AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i005_Pyrimidine_Biosynthesis_pyro_reg_100.orf -o005_pyro_100.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 =  	0.42
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RPH00395	91	Pyrococcus_OT3
#2	RPH01070	300	Pyrococcus_OT3

Motif number 1

GAGATATTTAAAGTTTACCAAAAACTTTTAGTATTG	1	39	0	AATTAAAACT	    0.988541	-53
TTTAGATCCAAATTTGAAACAGAGATGCCTAAGGTA	2	15	1	AATTAAAGAT	    0.965802	-286
TACAAGGCATAACTTTATACACAAACTCTGATATTT	2	56	1	AATTAAAAAC	    0.965784	-245
CTATTCCGCAAATTTAAGCTATAAATGGGTATTCGG	2	103	1	AATTAAAAAT	    0.971016	-198
ATTGTTAATAAATTTGAGCTATAGCCTGTCTAATCT	2	142	0	AATTAAAGCC	    0.983494	-159
TGTTGGTTTTAACGTTAAATTGAACTAAGCGTAATT	2	175	0	AAGTATAACT	    0.946647	-126
ATTTTTCCCAAAAGTAACGTAGAACCAAAAAAGAAA	2	223	1	AAGTAAAACC	    0.989365	-78
ACCAAAAAAGAAAGGTAGAAAAAACTTAAGAACCTT	2	246	1	AAGGAAAACT	    0.963433	-55
CCAAAGTTAGAAAGTTATTAAAAGGTTCTTAAGTTT	2	267	0	AAGTAAAGGT	    0.955212	-34
          ** ** *   * ****

Masking position 7
Map Score:   9.03303

Number of sites scoring better than the average of aligned sites = 114
Number in coding regions = 97
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 2

GTTTACCAAAAACTTTTAGTATTGATATCG	1	33	0	AACTTTTAGT	    0.904865	-59
TTGTAAGCACTACCTTAGGCATCTCTGTTT	2	31	0	TACCTTAGGC	    0.951861	-270
ACTATTCCGCAAATTTAAGCTATAAATGGG	2	102	1	AAATTTAAGC	    0.621732	-199
ATAGCCTGTCTAATCTTGGCCGAATACCCA	2	128	0	TAATCTTGGC	    0.954777	-173
TATTAACAATTACGCTTAGTTCAATTTAAC	2	168	1	TACGCTTAGT	    0.864731	-133
TATGGAGTGATACTGTTGGTTTTAACGTTA	2	194	0	TACTGTTGGT	     0.96048	-107
GGTTCTACGTTACTTTTGGGAAAAATATGG	2	219	0	TACTTTTGGG	    0.967682	-82
AATAACTTTCTAACTTTGGTGACCCAA   	2	284	1	TAACTTTGGT	    0.945897	-17
          **********

Masking position 2
Map Score:   3.03317

Number of sites scoring better than the average of aligned sites = 417
Number in coding regions = 366
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 3

CTGTTTCAAATTTGGATCTAAAGTGT    	2	7	0	TTTGGATCTA	    0.978552	-294
GAGTGATACTGTTGGTTTTAACGTTAAATT	2	190	0	GTTGGTTTTA	    0.978205	-111
ACCTTTCTTTTTTGGTTCTACGTTACTTTT	2	232	0	TTTGGTTCTA	      0.9914	-69
AGGTTCTTAAGTTTTTTCTACCTTTCTTTT	2	251	0	GTTTTTTCTA	    0.918675	-50
          **********

Masking position 7
Map Score:   1.74127

Number of sites scoring better than the average of aligned sites = 98
Number in coding regions = 89
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

GATATCGAAATCCGATATCGTGATTCGAT 	1	10	0	TCCGATATCG	    0.971916	-82
GATATCGGATTTCGATATCAATACTAAAAG	1	21	1	TTCGATATCA	    0.985872	-71
TTGGTAAACTTTAAATATCTCCTAATTATT	1	54	1	TTAAATATCT	    0.943232	-38
GTCGCAATCCTTAAATATCAGAGTTTGTGT	2	74	0	TTAAATATCA	    0.965884	-227
          **********

Masking position 5
Map Score:   0.720494

Number of sites scoring better than the average of aligned sites = 36
Number in coding regions = 30
Number in noncoding regions = 6
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:   -4.02005e-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:   -4.02005e-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:   -4.02005e-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