AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00430_hpyl_reg_100.orf -o00430_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	HP1118	210	gamma-glutamyltranspeptidase (ggt)

Motif number 1

ATAGCGTTTTGATCAAATAAGCCTTATTTA	1	22	1	GATCAAATAA	    0.819035	-189
AATAGATAGAGTTTAAAAAATAAGTTAAAT	1	47	0	GTTTAAAAAA	    0.970485	-164
TCAAAAATGAGTTTTAAAATAGATAGAGTT	1	64	0	GTTTTAAAAT	    0.924288	-147
TATAAAAAAGGCTCAAAAATGAGTTTTAAA	1	76	0	GCTCAAAAAT	     0.98691	-135
TTGAGCGCTAGCTATAAAAAAGGCTCAAAA	1	88	0	GCTATAAAAA	    0.970961	-123
TATAGCTAGCGCTCAAACCATTAATAGCAT	1	102	1	GCTCAAACCA	    0.934792	-109
ACACTCTCTCGCTTATAACTTACATGATGC	1	128	0	GCTTATAACT	    0.841059	-83
TATAACACAAGCTTTACAAAACACTCTCTC	1	148	0	GCTTTACAAA	    0.941284	-63
TAAAGCTTGTGTTATAATAACAAAGAAATT	1	162	1	GTTATAATAA	    0.776107	-49
AATCAGTTACGCTTAAAATTTCTTTGTTAT	1	178	0	GCTTAAAATT	    0.932332	-33
          **********

Masking position 3
Map Score:   9.36954

Number of sites scoring better than the average of aligned sites = 3587
Number in coding regions = 3159
Number in noncoding regions = 428
Number of orfs with sites within 600 bp upstream = 262
Fraction of orfs with sites within 600 bp upstream = 0.0420816


Motif number 2

GATCAAATAAGCCTTATTTAACTTATTTTT	1	32	1	GCCTTATTTA	    0.962498	-179
CTTATTTAACTTATTTTTTAAACTCTATCT	1	44	1	TTATTTTTTA	    0.881739	-167
TTTAAACTCTATCTATTTTAAAACTCATTT	1	60	1	ATCTATTTTA	     0.94422	-151
TCATTTTTGAGCCTTTTTTATAGCTAGCGC	1	84	1	GCCTTTTTTA	    0.983332	-127
TAATAGCATCATGTAAGTTATAAGCGAGAG	1	123	1	ATGTAAGTTA	    0.721451	-88
AAGCGAGAGAGTGTTTTGTAAAGCTTGTGT	1	144	1	GTGTTTTGTA	    0.933776	-67
CGCTTAAAATTTCTTTGTTATTATAACACA	1	169	0	TTCTTTGTTA	    0.963211	-42
          **********

Masking position 10
Map Score:   3.64387

Number of sites scoring better than the average of aligned sites = 1346
Number in coding regions = 1136
Number in noncoding regions = 210
Number of orfs with sites within 600 bp upstream = 151
Fraction of orfs with sites within 600 bp upstream = 0.0242531


Motif number 3

CTTATTTGATCAAAACGCTATGGGTAGAAA	1	13	0	CAAAACGCTA	    0.991851	-198
AGAGTTTAAAAAATAAGTTAAATAAGGCTT	1	40	0	AAATAAGTTA	    0.861514	-171
GCTAGCTATAAAAAAGGCTCAAAAATGAGT	1	82	0	AAAAAGGCTC	    0.927113	-129
AGCTAGCGCTCAAACCATTAATAGCATCAT	1	105	1	CAAACCATTA	    0.955761	-106
ACAAGCTTTACAAAACACTCTCTCGCTTAT	1	142	0	CAAAACACTC	    0.971508	-69
GTTTTCCTTTCAATCAGTTACGCTTAAAAT	1	189	0	CAATCAGTTA	    0.938367	-22
          **********

Masking position 3
Map Score:   2.45664

Number of sites scoring better than the average of aligned sites = 1326
Number in coding regions = 1193
Number in noncoding regions = 133
Number of orfs with sites within 600 bp upstream = 92
Fraction of orfs with sites within 600 bp upstream = 0.0147767


Motif number 4

          **********

No masking
Map Score:   3.71914e-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 5

          **********

No masking
Map Score:   3.71914e-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:   3.71914e-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