AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00590_hpyl_reg_100.orf -o00590_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

TAAATAAGGCTTATTTGATCAAAACGCTAT	1	22	0	TTATTTGATC	    0.839026	-189
ATTTAACTTATTTTTTAAACTCTATCTATT	1	47	1	TTTTTTAAAC	     0.97534	-164
AACTCTATCTATTTTAAAACTCATTTTTGA	1	64	1	ATTTTAAAAC	    0.913733	-147
TTTAAAACTCATTTTTGAGCCTTTTTTATA	1	76	1	ATTTTTGAGC	    0.978861	-135
TTTTGAGCCTTTTTTATAGCTAGCGCTCAA	1	88	1	TTTTTATAGC	    0.979503	-123
GAGAGAGTGTTTTGTAAAGCTTGTGTTATA	1	148	1	TTTGTAAAGC	    0.959512	-63
AATTTCTTTGTTATTATAACACAAGCTTTA	1	162	0	TTATTATAAC	     0.89481	-49
ATAACAAAGAAATTTTAAGCGTAACTGATT	1	178	1	AATTTTAAGC	    0.909153	-33
          **********

Masking position 8
Map Score:   9.25051

Number of sites scoring better than the average of aligned sites = 2306
Number in coding regions = 1977
Number in noncoding regions = 329
Number of orfs with sites within 600 bp upstream = 208
Fraction of orfs with sites within 600 bp upstream = 0.0334083


Motif number 2

ATCAAATAAGCCTTATTTAACTTATTTTTTAAAC	1	33	1	CTTATTATTA	    0.983156	-178
ATTTTTTAAACTCTATCTATTTTAAAACTCATTT	1	56	1	CCTATTATTA	    0.989222	-155
TTATAGCTAGCGCTCAAACCATTAATAGCATCAT	1	101	1	CCTCAACTTA	    0.967747	-110
CCATTAATAGCATCATGTAAGTTATAAGCGAGAG	1	119	1	CTCATTATTA	     0.95524	-92
CTTTACAAAACACTCTCTCGCTTATAACTTACAT	1	133	0	CCTCTTCTTA	    0.995612	-78
  CTGTTTTCCTTTCAATCAGTTACGCTTAAAAT	1	189	0	CTTCATCTTA	    0.987236	-22
          * **** **  ***

Masking position 12
Map Score:   4.12888

Number of sites scoring better than the average of aligned sites = 90
Number in coding regions = 81
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 3

TCTACCCATAGCGTTTTGATCAAATAAGCC	1	15	1	GCGTTTTGAT	    0.829051	-196
GATCAAATAAGCCTTATTTAACTTATTTTT	1	32	1	GCCTTATTTA	    0.971507	-179
CTTATTTAACTTATTTTTTAAACTCTATCT	1	44	1	TTATTTTTTA	    0.843875	-167
ATTTTAAAACTCATTTTTGAGCCTTTTTTA	1	74	1	TCATTTTTGA	    0.878472	-137
TCATTTTTGAGCCTTTTTTATAGCTAGCGC	1	84	1	GCCTTTTTTA	    0.987407	-127
ACCATTAATAGCATCATGTAAGTTATAAGC	1	118	1	GCATCATGTA	    0.921514	-93
AAGCGAGAGAGTGTTTTGTAAAGCTTGTGT	1	144	1	GTGTTTTGTA	    0.962729	-67
          **********

Masking position 4
Map Score:   3.00922

Number of sites scoring better than the average of aligned sites = 2680
Number in coding regions = 2386
Number in noncoding regions = 294
Number of orfs with sites within 600 bp upstream = 190
Fraction of orfs with sites within 600 bp upstream = 0.0305172


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