AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i112_Amino_Acid_Transport_3_aful_reg_100.orf -o112_aful_100.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	RAG49483	266	Archaeoglobus_fulgidus

Motif number 1

AAAAAAGAGGAAAAGTAAAAAACAATTGCTGCGAT	1	20	1	AAAATAACAA	    0.835059	-247
AAACGCCGGCAAAAACGATTATCGCAGCAATTGTT	1	40	0	AAAACAACGC	    0.994246	-227
GACAAGGAAACAAAACTCAGACCGACGAGAGTTTA	1	125	1	CAAACCACGA	    0.997206	-142
ACGAGAGTTTAAAACCGCCTAAAGCTCTTCTCCAG	1	149	1	AAAACCAAGC	    0.978853	-118
TCTTCTCCAGCAAATCCACCACCAAATTTATTCAT	1	174	1	CAAACAACAA	    0.979225	-93
TAACCGTTTAAAAATCCCCAAACGCCCAAACCTTA	1	216	1	AAAACCACGC	    0.997206	-51
CCTTAAATACCAAACCGCCCATCGAGAACCA    	1	246	1	CAAACCACGA	    0.997206	-21
          **** * *  * ***

Masking position 11
Map Score:   10.7824

Number of sites scoring better than the average of aligned sites = 101
Number in coding regions = 85
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 2

AAAACGCCGGCAAAAACGATTATCGCAGCA	1	46	0	CAAAAACGAT	    0.851939	-221
GTCTGATTTCAAAAAACGCCGGCAAAAACG	1	58	0	AAAAAACGCC	    0.986334	-209
GAAACAAAACTCAGACCGACGAGAGTTTAA	1	131	1	TCAGACCGAC	    0.923455	-136
GACGAGAGTTTAAAACCGCCTAAAGCTCTT	1	148	1	TAAAACCGCC	     0.99534	-119
TCTTCTCCAGCAAATCCACCACCAAATTTA	1	174	1	CAAATCCACC	    0.939233	-93
TTAACCGTTTAAAAATCCCCAAACGCCCAA	1	215	1	AAAAATCCCC	    0.903703	-52
ACCTTAAATACCAAACCGCCCATCGAGAAC	1	245	1	CCAAACCGCC	    0.996922	-22
          **********

Masking position 3
Map Score:   6.39023

Number of sites scoring better than the average of aligned sites = 710
Number in coding regions = 660
Number in noncoding regions = 50
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 3

TTTTACTTTTCCTCTTTTTTCTGAACACC  	1	9	0	CCTCTTTTTC	    0.931966	-258
TTACGTAATCCCACTTTAGTCTGATTTCAAA	1	75	0	CCACTTTATC	    0.984751	-192
TTTCCTTGTCACACTTTCCACAAATAAATTT	1	104	0	ACACTTTCAC	    0.934392	-163
AGGCGGTTTTAAACTCTCGTCGGTCTGAGTT	1	138	0	AAACTCTCTC	    0.969851	-129
AAACCGCCTAAAGCTCTTCTCCAGCAAATCC	1	160	1	AAGCTCTTTC	    0.945179	-107
AATCCACCACCAAATTTATTCATTAAGCTTT	1	186	1	CAAATTTATC	    0.874001	-81
TTTATTCATTAAGCTTTAACCGTTTAAAAAT	1	200	1	AAGCTTTACC	    0.930672	-67
          ******** **

Masking position 5
Map Score:   1.43475

Number of sites scoring better than the average of aligned sites = 794
Number in coding regions = 734
Number in noncoding regions = 60
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 4

          **********

No masking
Map Score:   -1.17788e-14

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:   -1.17788e-14

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:   -1.17788e-14

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