AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i018_non-Oxidative_glucose_Metabolism_aful_reg_300.orf -o018_aful_300.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/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	RAG19206	129	Archaeoglobus_fulgidus
#2	RAG19200	114	Archaeoglobus_fulgidus
#3	RAG49643	39	Archaeoglobus_fulgidus

Motif number 1

ACTGAAATATAAACCTTCAACAATTATTTC	1	15	0	AAACCTTCAA	    0.924652	-115
CAAGCAACCAAAACTGAAATATAAACCTTC	1	27	0	AAACTGAAAT	    0.966144	-103
TCCCTCTTAAAAACTTTCACCAGTACACAC	1	80	0	AAACTTTCAC	    0.956617	-50
TACAAAGAAAAGACTGTCATTA        	2	3	0	AGACTGTCAT	    0.965974	-112
TTTACCTTATAAACTGACGTTGGAGAGCAT	2	62	0	AAACTGACGT	    0.945209	-53
TTTATAAGGTAAACTTTATTTACAATGAAA	2	79	1	AAACTTTATT	    0.939281	-36
TTGGATTGTAACACTTTCATTGTAAATAAA	2	93	0	ACACTTTCAT	    0.956617	-22
          AAATCGTAATCTTTTTTAAT	3	1	1	AAATCGTAAT	    0.814767	-39
ACATCCTTAAAAACCTAATTAAAAAAGATT	3	18	0	AAACCTAATT	    0.870006	-22
          **********

Masking position 3
Map Score:   7.32653

Number of sites scoring better than the average of aligned sites = 462
Number in coding regions = 391
Number in noncoding regions = 71
Number of orfs with sites within 600 bp upstream = 81
Fraction of orfs with sites within 600 bp upstream = 0.01301


Motif number 2

AATTGGATTTTTCCCTCTTAAAAACTTTCAC	1	90	0	TTCCTCTTAA	    0.954211	-40
ATGACAGTCTTTTCTTTGTAATTGAAGTAGC	2	13	1	TTCTTTGTAA	    0.976806	-102
TAAATAAAGTTTACCTTATAAACTGACGTTG	2	70	0	TTCCTTATAA	    0.959769	-45
ATTGTAACACTTTCATTGTAAATAAAGTTTA	2	88	0	TTCATTGTAA	    0.846857	-27
        GGTTGGATTGTAACACTTTCATT	2	102	0	TTGATTGTAA	    0.966099	-13
CTTTTTTAATTAGGTTTTTAAGGATGTGC  	3	21	1	TAGTTTTTAA	     0.82634	-19
          ** ********

Masking position 6
Map Score:   4.60555

Number of sites scoring better than the average of aligned sites = 121
Number in coding regions = 100
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 3

        TGTTGAAATAATTGTTGAAGGTTT	1	3	1	TTGAAATATG	    0.987468	-127
TGCTCCACCTTCGAAGTAATTGGATTTTTCCC	1	106	0	TCGAAGTATG	    0.994584	-24
TTCTTTGTAATTGAAGTAGCTGTCTTTATCCA	2	24	1	TTGAAGTATG	    0.996816	-91
TAATTAGGTTTTTAAGGATGTGC         	3	27	1	TTTAAGGATG	    0.978822	-13
          ********  **

Masking position 5
Map Score:   2.59233

Number of sites scoring better than the average of aligned sites = 49
Number in coding regions = 45
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

TTGGTTGCTTGCTTTTCGTGTGTTTGAGCATT	1	46	1	GCTTTGTGTG	    0.996416	-84
GTGTGTTTGAGCATTGAGTGTGTACTGGTGAA	1	63	1	GCATTGTGTG	    0.997964	-67
ACGTTGGAGAGCATGCAGTATGGATAAAGACA	2	44	0	GCATGGTATG	    0.993424	-71
          *****  *****

Masking position 4
Map Score:   0.321439

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 13
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:   4.07441e-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:   4.07441e-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:   4.07441e-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