AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons027_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249806
 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
AGAGTGAAGGGCCCTCTGGATGGGGGTGCCGATGTACGG	0	19	1
TCTTCTAATTTGTTTCACGGCTAAGGTGGCTTGGATCTC	0	76	1
TATGAACCAAGTATTAAGGATGTAGGAGGAGTTTTGGAA	0	246	1
TGTAGGAGGAGTTTTGGAATCGGGGGAGGATCCGGGAGT	0	266	1
        CCTATCATGGGACGCGGGCGCGCTCAGGAGG	1	2	1
ACGCGGGCGCGCTCAGGAGGCGGGGGAGGCTACACGCTT	1	21	1
TAGGTATGTGGACCTGCTGTAGGAGACGGGACAAACGTG	2	14	0
GCAGGTCCACATACCTAAGTCGAGTGAGGCCAGTTTTTA	2	36	1
AGTGGCCGCTGATTATAGGTAGTGGGGGGTTAAGATCGG	2	127	1
          *  *    * ** *** **
MAP Score: 13.1907

Motif 3
AACACCTAGAGTGAAGGGCCCTCTGGATGGGGGTGCCG	0	12	1
GGGTGCCGATGTACGGTTCCCTGCGGCTGGACCTTCTT	0	42	1
TCTAATTTGTTTCACGGCTAAGGTGGCTTGGATCTCTT	0	79	1
GAACCAAGTATTAAGGATGTAGGAGGAGTTTTGGAATC	0	249	1
TGTAGGAGGAGTTTTGGAATCGGGGGAGGATCCGGGAG	0	266	1
        CCTATCATGGGACGCGGGCGCGCTCAGGAG	1	2	1
ACGCGGGCGCGCTCAGGAGGCGGGGGAGGCTACACGCT	1	21	1
TCCCTAGGAGGTACAGTGGCCGCTGATTATAGGTAGTG	2	113	1
TGGCCGCTGATTATAGGTAGTGGGGGGTTAAGATCGGC	2	129	1
          **   **   *** ** *
MAP Score: 4.6866

Motif 4
GTGAAGGGCCCTCTGGATGGGGGTGCCGATGTAC	0	22	1
GCCGATGTACGGTTCCCTGCGGCTGGACCTTCTT	0	46	1
GCTTGGATCTCTTGTTTGGCCGCTGTATGGCTTC	0	104	1
GAGGAGTTTTGGAATCGGGGGAGGATCCGGGAGT	0	271	1
  CCTATCATGGGACGCGGGCGCGCTCAGGAGGC	1	8	1
CGCGGGCGCGCTCAGGAGGCGGGGGAGGCTACAC	1	22	1
ATACCTAAGTCGAGTGAGGCCAGTTTTTAAATGT	2	46	1
TCCCTAGGAGGTACAGTGGCCGCTGATTATAGGT	2	113	1
CGCTGATTATAGGTAGTGGGGGGTTAAGATCGGC	2	133	1
          **   * *******
MAP Score: 4.36496

Motif 5
CAACACCTAGAGTGAAGGGCCCTCTGGATGGGGGTGCCGATGTA	0	11	1
GGGGTGCCGATGTACGGTTCCCTGCGGCTGGACCTTCTTCTAAT	0	41	1
ACGGCTAAGGTGGCTTGGATCTCTTGTTTGGCCGCTGTATGGCT	0	92	1
CAAGACAATCTGTATAGAGAGGAAGCATAGAAGCCATACAGCGG	0	123	0
CTATACAGATTGTCTTGTTGAGAAAACTCGGTGCTAATACGAAT	0	150	1
TAAACTATAAAATACTGTCTTCGAGACTTGAGCCTTACAGTAGG	0	201	1
ATGTAGGAGGAGTTTTGGAATCGGGGGAGGATCCGGGAGTTGTC	0	265	1
   CCTATCATGGGACGCGGGCGCGCTCAGGAGGCGGGGGAGGC	1	7	1
CCTCCACGTTTGTCCCGTCTCCTACAGCAGGTCCACATACCTAA	2	10	1
          ***   *    *   *   ** **
MAP Score: 4.27356

Motif 6
TAGAGTGAAGGGCCCTCTGGATGGGGGTGCCGAT	0	18	1
ATTAGAAGAAGGTCCAGCCGCAGGGAACCGTACA	0	51	0
TTGTTTCACGGCTAAGGTGGCTTGGATCTCTTGT	0	85	1
GAGGAGTTTTGGAATCGGGGGAGGATCCGGGAGT	0	271	1
   CCTATCATGGGACGCGGGCGCGCTCAGGAGG	1	7	1
GGCGCGCTCAGGAGGCGGGGGAGGCTACACGCTT	1	26	1
ATGTGGACCTGCTGTAGGAGACGGGACAAACGTG	2	14	0
ATCCCTAGGAGGTACAGTGGCCGCTGATTATAGG	2	112	1
CCGCTGATTATAGGTAGTGGGGGGTTAAGATCGG	2	132	1
          ** *  ***** **
MAP Score: 2.45383

Motif 7
CTAGAGTGAAGGGCCCTCTGGATGGGGGTGCCGA	0	17	1
TCTGGATGGGGGTGCCGATGTACGGTTCCCTGCG	0	33	1
ATTAGAAGAAGGTCCAGCCGCAGGGAACCGTACA	0	51	0
GATCTCTTGTTTGGCCGCTGTATGGCTTCTATGC	0	109	1
CCTATCATGGGACGCGGGCGCGCTCAGGAGGCGG	1	10	1
GGCGCGCTCAGGAGGCGGGGGAGGCTACACGCTT	1	26	1
TTAGGTATGTGGACCTGCTGTAGGAGACGGGACA	2	20	0
AGGAGGTACAGTGGCCGCTGATTATAGGTAGTGG	2	118	1
          ** ** **** * *
MAP Score: 0.759836