AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -igalR_hpyl_opreg_100.orf -g0.389 -x5 
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 =  	0.389
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HP0360	216	UDP-glucose 4-epimerase

Motif number 1

TTTTACAATCTTTGGGGAATTAGC       	1	4	0	TTTGGGGATT	    0.953185	-213
ATGGTGGGCTTAGGAGGAGTTGAACCTCCGA	1	35	1	TAGGAGGATT	    0.970294	-182
ACCTCACCCTTATCAGGGGTGCGCTCTAACC	1	65	1	TATCAGGGTG	    0.961595	-152
TTTATTGGCTTTTAAGGGCTTATAGCTCAGG	1	97	0	TTTAAGGGTT	    0.992843	-120
CCATTTATTATTTAAGGATTTTTTAAGAAAA	1	147	0	TTTAAGGATT	     0.98533	-70
CCTTAAATAATAAATGGGATTAAGATGTTAT	1	161	1	TAAATGGGTT	    0.959814	-56
TTTTTCATTTTAAAAGGGGTTTT        	1	204	1	TAAAAGGGTT	    0.989776	-13
          ******** **

Masking position 10
Map Score:   7.66275

Number of sites scoring better than the average of aligned sites = 1048
Number in coding regions = 912
Number in noncoding regions = 136
Number of orfs with sites within 600 bp upstream = 101
Fraction of orfs with sites within 600 bp upstream = 0.0162223


Motif number 2

CTAAGCCCACCATTTTTACAATCTTTGGGG	1	18	0	CATTTTTACA	    0.959909	-199
AAATTTAATCTATAATTTCATCTTTATTGG	1	120	0	TATAATTTCA	    0.959372	-97
ATTATTTAAGGATTTTTTAAGAAAATTTAA	1	142	0	GATTTTTTAA	    0.937894	-75
TAATCCCATTTATTATTTAAGGATTTTTTA	1	153	0	TATTATTTAA	    0.970691	-64
AAATAACAACTATTATAACATCTTAATCCC	1	176	0	TATTATAACA	    0.903568	-41
TAATAGTTGTTATTTTTTCATTTTAAAAGG	1	191	1	TATTTTTTCA	    0.990004	-26
          **********

Masking position 6
Map Score:   5.88413

Number of sites scoring better than the average of aligned sites = 472
Number in coding regions = 409
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 3

AAATGGTGGGCTTAGGAGGAGTTGAACCTCC	1	33	1	CTTAGAGGAG	    0.990823	-184
CGACCTCACCCTTATCAGGGGTGCGCTCTAA	1	63	1	CTTACAGGGG	    0.997593	-154
TCTTTATTGGCTTTTAAGGGCTTATAGCTCA	1	99	0	CTTTAAGGGC	    0.987055	-118
ATTTTTTCATTTTAAAAGGGGTTTT      	1	202	1	TTTAAAGGGG	    0.992366	-15
          **** ******

Masking position 7
Map Score:   2.72511

Number of sites scoring better than the average of aligned sites = 102
Number in coding regions = 92
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

AAATGGTGGGCTTAGGAGGAGTTGAACCTC	1	33	1	CTTAGGAGGA	    0.964742	-184
CGCACCCCTGATAAGGGTGAGGTCGGAGGT	1	58	0	ATAAGGGTGA	    0.991587	-159
TTAAAAGCCAATAAAGATGAAATTATAGAT	1	113	1	ATAAAGATGA	    0.980104	-104
TCCTTAAATAATAAATGGGATTAAGATGTT	1	160	1	ATAAATGGGA	     0.96739	-57
          **********

Masking position 4
Map Score:   1.07954

Number of sites scoring better than the average of aligned sites = 151
Number in coding regions = 132
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 5

          **********

No masking
Map Score:   2.15595e-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:   2.15595e-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:   2.15595e-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