AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID021_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391058
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	cydA	300	cytochrome d terminal oxidase, polypeptide subunit I
#1	appC	133	probable third cytochrome oxidase, subunit I

Motif 1
CAATTTGATCGAGAACAATTTATCT      	0	4	0
TAAATTGTTCTCGATCAAATTGGCTGAAAGG	0	13	1
TTTTTCGACGGTGATCAATTTATAGCTAAAT	0	49	0
ATATATACGTGGGATCAATTTGAGTTTTTAT	0	131	1
AGAAATTTGTTTGAACACTTTCATCATACCA	0	209	0
CTTTCTAACGGGGTTCACTCTCGGAGTCTTC	0	260	1
          * *********
MAP Score: 7.21853

Motif 2
 AGATAAATTGTTCTCGATCAAATTGGCTGAAAGG	0	9	1
GCTATAAATTGATCACCGTCGAAAAATGCAAATTT	0	54	1
AAATTTGTTTGAACACTTTCATCATACCATGTGAA	0	203	0
TTCTAACGGGGTTCACTCTCGGAGTCTTCATGCGA	0	262	1
AGACGGTAAGTATCGCTTTCAGTCTTATGAATATC	1	12	1
GTCTTATGAATATCGCAATCGGCGAATACCTCTGG	1	33	1
GATAATGGTAGATCTCCCTCTTTATCCTGAAACTC	1	73	0
TCGGGTTATTTTTCTCTCTTCGCCTACAGGAGTGC	1	106	1
          **** *  ** ** *
MAP Score: 3.65238

Motif 3
    AGATAAATTGTTCTCGATCAAATTGGCTGAAA	0	6	1
TTAGCTATAAATTGATCACCGTCGAAAAATGCAAAT	0	51	1
AAAAACTCAAATTGATCCCACGTATATATTACGCCG	0	124	0
CGGCGTAAAGAAAGGTTGCAAACATGTTAATAAAAA	0	155	0
TTACGCCGTTTTTGTGTGCATTCACATGGTATGATG	0	183	1
TGGTATGATGAAAGTGTTCAAACAAATTTCTATTGG	0	209	1
CCCCGTTAGAAAGGGTCACACGCATGCCCCAATAGA	0	237	0
ACCCTTTCTAACGGGGTTCACTCTCGGAGTCTTCAT	0	257	1
GACGGTAAGTATCGCTTTCAGTCTTATGAATATCGC	1	13	1
          *  * ** ** *** *
MAP Score: 2.04188