AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i234_sensory_cassete_hpyl_reg_100.orf -o234_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	RHP01119	235	AE000511

Motif number 1

AAGGAATTGTTTAAAAACATTAAAAAATAA	1	21	1	TTAAAAACAT	    0.985045	-215
TTAAAAACATTAAAAAATAAGACTTTATTT	1	31	1	TAAAAAATAA	     0.93507	-205
CATGGAATATTGAAAAATAAAGTCTTATTT	1	45	0	TGAAAAATAA	    0.955293	-191
TCAATATTCCATGAAAACAAAGCCTTAAAT	1	62	1	ATGAAAACAA	    0.909172	-174
TAAATTTCCATTAATAACTATGATAATGTT	1	87	1	TTAATAACTA	    0.863241	-149
AAAATAAAAATTCAAAACATTATCATAGTT	1	102	0	TTCAAAACAT	     0.94609	-134
TGAAAATATCTTAAAAATAAAAATTCAAAA	1	115	0	TTAAAAATAA	    0.988507	-121
TAAAGATACCTTGAAAATATCTTAAAAATA	1	126	0	TTGAAAATAT	    0.952801	-110
CAAGGTATCTTTAATAATAAAATGCTAGAA	1	143	1	TTAATAATAA	    0.941038	-93
TTCTGCAACTTTAAAAACGATTAACTTTGT	1	192	0	TTAAAAACGA	    0.971494	-44
          **********

Masking position 6
Map Score:   16.5903

Number of sites scoring better than the average of aligned sites = 1244
Number in coding regions = 1003
Number in noncoding regions = 241
Number of orfs with sites within 600 bp upstream = 182
Fraction of orfs with sites within 600 bp upstream = 0.0292323


Motif number 2

   AAAACGATCAAAGGAATTGTTTAAAAA	1	8	1	TCAAAGGAAT	    0.919392	-228
AGTCTTATTTTTTAATGTTTTTAAACAATT	1	25	0	TTTAATGTTT	    0.863553	-211
AGGCTTTGTTTTCATGGAATATTGAAAAAT	1	57	0	TTCATGGAAT	    0.981687	-179
TTAATGGAAATTTAAGGCTTTGTTTTCATG	1	71	0	TTTAAGGCTT	    0.896903	-165
ATCATAGTTATTAATGGAAATTTAAGGCTT	1	81	0	TTAATGGAAA	    0.896055	-155
TTAAGATATTTTCAAGGTATCTTTAATAAT	1	131	1	TTCAAGGTAT	    0.977533	-105
ATTAACTTTGTTAATGTTTTAGGGGACTAA	1	173	0	TTAATGTTTT	    0.795013	-63
ATTAACAAAGTTAATCGTTTTTAAAGTTGC	1	188	1	TTAATCGTTT	    0.895114	-48
AATTAACTCCTTCAATGATTTCTGCAACTT	1	211	0	TTCAATGATT	    0.946147	-25
ATTGAAGGAGTTAATTGAAGT         	1	225	1	TTAATTGAAG	     0.80724	-11
          **********

Masking position 4
Map Score:   7.09923

Number of sites scoring better than the average of aligned sites = 1815
Number in coding regions = 1531
Number in noncoding regions = 284
Number of orfs with sites within 600 bp upstream = 228
Fraction of orfs with sites within 600 bp upstream = 0.0366206


Motif number 3

          **********

No masking
Map Score:   3.64809e-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 4

          **********

No masking
Map Score:   3.64809e-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:   3.64809e-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