AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00471_hpyl_reg_100.orf -o00471_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	HP0493	124	phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY)
#2	HP0549	37	glutamate racemase (glr)
#3	HP0550	263	transcription termination factor Rho (rho)
#4	HP0624	119	solute-binding signature and mitochondrial signature protein (aspB)

Motif number 1

GGATAGAAGCTTATTTTAATTTTTAGGAATCTT	1	13	0	TTTTTAATTT	    0.978771	-112
CTATTCATGCTATTTTTAAGTAAATCAATTTGC	1	50	1	TTTTTAATAA	    0.952215	-75
ACAATTTTCTTTTTTCTAAATTTCAAGCATGGC	1	86	1	TTTCTAATTT	    0.926053	-39
     GACACTATTTTTAATTTAATGGGATTAA	2	20	0	TTTTTAATTA	    0.918138	-18
AAGTATCCTTTATTTTTAAATTTAAACTTAAAA	3	12	1	TTTTTAATTT	    0.914812	-252
ACTTATGCTATAATTTTAAGTTTAAATTTAAAA	3	25	0	TTTTTAATTT	    0.983103	-239
AACTTTAGAGTGGTTTTAATTTATTATGACTTA	3	53	0	TTTTTAATTA	     0.98561	-211
AAAGTCAAATTTTATTTAACTTTAGAGTGGTTT	3	70	0	TATTTAATTT	    0.894466	-194
GCTATCATAATTTTTTTAACAAAGTCAAATTTT	3	90	0	TTTTTAAAAA	    0.928982	-174
GGTTACACTAATTTTTTAAGAATGCTTTAGCTT	3	181	1	ATTTTAAAAT	    0.665461	-83
TAGCTTTTTGTATTTTTATCTTAATTGCAACAA	3	208	1	TTTTTATTTA	    0.880378	-56
    TAAATTTCCTTTTAACAAAAAGAGATTTC	3	245	0	TTTTTAAAAA	    0.936971	-19
ATTAACTATTCCATTTTAAGATTAAAGTAGCCC	4	96	1	CTTTTAAATT	    0.864689	-24
          *  ****** ***

Masking position 8
Map Score:   22.7485

Number of sites scoring better than the average of aligned sites = 409
Number in coding regions = 273
Number in noncoding regions = 136
Number of orfs with sites within 600 bp upstream = 124
Fraction of orfs with sites within 600 bp upstream = 0.0199165


Motif number 2

AAATAGCATGAATAGGGTAGGATAGAAGCTTATT	1	31	0	AATATAGATA	    0.882672	-94
AAATTTAGAAAAAAGAAAATTGTAGCGCAAATTG	1	75	0	AAAAAATGTA	    0.961119	-50
GTTTAAATTTAAAAATAAAGGATACTTG      	3	5	0	AAAAAAGATA	    0.981562	-259
ATTTAAACTTAAAATTATAGCATAAGTCATAATA	3	31	1	AAAATAGATA	    0.981605	-233
GACTTTGTTAAAAAAATTATGATAGCATAGCAAA	3	97	1	AAAATATATA	    0.958011	-167
AAGCATTCTTAAAAAATTAGTGTAACCAAAAGAT	3	174	0	AAAATAGGTA	    0.983013	-90
AAAAATACAAAAAGCTAAAGCATTCTTAAAAAAT	3	191	0	AAAGAAGATT	    0.807623	-73
AAACCACCAAGAAAGAGTATAATAGCGCATAAGA	4	33	0	GAAATATATA	    0.826341	-87
AATCTTACCTAAAATTTAAGCGTTATGGTATGAA	4	65	0	AAAAAAGGTT	     0.96303	-55
CTTTAATCTTAAAATGGAATAGTTAATCTTACCT	4	89	0	AAAAAATGTT	    0.917988	-31
          ****   *** ***

Masking position 9
Map Score:   9.9016

Number of sites scoring better than the average of aligned sites = 372
Number in coding regions = 291
Number in noncoding regions = 81
Number of orfs with sites within 600 bp upstream = 68
Fraction of orfs with sites within 600 bp upstream = 0.0109219


Motif number 3

         AAAAGATTCCTAAAAATTAAAATAA	1	2	1	AAACCTAAAA	    0.982745	-123
CCTAAAAATTAAAATAAGCTTCTATCCTACCCTA	1	19	1	AAAGCTTCTA	    0.821897	-106
TAAGTAAATCAATTTGCGCTACAATTTTCTTTTT	1	66	1	AATGCTACAA	     0.93591	-59
          AAAATCCCCTAAAATCGCCATGCT	1	111	0	AAACCTAAAA	    0.982745	-14
TTTATTTTTAAATTTAAACTTAAAATTATAGCAT	3	20	1	AATACTTAAA	    0.797753	-244
TAATAAATTAAAACCACTCTAAAGTTAAATAAAA	3	60	1	AAATCTAAAG	    0.855196	-204
TAGTGTAACCAAAAGATGCTAATAAGTGGCCCAT	3	157	0	AAAGCTAATA	    0.947361	-107
ACAAAAAGCTAAAGCATTCTTAAAAAATTAGTGT	3	185	0	AAATCTTAAA	    0.929872	-79
TGGAATAGTTAATCTTACCTAAAATTTAAGCGTT	4	75	0	AATCCTAAAA	    0.967612	-45
          ***    *******

Masking position 10
Map Score:   5.2025

Number of sites scoring better than the average of aligned sites = 886
Number in coding regions = 712
Number in noncoding regions = 174
Number of orfs with sites within 600 bp upstream = 146
Fraction of orfs with sites within 600 bp upstream = 0.02345


Motif number 4

          **********

No masking
Map Score:   4.50646e-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 5

          **********

No masking
Map Score:   4.50646e-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:   4.50646e-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