AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i035_Sugars_Metabolism_aful_reg_300.orf -o035_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	RAG10014	73	Archaeoglobus_fulgidus
#2	RAG02871	72	Archaeoglobus_fulgidus
#3	RAG02870	77	Archaeoglobus_fulgidus

Motif number 1

CTCGGCTTTAAAGTTATTTTCTAAAAAAGAT	1	26	1	AATTATTTTC	    0.985564	-48
     AGGAAAATTGAGTTTGGCAAATCAAT	2	6	1	AATGAGTTTG	    0.953523	-67
GAGTTCGCCGAATTGATTTGCCAAACTCAAT	2	17	0	AATGATTTGC	    0.994111	-56
GATATGTAATAAATTTTTTGGAGTTCGCCGA	2	37	0	AATTTTTTGG	    0.982489	-36
TTACGCTAATATCTGTTTTGCTTAACGAAAA	3	26	1	ATTGTTTTGC	     0.97655	-52
GCCATTTTAAAATTTTTTTTCGTTAAGCAAA	3	42	0	AATTTTTTTC	    0.985564	-36
          ** ********

Masking position 4
Map Score:   6.93348

Number of sites scoring better than the average of aligned sites = 98
Number in coding regions = 73
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 2

AAAAGATTAAATTTCCCCAAATCGAAGGTAGGT	1	50	1	ATTCCCAATC	    0.997297	-24
CGCCGAATTGATTTGCCAAACTCAATTTTCCT 	2	10	0	ATTGCCAATC	    0.998994	-63
TGGCAAATCAATTCGGCGAACTCCAAAAAATTT	2	25	1	ATTGGCAATC	    0.997307	-48
CAAAACAGATATTAGCGTAAATCAAAAAGTCCT	3	13	0	ATTGCGAATC	    0.997307	-65
          *** *** ** **

Masking position 9
Map Score:   5.70586

Number of sites scoring better than the average of aligned sites = 6
Number in coding regions = 3
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 3

TTCGATTTGGGGAAATTTAATCTTTTTTAG	1	46	0	GGAAATTTAA	    0.987727	-28
         AGGAAAATTGAGTTTGGCAAA	2	2	1	GGAAAATTGA	    0.967414	-71
TTACGTCTCCGGATATGTAATAAATTTTTT	2	49	0	GGATATGTAA	      0.9874	-24
TTACATATCCGGAGACGTAAGGCC      	2	59	1	GGAGACGTAA	    0.989876	-14
          **********

Masking position 5
Map Score:   2.84849

Number of sites scoring better than the average of aligned sites = 65
Number in coding regions = 54
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 4

          **********

No masking
Map Score:   -1.82309e-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:   -1.82309e-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:   -1.82309e-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