AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i146_NADH-formate_Dehydrogenase_hpyl_reg_300.orf -o146_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -x5 -e 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.39
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RHP00650	116	AE000511
#2	RHP00654	69	AE000511
#3	RHP00655	101	AE000511

Motif number 1

AATTTAGTTTTAATTTCAAGCGTGGTGCGTTA	1	22	0	TAATCAAGCG	    0.993591	-95
AAATTAAAACTAAATTTTAGTGTATTCTTAGC	1	38	1	TAATTTAGTG	    0.975158	-79
AAATTTTAGATAAGATCAAGCGTGATTTTTTC	1	70	1	TAATCAAGCG	    0.993591	-47
CTTAAATGCCTAAAATTTAGAAAAAATCACGC	1	89	0	TAATTTAGAA	    0.964358	-28
 AAAATTTAGTAATCTTAAGCGGGGCTGGTAT	2	10	1	TAATTAAGCG	    0.993717	-60
AGCGGGATTAAAACCTTTAGAGACGCTG    	2	52	1	AAATTTAGAG	    0.925399	-18
TTTTTTCAGCTAACGATTAGCAAAAACATGGT	3	32	1	TAAATTAGCA	    0.973197	-70
CAAACTCCTTTAATTACTAGCAAATGACAAAG	3	72	0	TAAACTAGCA	    0.972656	-30
          ***  *******

Masking position 9
Map Score:   13.4159

Number of sites scoring better than the average of aligned sites = 285
Number in coding regions = 258
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 2

AGAATACACTAAAATTTAGTTTTAATTTCA	1	36	0	AAAATTTAGT	     0.99132	-81
TATTCTTAGCAAATTTTAGATAAGATCAAG	1	60	1	AAATTTTAGA	    0.982401	-57
GATTTTTTCTAAATTTTAGGCATTTAAGGA	1	93	1	AAATTTTAGG	    0.979131	-24
          AAAATTTAGTAATCTTAAGC	2	1	1	AAAATTTAGT	     0.99132	-69
GCGGGATTAAAACCTTTAGAGACGCTG   	2	53	1	AACCTTTAGA	    0.944919	-17
CTGAAAAAATAAAAATTATTTTAACATTTC	3	11	0	AAAAATTATT	    0.803992	-91
          **********

Masking position 6
Map Score:   7.2354

Number of sites scoring better than the average of aligned sites = 436
Number in coding regions = 358
Number in noncoding regions = 78
Number of orfs with sites within 600 bp upstream = 67
Fraction of orfs with sites within 600 bp upstream = 0.0107613


Motif number 3

TCAAGCGTGGTGCGTTAAAGGCGGTGGT   	1	8	0	TGGTTAAAGG	    0.937405	-109
CACCACGCTTGAAATTAAAACTAAATTTTAG	1	27	1	GAATTAAAAC	    0.944862	-90
CTAAATTTTAGGCATTTAAGGAATCA     	1	101	1	GGATTTAAGG	    0.993002	-16
AAGCGGGGCTGGTATTTCAGCAGAAAGCGGG	2	27	1	GGATTTCAGC	    0.981063	-43
AGCAGAAAGCGGGATTAAAACCTTTAGAGAC	2	45	1	GGATTAAAAC	    0.988926	-25
TCATTTGCTAGTAATTAAAGGAGTTTGAGAG	3	77	1	GTATTAAAGG	    0.980668	-25
          ** ********

Masking position 6
Map Score:   4.20646

Number of sites scoring better than the average of aligned sites = 548
Number in coding regions = 491
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 4

AAATCACGCTTGATCTTATCTAAAATTTGC	1	68	0	TGATCTTATC	    0.977025	-49
AGATCAAGCGTGATTTTTTCTAAATTTTAG	1	82	1	TGATTTTTTC	    0.985806	-35
AAAAATTATTTTAACATTTC          	3	1	0	TTAACATTTC	     0.91578	-101
AAAATAATTTTTATTTTTTCAGCTAACGAT	3	19	1	TTATTTTTTC	    0.978215	-83
          **********

Masking position 7
Map Score:   1.86106

Number of sites scoring better than the average of aligned sites = 181
Number in coding regions = 163
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 5

          **********

No masking
Map Score:   -2.39152e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 6

          **********

No masking
Map Score:   -2.39152e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 7

          **********

No masking
Map Score:   -2.39152e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0