AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID101_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391828
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	cyoB	21	cytochrome o ubiquinol oxidase subunit I
#1	cyoA	300	cytochrome o ubiquinol oxidase subunit II

Motif 1
TGAGTCTTTATTTTCTCATCACCCAGTTGTCACTCTA	1	10	1
ATTGGTTATACCAATTGCCCGCCCAGACTCCTTCAGC	1	83	1
CGCCCAGACTCCTTCAGCACTCCCCTTTTGTTATAAC	1	102	1
CACTCCCCTTTTGTTATAACGCCCTTTTGCAACAGCT	1	119	1
TGCAACAGCTTCTTAAAATCAACCTGATATGTTTTGC	1	146	1
ATGTTTACAGTAATGTAACCTTCCCGTAAAATGCCCA	1	229	1
TGCCCACACACTTTAAACGCCACCAGATCCCGTGGAA	1	260	1
          *  * * * * *** **
MAP Score: 2.73467

Motif 2
         AGGGGTTGAGGAAGAATAAAG	0	1	1
TCATTAGAGTGACAACTGGGTGATGAGAAA	1	21	0
AGTCTGGGCGGGCAATTGGTATAACCAATG	1	82	0
GAGTGCTGAAGGAGTCTGGGCGGGCAATTG	1	94	0
CCAAGTAACAGGAATTTAATCATGTTTACA	1	208	1
GGGATCTGGTGGCGTTTAAAGTGTGTGGGC	1	261	0
TCAATTCCACGGGATCTGGTGGCGTTTAAA	1	271	0
CAGATCCCGTGGAATTGAGGTCGTTAA   	1	283	1
          **********
MAP Score: 2.66979

Motif 3
TGGTTATACCAATTGCCCGCCCAGACTCCTT	1	85	1
CCTTTTGTTATAACGCCCTTTTGCAACAGCT	1	125	1
CCTTCCCGTAAAATGCCCACACACTTTAAAC	1	247	1
CACACACTTTAAACGCCACCAGATCCCGTGG	1	264	1
         TTAACGACCTCAATTCCACGGG	1	288	0
          ******** **
MAP Score: 2.19146