AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i007_Pyrimidine_Nucleotides_Biosynthesis_aquae_reg_300.orf -o007_aquae_300.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 =  	0.44
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RAA01558	69	Aquifex_aeolicus
#2	RAA01695	145	Aquifex_aeolicus
#3	RAA00806	113	Aquifex_aeolicus

Motif number 1

TAGTATATTCTAACCCACTACATAATAAAAATAAATTA	1	26	1	TAACATATAA	    0.880834	-44
TACATAATAAAAATAAATTAAAGGATAATTAAGTAA  	1	44	1	AAAAATATAA	    0.821589	-26
ATACTTATAGAAAGAACTTTTCTCAAGAAATC      	2	5	0	AAAACTAAGA	    0.962503	-141
CAATTCCGCCACACCCCCTAACTAAAGAAATATATTAT	2	41	0	ACACCTAAGA	    0.984796	-105
GGGGGACTTAAAATCCCCTGGGCGAAAAGCCCGTGAGG	2	87	1	AAACCTAAAA	    0.992233	-59
AAGCTTTTTAAAACCGCGTTATAATAAACCAATT    	3	7	0	AAACCTTAAA	    0.947309	-107
ACGCGGTTTTAAAAAGCTTGTGATAAAAAGCAATGATT	3	26	1	AAAACTAAAA	    0.973011	-88
AGCAATGATTTAGCCAAGTGGACAAAAATCTTACAGCG	3	54	1	TAGCATAAAA	    0.772954	-60
CAAAAATCTTACAGCGCCTATTTAATAAATTCTTAACG	3	76	1	ACACCTATAA	    0.976294	-38
          TCATCACCTCCGTTAAGAATTTATTAAA	3	96	0	TCACCTAAGA	    0.963428	-18
          *** * * *     ****

Masking position 9
Map Score:   8.82328

Number of sites scoring better than the average of aligned sites = 679
Number in coding regions = 630
Number in noncoding regions = 49
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 2

          CTTTCCACCTCCGGTTAGTATA	1	1	1	CTTCACCTCC	    0.984315	-69
CGGTTAGTATATTCTAACCCACTACATAATAA	1	22	1	ATCAACCCAC	    0.974118	-48
CTGCCAATTCCGCCACACCCCCTAACTAAAGA	2	51	0	CCCCACCCCC	    0.998682	-95
ACGCGGGGGACTTAAAATCCCCTGGGCGAAAA	2	83	1	CTAAATCCCC	    0.957687	-63
GGGTGGAGGGAGTCGAACCCTCACGGGCTTTT	2	111	0	ATCAACCCTC	    0.974118	-35
GGGTTCGACTCCCTCCACCCCCACCACCCAAC	2	123	1	CCTCACCCCC	    0.997035	-23
          * ** *******

Masking position 7
Map Score:   4.73802

Number of sites scoring better than the average of aligned sites = 139
Number in coding regions = 113
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 3

GTAGTGGGTTAGAATATACTAACCGGAGGTGG	1	15	0	AGAATATAAA	    0.970887	-55
AACCCACTACATAATAAAAATAAATTAAAGGA	1	37	1	ATAATAAATA	    0.956231	-33
AAATTAAAGGATAATTAAGTAA          	1	58	1	ATAATTAAAA	    0.953346	-12
CTAAAGAAATATATTATACTTATAGAAAGAAC	2	26	0	ATATTATATA	    0.843291	-120
AAACCGCGTTATAATAAACCAATT        	3	3	0	ATAATAAAAA	    0.975932	-111
ACCTCCGTTAAGAATTTATTAAATAGGCGCTG	3	87	0	AGAATTTAAA	    0.941112	-27
          ********  **

Masking position 5
Map Score:   3.28806

Number of sites scoring better than the average of aligned sites = 106
Number in coding regions = 82
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 4

AAATCCCCTGGGCGAAAAGCCCGTGAGGGT	2	97	1	GGCGAAAAGC	    0.988105	-49
ATAACGCGGTTTTAAAAAGCTTGTGATAAA	3	23	1	TTTAAAAAGC	    0.939578	-91
AAAAGCTTGTGATAAAAAGCAATGATTTAG	3	37	1	GATAAAAAGC	    0.990778	-77
TAGCCAAGTGGACAAAAATCTTACAGCGCC	3	64	1	GACAAAAATC	      0.9769	-50
          **********

Masking position 5
Map Score:   1.07941

Number of sites scoring better than the average of aligned sites = 76
Number in coding regions = 68
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 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


Motif number 7

          **********

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