AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID101_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943392184
 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
     CTTTATTCTTCCTCAACCCCT    	0	6	0
GAGTCTTTATTTTCTCATCACCCAGTTGTC	1	11	1
AATAAAACAATTATTTAACAAATAATTATC	1	49	0
AATAATTGTTTTATTTCACATTGGTTATAC	1	64	1
TATAACGCCCTTTTGCAACAGCTTCTTAAA	1	133	1
ACCTGATATGTTTTGCAACATATGTGACCT	1	167	1
          **********
MAP Score: 4.75433

Motif 2
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 3
TTTCTCATCACCCAGTTGTCACTCTAATGAT	1	21	1
TGTTTTATTTCACATTGGTTATACCAATTGC	1	70	1
TTCAGCACTCCCCTTTTGTTATAACGCCCTT	1	114	1
TGTTATAACGCCCTTTTGCAACAGCTTCTTA	1	130	1
GCTGCCAGGTCACATATGTTGCAAAACATAT	1	172	0
          ********* *
MAP Score: 2.45631