AlignACE 3.0 10/20/99
AlignACE2 -i EC_operons050_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943441873
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yciV	137	putative enzymes
#1	yrdD	62	putative DNA topoisomerase
#2	smf_2	53	orf, fragment 2
#3	smf_1	129	orf, fragment 1
#4	atpD	26	membrane-bound ATP synthase, F1 sector, beta-subunit
#5	atpG	50	membrane-bound ATP synthase, F1 sector, gamma-subunit
#6	atpF	61	membrane-bound ATP synthase, F0 sector, subunit b
#7	atpE	46	membrane-bound ATP synthase, F0 sector, subunit c
#8	atpI	300	membrane-bound ATP synthase, dispensable protein, affects expression of atpB

Motif 1
TTTCAGAATATTTGCCAGAACCGTTATGATGTC	0	79	1
GCAAAAAACATTATCCAGAACGGGAGTGCGCC 	0	115	1
ATTACGCACCGTGAACAGTGCTGATTTCGCCAT	1	38	0
CCTTGTTTTATTAACCAGTGAGGCCCTTCGCTT	2	20	0
        AAATCTCCAGAGATGTGTTCAGGAG	3	2	1
ATCTTTGCGATTGGTCAGTGATGCTGTCAATCA	3	75	0
AAGGCATCATTTGCCAAGTAAATAAATATGCTG	8	10	1
AGCACGCTTTATCACCAGTGTTTACGCGTTATT	8	72	1
ATCGAACAGGGTTAGCAGAAAAGTCGCAATTGT	8	119	1
GTTTAAATATTTTTCCAGTGCATACAATTGCGA	8	142	0
          **  ******* *
MAP Score: 4.44573

Motif 2
TAACCAGTGAGGCCCTTCGCTTCCCGGATT	2	12	0
TTCTATTCTAGACAAATCCCCCTCTGATTG	3	51	1
CAGCATCACTGACCAATCGCAAAGATTGCT	3	82	1
CCTGCCCTAAGGCAAGCCGCCAGACG    	5	6	0
CTTGCCTTAGGGCAGGCCGCAAGGCATTGA	5	20	1
AGGGTTAGCAGAAAAGTCGCAATTGTATGC	8	126	1
AGTTTTATACGACACGCGGCATACCTCGAA	8	270	1
          **********
MAP Score: 4.38498

Motif 3
      GGAATCCGGGAAGCGAAGGGCCTCACTG	2	4	1
AGGGGGATTTGTCTAGAATAGAAGAAATAATCTT	3	40	0
CAGCATCACTGACCAATCGCAAAGATTGCTAAGG	3	82	1
GGCTGCTTATGGCAGGGAGATAAGG         	3	114	1
CCTGCCCTAAGGCAAGCCGCCAGACG        	5	2	0
CTTGCCTTAGGGCAGGCCGCAAGGCATTGAGGAG	5	20	1
GATCGAACAGGGTTAGCAGAAAAGTCGCAATTGT	8	118	1
CGCTTTTTGATGCTTGACTCTAAGCCTTAAAGAA	8	236	1
TACGACACGCGGCATACCTCGAAGGGAGCAGGA 	8	277	1
          ***  * *** ***
MAP Score: 4.29187

Motif 4
ATGGCGAAATCAGCACTGTTCACGGTGCGTA	1	38	1
AAGCGAAGGGCCTCACTGGTTAATAAAACAA	2	20	1
TAGACAAATCCCCCTCTGATTGACAGCATCA	3	59	1
TGATTGACAGCATCACTGACCAATCGCAAAG	3	75	1
  GAGCTTCTCCTCAATGCCTTGCGGCCTGC	5	31	0
CACGCTTTATCACCAGTGTTTACGCGTTATT	8	74	1
ATACGGTGCGCCCCCGTGATTTCAAACAATA	8	197	0
          ******** **
MAP Score: 2.6153

Motif 5
       TCATTTCTTTAATTCAGCATAAGT	1	3	1
AGAATCGCACCTTGTTTTATTAACCAGTGAG	2	31	0
AGAAAGATTATTTCTTCTATTCTAGACAAAT	3	37	1
    TAAGCGTTGCTTTTATTTAAAGAGCAA	6	6	1
CAGTCTCCAGTTTGTTTCAGTTAAAACGTAG	7	23	0
CGTATAAAACTTTCTTTAAGGCTTAGAGTCA	8	250	0
          ******* ***
MAP Score: 0.553653