AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i006_Pyrimidine_Biosynthesis_II_pyro_reg_300.orf -o006_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	RPH01395	71	Pyrococcus_OT3
#2	RPH01070	300	Pyrococcus_OT3

Motif number 1

CCTTTTCACCATTCAAAGTTTCAAATAAGG	1	52	0	ATTCAAAGTT	    0.904846	-20
GGCATCTCTGTTTCAAATTTGGATCTAAAG	2	14	0	TTTCAAATTT	    0.938073	-287
TGCCTTGTAAGCACTACCTTAGGCATCTCT	2	35	0	GCACTACCTT	    0.872681	-266
CAGAGTTTGTGTATAAAGTTATGCCTTGTA	2	56	0	GTATAAAGTT	    0.828214	-245
CCCATTTATAGCTTAAATTTGCGGAATAGT	2	102	0	GCTTAAATTT	    0.856714	-199
ACAGGCTATAGCTCAAATTTATTAACAATT	2	149	1	GCTCAAATTT	    0.954936	-152
ATACTGTTGGTTTTAACGTTAAATTGAACT	2	185	0	TTTTAACGTT	    0.905339	-116
TTCTTTTTTGGTTCTACGTTACTTTTGGGA	2	228	0	GTTCTACGTT	    0.978489	-73
TCTTAAGTTTTTTCTACCTTTCTTTTTTGG	2	247	0	TTTCTACCTT	    0.946314	-54
TTTTAATAACTTTCTAACTTTGGTGACCCA	2	280	1	TTTCTAACTT	    0.942095	-21
          **********

Masking position 6
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

TATTAAACTGTAATTCTAAAATTAGGTGATCTGA	1	12	0	TACTAAATTA	    0.915176	-60
TAAATGGGTATTCGGCCAAGATTAGACAGGCTAT	2	124	1	TTCCAAATTA	    0.987642	-177
TAACGTTAAATTGAACTAAGCGTAATTGTTAATA	2	168	0	TTCTAACGTA	     0.97334	-133
AATTTAACGTTAAAACCAACAGTATCACTCCATA	2	190	1	TACCAAAGTA	    0.991999	-111
CACTCCATATTTTTCCCAAAAGTAACGTAGAACC	2	215	1	TTCCAAAGTA	    0.994535	-86
          **   **** ****

Masking position 8
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	     0.92429	-51
TCAAAGTTTCAAATAAGGTTTTTATATTAAA	1	39	0	AAATAAGGTT	    0.934289	-33
CCTTTTCACCATTCAAAGTTTCAAATAAGGT	1	51	0	ATTCAAAGTT	    0.942609	-21
TCAAATTTGGATCTAAAGTGT          	2	1	0	ATCTAAAGGT	    0.917302	-300
AAACTCTGATATTTAAGGATTGCGACTATTC	2	78	1	ATTTAAGGTT	    0.981301	-223
CCGAATACCCATTTATAGCTTAAATTTGCGG	2	108	0	ATTTATAGTT	    0.958855	-193
CTTTTGGGAAAAATATGGAGTGATACTGTTG	2	206	0	AAATATGGGT	    0.778123	-95
TTAGAAAGTTATTAAAAGGTTCTTAAGTTTT	2	266	0	ATTAAAAGTT	    0.917501	-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

TAAGGTTTTTATATTAAACTGTAATTCTAA	1	27	0	ATATTAAACT	    0.910732	-45
TAAAAACCTTATTTGAAACTTTGAATGGTG	1	46	1	ATTTGAAACT	    0.952916	-26
TCTGTTTCAAATTTGGATCTAAAGTGT   	2	8	0	ATTTGGATCT	    0.937501	-293
CTATTCCGCAAATTTAAGCTATAAATGGGT	2	103	1	AATTTAAGCT	    0.963483	-198
ATTGTTAATAAATTTGAGCTATAGCCTGTC	2	148	0	AATTTGAGCT	    0.979809	-153
TTTTAACGTTAAATTGAACTAAGCGTAATT	2	175	0	AAATTGAACT	    0.958685	-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