AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i160_Porphyrin_Biosynthesis_hpyl_reg_100.orf -o160_hpyl_100.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	RHP00038	117	AE000511
#2	RHP00039	44	AE000511
#3	RHP00040	65	AE000511

Motif number 1

CGCTTTAAGCGTTGGCTTTTTGCTTTAATT	1	40	1	GTTGGCTTTT	    0.949835	-78
CTTTAATTTTTACTTCTTTTTTAATAAAAT	1	62	1	TACTTCTTTT	    0.962049	-56
TTTAATAAAATACTCTTTTTGATTCCTTTT	1	81	1	TACTCTTTTT	    0.970595	-37
TACTCTTTTTGATTCCTTTTTATTATAGGC	1	91	1	GATTCCTTTT	    0.990217	-27
    TTTTTAGATTTTTCTTAATCTTAAGC	2	7	1	GATTTTTCTT	    0.807689	-38
TTCTTAATCTTAAGCCTTTTAAAAGGCGTT	2	22	1	TAAGCCTTTT	    0.963001	-23
       TAAAACGCCTTTTAAAAGGCTTA	2	32	0	AACGCCTTTT	    0.962281	-13
        AATATTCATTTTAAAAAACAAC	3	3	1	TATTCATTTT	    0.924031	-63
ATACTCCATAGTTGTTTTTTAAAATGAATA	3	13	0	GTTGTTTTTT	    0.899269	-53
TTTGTCTAATTATGGTTTTTATACTCCATA	3	33	0	TATGGTTTTT	    0.964194	-33
          **********

Masking position 7
Map Score:   11.7076

Number of sites scoring better than the average of aligned sites = 1500
Number in coding regions = 1318
Number in noncoding regions = 182
Number of orfs with sites within 600 bp upstream = 148
Fraction of orfs with sites within 600 bp upstream = 0.0237713


Motif number 2

CCAACGCTTAAAGCGTTAGCCCCATACAAA	1	25	0	AAGCGTTAGC	    0.996764	-93
CTAACGCTTTAAGCGTTGGCTTTTTGCTTT	1	36	1	AAGCGTTGGC	    0.997905	-82
GATTTTTCTTAATCTTAAGCCTTTTAAAAG	2	17	1	AATCTTAAGC	    0.952003	-28
 AAATCCTTAAAGGTTTGTCTAATTATGGT	3	47	0	AAGGTTTGTC	    0.966576	-19
          **********

Masking position 6
Map Score:   3.07719

Number of sites scoring better than the average of aligned sites = 325
Number in coding regions = 300
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 3

ATACAAACACCTTTCTTAAAA         	1	2	0	CTTTCTTAAA	    0.980061	-116
GCGTTGGCTTTTTGCTTTAATTTTTACTTC	1	48	1	TTTGCTTTAA	    0.933493	-70
AAAAAGAGTATTTTATTAAAAAAGAAGTAA	1	71	0	TTTTATTAAA	    0.658442	-47
TTTGATTCCTTTTTATTATAGGCGGTTATT	1	98	1	TTTTATTATA	    0.902721	-20
 TTTTTAGATTTTTCTTAATCTTAAGCCTT	2	10	1	TTTTCTTAAT	    0.972035	-35
TCCATAGTTGTTTTTTAAAATGAATATT  	3	9	0	TTTTTTAAAA	    0.631027	-57
          **********

Masking position 6
Map Score:   5.84332

Number of sites scoring better than the average of aligned sites = 1106
Number in coding regions = 895
Number in noncoding regions = 211
Number of orfs with sites within 600 bp upstream = 168
Fraction of orfs with sites within 600 bp upstream = 0.0269836


Motif number 4

          **********

No masking
Map Score:   1.65857e-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:   1.65857e-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:   1.65857e-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