AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00480_aful_reg_300.orf -o00480_aful_300.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -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 =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	AF0645	232	translation initiation factor eIF-5A (eif5A)
#2	AF0647	132	isocitrate dehydrogenase, NADP (icd)

Motif number 1

CTCGGATTCCAGAAGTCGTTCTGGCAGGAT       	1	4	0	AGAATTCGAG	    0.990339	-229
ACCAGCTGCCCTGATTTGGCCCGTGAGGCCAGAGGTA	1	45	1	CTGATGCGAG	    0.912794	-188
CCAGAGGTAAAGCAGTATTCCGGTAAAGGCTATAATT	1	73	1	AGCATTCGAA	    0.980822	-160
GGTAAAGGCTATAATTACTCCTGAAAGCACCATGAAG	1	94	1	ATAATTCGAG	    0.978494	-139
TGAAGCTCGCAAAAATCAGACGGCTGGTTCTGTTCTA	1	131	0	AAAATGCGGG	    0.962314	-102
AAGAAGAGTTAAAAATGCGACTGAGAAGAAAAAGCAT	1	167	0	AAAATGCGAA	    0.982341	-66
TCGCATTTTTAACTCTTCTTCAGAAAAATTTAAATTA	1	184	1	AACTTTCGAA	    0.869728	-49
TAAATTAACGCAAAATTAGGCAGCAAGGT        	1	214	1	CAAATGCGAG	    0.981625	-19
TGAGGCTTAAAGCAATTATACCGTAAAAACTTTTGCA	2	41	1	AGCATTCGAA	    0.980822	-92
          **** *  * * *  **

Masking position 6
Map Score:   7.18328

Number of sites scoring better than the average of aligned sites = 239
Number in coding regions = 220
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 2

CTTTACCTCTGGCCTCACGGGCCAAATCAG	1	55	0	GGCCTCACGG	    0.943441	-178
TACTTCATGGTGCTTTCAGGAGTAATTATA	1	103	0	TGCTTTCAGG	    0.967593	-130
GGTTCTGTTCTACTTCATGGTGCTTTCAGG	1	113	0	TACTTCATGG	      0.7784	-120
GATTTTTGCGAGCTTCATGCTTTTTCTTCT	1	151	1	AGCTTCATGC	    0.964638	-82
         AAGCTTTCAGCATCGAAATTC	2	2	1	AGCTTTCAGC	    0.984436	-131
ACGGTATAATTGCTTTAAGCCTCACATGAG	2	35	0	TGCTTTAAGC	     0.96838	-98
AGTTTATAAAATCCTTCCGCTCTTGGTTGA	2	97	0	ATCCTTCCGC	    0.937817	-36
AAACTACCACAACCTTCCGCT         	2	122	1	AACCTTCCGC	    0.963761	-11
          **********

Masking position 5
Map Score:   6.30829

Number of sites scoring better than the average of aligned sites = 1301
Number in coding regions = 1239
Number in noncoding regions = 62
Number of orfs with sites within 600 bp upstream = 52
Fraction of orfs with sites within 600 bp upstream = 0.00835207


Motif number 3

GGCCAAATCAGGGCAGCTGGTAATTCTCGG	1	36	0	GGGCAGCTGG	     0.99711	-197
CGCAAAAATCAGACGGCTGGTTCTGTTCTA	1	131	0	AGACGGCTGG	    0.988617	-102
ACGCAAAATTAGGCAGCAAGGT        	1	221	1	AGGCAGCAAG	    0.982501	-12
ACTCAACCAAGAGCGGAAGGATTTTATAAA	2	95	1	GAGCGGAAGG	    0.971274	-38
          **********

Masking position 6
Map Score:   1.24846

Number of sites scoring better than the average of aligned sites = 223
Number in coding regions = 216
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

          **********

No masking
Map Score:   -7.29427e-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 5

          **********

No masking
Map Score:   -7.29427e-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:   -7.29427e-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