AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i006_Pyrimidine_Biosynthesis_II_aquae_reg_300.orf -o006_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	RAA01005	125	Aquifex_aeolicus
#2	RAA00241	67	Aquifex_aeolicus

Motif number 1

TTTGGTTTACTTAAATTTCAGGAGGTGGTA	1	13	0	TTAAATTTCA	    0.632902	-113
CCGCCGAGTAGTAAAATATAGTTTGGTTTA	1	34	0	GTAAAATATA	    0.957548	-92
TAACGAAATTTTTATAAAAATTTTCACCGC	1	60	0	TTTATAAAAA	    0.568845	-66
TAAAAATTTCGTTATATATACATAAAGTTA	1	76	1	GTTATATATA	    0.881206	-50
TATACATAAAGTTAATTAAAGGTTAGGAAG	1	92	1	GTTAATTAAA	    0.613692	-34
GGTTAGGAAGTTAAAATAAACTTG      	1	112	1	TTAAAATAAA	    0.537644	-14
AAATGTTGTTTTAAAATTAAGTTTCAGGAG	2	19	0	TTAAAATTAA	    0.528964	-49
TTTATTGTATTTTAATTAAAATAAATCAAG	2	47	1	TTTAATTAAA	      0.4997	-21
          **********

Masking position 4
Map Score:   8.71342

Number of sites scoring better than the average of aligned sites = 228
Number in coding regions = 158
Number in noncoding regions = 70
Number of orfs with sites within 600 bp upstream = 80
Fraction of orfs with sites within 600 bp upstream = 0.0128493


Motif number 2

   AATACCACCTCCTGAAATTTAAGTAAA	1	8	1	CCTCCTGAAA	    0.997447	-118
   TCTCCTTCCTCCTGAAACTTAATTTTA	2	8	1	CCTCCTGAAA	    0.997447	-60
          **********

Masking position 6
Map Score:   3.41122

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 3

TAAGTAAACCAAACTATATTTTACTACTCG	1	30	1	AAACTATATT	    0.973139	-96
TTAACTTCCTAACCTTTAATTAACTTTATG	1	96	0	AACCTTTAAT	    0.772768	-30
TTAGGAAGTTAAAATAAACTTG        	1	114	1	AAAATAAACT	    0.936606	-12
CTTCCTCCTGAAACTTAATTTTAAAACAAC	2	15	1	AAACTTAATT	    0.967152	-53
CTTAATTTTAAAACAACATTTTATTGTATT	2	28	1	AAACAACATT	    0.938126	-40
TATTTTAATTAAAATACAATAAAATGTTGT	2	40	0	AAAATACAAT	      0.9499	-28
TATTTTAATTAAAATAAATCAAGT      	2	54	1	AAAATAAATC	    0.909914	-14
          **********

Masking position 8
Map Score:   5.26235

Number of sites scoring better than the average of aligned sites = 206
Number in coding regions = 171
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 4

        AATACCACCTCCTGAAATTTAA	1	3	1	TACCACCTCC	    0.994786	-123
TTATAAAAATTTTCACCGCCGAGTAGTAAA	1	49	0	TTTCACCGCC	    0.992223	-77
 CAAGTTTATTTTAACTTCCTAACCTTTAA	1	107	0	TTTAACTTCC	    0.952539	-19
        TCTCCTTCCTCCTGAAACTTAA	2	3	1	TCCTTCCTCC	    0.976208	-65
          **********

Masking position 1
Map Score:   1.09552

Number of sites scoring better than the average of aligned sites = 430
Number in coding regions = 325
Number in noncoding regions = 105
Number of orfs with sites within 600 bp upstream = 115
Fraction of orfs with sites within 600 bp upstream = 0.0184709


Motif number 5

          **********

No masking
Map Score:   4.00336e-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:   4.00336e-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:   4.00336e-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