AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i006_Pyrimidine_Biosynthesis_II_aquae_reg_100.orf -o006_aquae_100.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	    0.649984	-113
CCGCCGAGTAGTAAAATATAGTTTGGTTTA	1	34	0	GTAAAATATA	    0.942336	-92
TTATATATACATAAAGTTAATTAAAGGTTA	1	87	1	ATAAAGTTAA	    0.903018	-39
ATAAAGTTAATTAAAGGTTAGGAAGTTAAA	1	97	1	TTAAAGGTTA	    0.903616	-29
GGTTAGGAAGTTAAAATAAACTTG      	1	112	1	TTAAAATAAA	    0.958468	-14
AAATGTTGTTTTAAAATTAAGTTTCAGGAG	2	19	0	TTAAAATTAA	    0.671245	-49
TTTATTTTAATTAAAATACAATAAAATGTT	2	42	0	TTAAAATACA	    0.986732	-26
TGTATTTTAATTAAAATAAATCAAGT    	2	52	1	TTAAAATAAA	    0.958468	-16
          **********

Masking position 5
Map Score:   14.3276

Number of sites scoring better than the average of aligned sites = 138
Number in coding regions = 97
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 59
Fraction of orfs with sites within 600 bp upstream = 0.00947639


Motif number 2

   AATACCACCTCCTGAAATTTAAGTAAA	1	8	1	CCTCCTGAAA	    0.997406	-118
   TCTCCTTCCTCCTGAAACTTAATTTTA	2	8	1	CCTCCTGAAA	    0.997406	-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

AATTTAAGTAAACCAAACTATATTTTACTAC	1	26	1	AACAAACTAT	     0.96823	-100
CGAAATTTTTATAAAAATTTTCACCGCCGAG	1	56	0	ATAAAATTTT	    0.914409	-70
ATGTATATATAACGAAATTTTTATAAAAATT	1	68	0	AACAAATTTT	    0.989152	-58
TCCTAACCTTTAATTAACTTTATGTATATAT	1	89	0	TAATAACTTT	    0.861525	-37
TAGGAAGTTAAAATAAACTTG          	1	115	1	AAAAAACTTG	    0.956139	-11
TTCCTCCTGAAACTTAATTTTAAAACAACAT	2	16	1	AACTAATTTT	     0.97772	-52
TTAATTTTAAAACAACATTTTATTGTATTTT	2	29	1	AACACATTTT	    0.971793	-39
          *** *******

Masking position 7
Map Score:   7.54031

Number of sites scoring better than the average of aligned sites = 213
Number in coding regions = 182
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 4

        AATACCACCTCCTGAAATTTAA	1	3	1	TACCACCTCC	    0.995036	-123
TTATAAAAATTTTCACCGCCGAGTAGTAAA	1	49	0	TTTCACCGCC	    0.992595	-77
 CAAGTTTATTTTAACTTCCTAACCTTTAA	1	107	0	TTTAACTTCC	    0.954722	-19
        TCTCCTTCCTCCTGAAACTTAA	2	3	1	TCCTTCCTCC	    0.977328	-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