCGA	4	38	1
ATTACACCAACTGCGAATTATCGCCAGAAATGTAGCTC	4	58	0
TATTAAAAATCCTACGATGTCGGCAAAATGCCTCAAAA	4	95	1
CGGCAAAATGCCTCAAAATTTTGCCAAATGCAAAGCCT	4	115	1
AATATTCTATCCTTAAAATTTCGCTCCAAATGGCAAAA	4	216	1
          **   ** **  ** * *
MAP Score: 2.93663

Motif 3
CCTGTCGGGTGCTTTTTTCATTTCTCTAAT	0	43	1
CTGCCTCGCAGAGTTTTGAACAGTTTTCAC	0	86	1
AACAAATGCTGGTTTTTTGA          	1	26	1
ATTATGATAAGATTTATGCATTCATAACCC	3	13	1
CAGATGGATCGGGTTATGAATGCATAAATC	3	23	0
CGACATCGTAGGATTTTTAATATTACACCA	4	87	0
AAATTTTGAGGCATTTTGCCGACATCGTAG	4	106	0
TTTAGGCTTTGCATTTGGCAAAATTTTGAG	4	126	0
CATTTGGAGCGAAATTTTAAGGATAGAATA	4	218	0
          **********
MAP Score: 1.43882