AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i005_Pyrimidine_Biosynthesis_pyro_reg_300.orf -o005_pyro_300.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

CAATACTAAAAGTTTTTGGTAAACTTTAAATATCTC	1	39	1	AGTTTTAATT	    0.986062	-53
TACCTTAGGCATCTCTGTTTCAAATTTGGATCTAAA	2	15	0	ATCTTTAATT	    0.958408	-286
AAATATCAGAGTTTGTGTATAAAGTTATGCCTTGTA	2	56	0	GTTTTTAATT	    0.958394	-245
CCGAATACCCATTTATAGCTTAAATTTGCGGAATAG	2	103	0	ATTTTTAATT	     0.96495	-198
AGATTAGACAGGCTATAGCTCAAATTTATTAACAAT	2	142	1	GGCTTTAATT	    0.979847	-159
AATTACGCTTAGTTCAATTTAACGTTAAAACCAACA	2	175	1	AGTTATACTT	    0.935427	-126
TTTCTTTTTTGGTTCTACGTTACTTTTGGGAAAAAT	2	223	0	GGTTTTACTT	    0.986996	-78
AAGGTTCTTAAGTTTTTTCTACCTTTCTTTTTTGGT	2	246	0	AGTTTTCCTT	    0.955551	-55
AAACTTAAGAACCTTTTAATAACTTTCTAACTTTGG	2	267	1	ACCTTTACTT	    0.945658	-34
          **** *   * ** **

Masking position 10
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	    0.908646	-59
TTGTAAGCACTACCTTAGGCATCTCTGTTT	2	31	0	TACCTTAGGC	    0.953869	-270
ACTATTCCGCAAATTTAAGCTATAAATGGG	2	102	1	AAATTTAAGC	     0.63219	-199
ATAGCCTGTCTAATCTTGGCCGAATACCCA	2	128	0	TAATCTTGGC	    0.956669	-173
TATTAACAATTACGCTTAGTTCAATTTAAC	2	168	1	TACGCTTAGT	    0.869877	-133
TATGGAGTGATACTGTTGGTTTTAACGTTA	2	194	0	TACTGTTGGT	    0.962143	-107
GGTTCTACGTTACTTTTGGGAAAAATATGG	2	219	0	TACTTTTGGG	    0.969052	-82
AATAACTTTCTAACTTTGGTGACCCAA   	2	284	1	TAACTTTGGT	     0.94814	-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

     ACACTTTAGATCCAAATTTGAAACA	2	6	1	TTAGATCCAA	    0.838979	-295
CAATTTAACGTTAAAACCAACAGTATCACT	2	189	1	TTAAAACCAA	    0.966817	-112
CAAAAGTAACGTAGAACCAAAAAAGAAAGG	2	231	1	GTAGAACCAA	    0.993555	-70
AAAAAGAAAGGTAGAAAAAACTTAAGAACC	2	250	1	GTAGAAAAAA	    0.920866	-51
          **********

Masking position 5
Map Score:   1.74127

Number of sites scoring better than the average of aligned sites = 89
Number in coding regions = 77
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 4

TTTTAGTATTGATATCGAAATCCGATATCGT	1	19	0	GATATCAAAT	    0.931091	-73
TTTCGATATCAATACTAAAAGTTTTTGGTAA	1	30	1	AATACTAAAG	    0.931091	-62
ATAATTAGGAGATATTTAAAGTTTACCAAAA	1	52	0	GATATTAAAG	    0.990598	-40
TTGAAACAGAGATGCCTAAGGTAGTGCTTAC	2	28	1	GATGCCAAGG	    0.956428	-273
CACAAACTCTGATATTTAAGGATTGCGACTA	2	75	1	GATATTAAGG	    0.988681	-226
AAGTTAGAAAGTTATTAAAAGGTTCTTAAGT	2	269	0	GTTATTAAAG	    0.962944	-32
          ****** ****

Masking position 8
Map Score:   3.60714

Number of sites scoring better than the average of aligned sites = 207
Number in coding regions = 190
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


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