AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i279_hypothetical4_aful_reg_300.orf -o279_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	RAG48295	148	Archaeoglobus_fulgidus

Motif number 1

CACTGTTAGGTAACAGTGTTTGGGGTGGTG	1	16	0	TAACAGTGTT	    0.997627	-133
CACTGTTACCTAACAGTGTTTATATTTAAC	1	28	1	TAACAGTGTT	    0.997627	-121
GTTGGCCTAAAATCGGTTTTGAAAATGCAA	1	82	0	AATCGGTTTT	    0.976671	-67
GCCTAAATTTAAAAAGTTTTTGGTTGGCCT	1	104	0	AAAAAGTTTT	    0.891201	-45
ATCCTAAACATAACGGTGTTAAAA      	1	135	1	TAACGGTGTT	      0.9978	-14
          **********

Masking position 7
Map Score:   11.217

Number of sites scoring better than the average of aligned sites = 61
Number in coding regions = 50
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 2

GGTAACAGTGTTTGGGGTGGTGATGGG    	1	7	0	TTTGGGTGGT	    0.993802	-142
GCATTATGCATTTTTGATTGCATTTTCAAAA	1	65	1	TTTTTGTTGC	    0.985904	-84
TTTAAAAAGTTTTTGGTTGGCCTAAAATCGG	1	96	0	TTTTGGTGGC	    0.998682	-53
CACCGTTATGTTTAGGATAGCCTAAATTTAA	1	122	0	TTTAGGTAGC	     0.99367	-27
          ****** ****

Masking position 8
Map Score:   4.33684

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 24
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 3

GCTTATAATGTTAAATATAAACACTGTTAG	1	37	0	TTAAATATAA	    0.566747	-112
TTAGGATAGCCTAAATTTAAAAAGTTTTTG	1	112	0	CTAAATTTAA	    0.569239	-37
TTAGGCTATCCTAAACATAACGGTGTTAAA	1	128	1	CTAAACATAA	    0.968146	-21
          **********

Masking position 5
Map Score:   2.64239

Number of sites scoring better than the average of aligned sites = 9
Number in coding regions = 5
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 4

          **********

No masking
Map Score:   2.43208e-15

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:   2.43208e-15

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:   2.43208e-15

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