AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons027_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249818
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE0792	300	234aa long hypothetical cytochrome C oxidase polypeptide II
#1	APE1570	52	284aa long hypothetical 4-hydroxybenzeoate octaprenyl transferase
#2	APE1878	157	305aa long hypothetical cytochrome C oxidase assembly factor

Motif 1
AGGGCCCTCTGGATGGGGGTGCCGATGTACGGTT	0	26	1
CAAGTATTAAGGATGTAGGAGGAGTTTTGGAATC	0	253	1
GAGGAGTTTTGGAATCGGGGGAGGATCCGGGAGT	0	271	1
AATCGGGGGAGGATCCGGGAGTTGTCT       	0	283	1
 CCTATCATGGGACGCGGGCGCGCTCAGGAGGCG	1	9	1
GGCGCGCTCAGGAGGCGGGGGAGGCTACACGCTT	1	26	1
GCTGATTATAGGTAGTGGGGGGTTAAGATCGGC 	2	134	1
          *** ***** *  *
MAP Score: 19.3048

Motif 2
AACACCTAGAGTGAAGGGCCCTCTGGATGGGGGTGCCGAT	0	12	1
GGGTGCCGATGTACGGTTCCCTGCGGCTGGACCTTCTTCT	0	42	1
CGGCTAAGGTGGCTTGGATCTCTTGTTTGGCCGCTGTATG	0	93	1
CTGTCTTCGAGACTTGAGCCTTACAGTAGGGTATGAACCA	0	215	1
TTTGGAATCGGGGGAGGATCCGGGAGTTGTCT        	0	278	1
TCATGGGACGCGGGCGCGCTCAGGAGGCGGGGGAGGCTAC	1	14	1
CTCCACGTTTGTCCCGTCTCCTACAGCAGGTCCACATACC	2	11	1
AATGTGAGTTGAATAGGTCTCAAAAGAACGATAATAAATC	2	75	1
          * *  *  ***   **  **
MAP Score: 6.62578

Motif 3
CTAGAGTGAAGGGCCCTCTGGATGGGGGTGCC	0	17	1
GCCATACAGCGGCCAAACAAGAGATCCAAGCC	0	103	0
TGGGACGCGGGCGCGCTCAGGAGGCGGGGGAG	1	17	1
TTTAAAAACTGGCCTCACTCGACTTAGGTATG	2	45	0
GAGTTGAATAGGTCTCAAAAGAACGATAATAA	2	80	1
CCTATAATCAGCGGCCACTGTACCTCCTAGGG	2	114	0
          **** **** **
MAP Score: 1.1272