AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i007_Pyrimidine_Nucleotides_Biosynthesis_hpyl_reg_300.orf -o007_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 =  	0.39
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RHP00752	28	AE000511
#2	RHP00753	56	AE000511
#3	RHP00757	83	AE000511
#4	RHP00760	300	AE000511

Motif number 1

AAACTTTTCAGGGGGCGTTTGAACTTCTTAC	2	17	1	GGGGGCGTTG	    0.993517	-40
TCTTTTTTAAGGGAGTGTTTTTTTATAACCG	3	26	1	GGGAGTGTTT	    0.995673	-58
          GGGGGTATTGTAGCGCTAATT	3	73	0	GGGGGTATTT	    0.997953	-11
ATGTTTTTTAAGGAGCGTTATAATGAAAACG	4	54	0	AGGAGCGTTT	    0.961809	-247
AAAAAACATAGGAAGTATTATAACAAAGCCC	4	76	1	GGAAGTATTT	     0.95511	-225
CGCTTAATGAGCGGGCTTTGTTATAATACTT	4	88	0	GCGGGCTTTT	    0.960055	-213
TTTTTTGCATGGGGGTATTGTAGCGCTTAAT	4	111	0	GGGGGTATTT	    0.997953	-190
ACAATGAAATGGGGGTATTTTAAAAAAATGA	4	228	0	GGGGGTATTT	    0.997953	-73
          ********* *

Masking position 8
Map Score:   18.0406

Number of sites scoring better than the average of aligned sites = 343
Number in coding regions = 305
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 2

  AAAAGTCATTTTATTAGGGATCAAATCA	1	9	1	TTTTATTAGG	    0.936939	-20
AGACAAAACTTTTCAGGGGGCGTTTGAACT	2	12	1	TTTCAGGGGG	    0.959464	-45
GCGGTGTCTTTTTTAAGGGAGTGTTTTTTT	3	20	1	TTTTAAGGGA	    0.946394	-64
TTATAACCGCTTTTAGTATAAAGGCAATTA	3	48	1	TTTTAGTATA	    0.560877	-36
CGAAGCGCAATTTTATGAAGTTTTAGAAAA	4	22	0	TTTTATGAAG	    0.875987	-279
CTTCGTTCGTTTTCATTATAACGCTCCTTA	4	47	1	TTTCATTATA	    0.803392	-254
TTCCTATGTTTTTTAAGGAGCGTTATAATG	4	60	0	TTTTAAGGAG	    0.918564	-241
AAATCTTTTTTTGCATGGGGGTATTGTAGC	4	118	0	TTGCATGGGG	    0.881667	-183
AAAAAGATTTTTTTATTAGAAGACGATTAC	4	138	1	TTTTATTAGA	    0.913131	-163
GACGATTACCTTTTAAGCGAGAGCGTTAAG	4	159	1	TTTTAAGCGA	    0.843191	-142
CAATCTAAATTTTCAATGAGTCAAACTCCT	4	187	0	TTTCAATGAG	    0.918564	-114
AATACCCCCATTTCATTGTAAAATTCTTTC	4	240	1	TTTCATTGTA	    0.886216	-61
TGTAAAATTCTTTCATGCAAAACCCATTGA	4	256	1	TTTCATGCAA	    0.558534	-45
TTTTATTAAACTTCAATGGGTTTTGCATGA	4	268	0	CTTCAATGGG	    0.771776	-33
TATTTTTACCTTTTATTAAACTTCAATGGG	4	278	0	TTTTATTAAA	    0.821149	-23
          **********

Masking position 5
Map Score:   16.4461

Number of sites scoring better than the average of aligned sites = 2080
Number in coding regions = 1832
Number in noncoding regions = 248
Number of orfs with sites within 600 bp upstream = 166
Fraction of orfs with sites within 600 bp upstream = 0.0266624


Motif number 3

TCCCTAATAAAATGACTTTT          	1	1	0	AATGACTTTT	    0.898302	-28
TGTAGCGCTAATTGCCTTTATACTAAAAGC	3	56	0	ATTGCCTTTA	    0.970019	-28
GAAGTTTTAGAAAACCTTTTCATAG     	4	6	0	AAAACCTTTT	    0.935413	-295
TTCTAATAAAAAAATCTTTTTTTGCATGGG	4	129	0	AAAATCTTTT	    0.746467	-172
TTAGAAGACGATTACCTTTTAAGCGAGAGC	4	153	1	ATTACCTTTT	    0.983982	-148
GAAAATTTAGATTGCCTTGACTGACTCATT	4	203	1	ATTGCCTTGA	    0.908721	-98
   TCTTATTTTTACCTTTTATTAAACTTC	4	284	0	TTTACCTTTT	    0.927446	-17
          **********

Masking position 7
Map Score:   4.99893

Number of sites scoring better than the average of aligned sites = 894
Number in coding regions = 788
Number in noncoding regions = 106
Number of orfs with sites within 600 bp upstream = 87
Fraction of orfs with sites within 600 bp upstream = 0.0139737


Motif number 4

TTAAAAAAGACACCGCTTTATTTTA     	3	6	0	CACCGCTTTA	    0.948412	-78
GTTTTTTTATAACCGCTTTTAGTATAAAGG	3	42	1	AACCGCTTTT	    0.943502	-42
TAAAGGCAATTAGCGCTACAATACCCCC  	3	66	1	TAGCGCTACA	    0.973478	-18
AAAACGAACGAAGCGCAATTTTATGAAGTT	4	30	0	AAGCGCAATT	    0.936376	-271
GTTTTTTAAGGAGCGTTATAATGAAAACGA	4	53	0	GAGCGTTATA	    0.910364	-248
CCCGCTCATTAAGCGCTACAATACCCCCAT	4	104	1	AAGCGCTACA	    0.989331	-197
          **********

Masking position 2
Map Score:   2.25955

Number of sites scoring better than the average of aligned sites = 681
Number in coding regions = 624
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 5

          **********

No masking
Map Score:   8.764e-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:   8.764e-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:   8.764e-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