AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i006_Pyrimidine_Biosynthesis_II_pyro_reg_100.orf -o006_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	RPH01395	71	Pyrococcus_OT3
#2	RPH01070	300	Pyrococcus_OT3

Motif number 1

CCTTATTTGAAACTTTGAATGGTGAAAAGG	1	52	1	AACTTTGAAT	    0.905315	-20
CTTTAGATCCAAATTTGAAACAGAGATGCC	2	14	1	AAATTTGAAA	     0.93839	-287
AGAGATGCCTAAGGTAGTGCTTACAAGGCA	2	35	1	AAGGTAGTGC	    0.873286	-266
TACAAGGCATAACTTTATACACAAACTCTG	2	56	1	AACTTTATAC	    0.828989	-245
ACTATTCCGCAAATTTAAGCTATAAATGGG	2	102	1	AAATTTAAGC	    0.857382	-199
AATTGTTAATAAATTTGAGCTATAGCCTGT	2	149	0	AAATTTGAGC	     0.95517	-152
AGTTCAATTTAACGTTAAAACCAACAGTAT	2	185	1	AACGTTAAAA	    0.905805	-116
TCCCAAAAGTAACGTAGAACCAAAAAAGAA	2	228	1	AACGTAGAAC	    0.978603	-73
CCAAAAAAGAAAGGTAGAAAAAACTTAAGA	2	247	1	AAGGTAGAAA	     0.94659	-54
TGGGTCACCAAAGTTAGAAAGTTATTAAAA	2	280	0	AAGTTAGAAA	    0.942392	-21
          **********

Masking position 5
Map Score:   9.12064

Number of sites scoring better than the average of aligned sites = 758
Number in coding regions = 668
Number in noncoding regions = 90
Number of orfs with sites within 600 bp upstream = 92
Fraction of orfs with sites within 600 bp upstream = 0.0147767


Motif number 2

TCAGATCACCTAATTTTAGAATTACAGTTTAATA	1	12	1	TAATTTAGTA	    0.914342	-60
ATAGCCTGTCTAATCTTGGCCGAATACCCATTTA	2	124	0	TAATTTGGAA	    0.988595	-177
TATTAACAATTACGCTTAGTTCAATTTAACGTTA	2	168	1	TACGTTAGAA	     0.97543	-133
TATGGAGTGATACTGTTGGTTTTAACGTTAAATT	2	190	0	TACTTTGGTA	    0.992601	-111
GGTTCTACGTTACTTTTGGGAAAAATATGGAGTG	2	215	0	TACTTTGGAA	    0.994969	-86
          **** ****   **

Masking position 7
Map Score:   2.05999

Number of sites scoring better than the average of aligned sites = 19
Number in coding regions = 14
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

CTAATTTTAGAATTACAGTTTAATATAAAAA	1	21	1	AATTACAGTT	    0.932815	-51
TCAAAGTTTCAAATAAGGTTTTTATATTAAA	1	39	0	AAATAAGGTT	    0.941739	-33
CCTTTTCACCATTCAAAGTTTCAAATAAGGT	1	51	0	ATTCAAAGTT	    0.949137	-21
TCAAATTTGGATCTAAAGTGT          	2	1	0	ATCTAAAGGT	    0.926555	-300
AAACTCTGATATTTAAGGATTGCGACTATTC	2	78	1	ATTTAAGGTT	    0.983519	-223
CCGAATACCCATTTATAGCTTAAATTTGCGG	2	108	0	ATTTATAGTT	    0.963643	-193
CTTTTGGGAAAAATATGGAGTGATACTGTTG	2	206	0	AAATATGGGT	    0.799536	-95
TTAGAAAGTTATTAAAAGGTTCTTAAGTTTT	2	266	0	ATTAAAAGTT	    0.926732	-35
          ******** **

Masking position 5
Map Score:   4.20965

Number of sites scoring better than the average of aligned sites = 230
Number in coding regions = 168
Number in noncoding regions = 62
Number of orfs with sites within 600 bp upstream = 80
Fraction of orfs with sites within 600 bp upstream = 0.0128493


Motif number 4

TTAGAATTACAGTTTAATATAAAAACCTTA	1	27	1	AGTTTAATAT	    0.909722	-45
CACCATTCAAAGTTTCAAATAAGGTTTTTA	1	46	0	AGTTTCAAAT	    0.951813	-26
   ACACTTTAGATCCAAATTTGAAACAGA	2	8	1	AGATCCAAAT	    0.935417	-293
ACCCATTTATAGCTTAAATTTGCGGAATAG	2	103	0	AGCTTAAATT	    0.962618	-198
GACAGGCTATAGCTCAAATTTATTAACAAT	2	148	1	AGCTCAAATT	    0.979127	-153
AATTACGCTTAGTTCAATTTAACGTTAAAA	2	175	1	AGTTCAATTT	     0.95742	-126
          **********

Masking position 4
Map Score:   5.4816

Number of sites scoring better than the average of aligned sites = 169
Number in coding regions = 146
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 5

          **********

No masking
Map Score:   4.92707e-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:   4.92707e-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:   4.92707e-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