AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -icoldbox_hpyl_opreg_300.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	HP0247	188	ATP-dependent RNA helicase, DEAD-box family (deaD)

Motif number 1

TCTTATTCCCTAAATTCTAATTATTTTAGC	1	21	1	TAAATTCTAA	     0.94035	-168
AAGTTTTTATAAAAGGCTTATGCTAAAATA	1	42	0	AAAAGGCTTA	    0.981936	-147
GCCTTTTATAAAAACTTTAAACCTAATTGA	1	55	1	AAAACTTTAA	    0.933809	-134
ATAGCATAAAAATACGCTCAATTAGGTTTA	1	72	0	AATACGCTCA	    0.904321	-117
TGCTATACTCAAAAATCTTATAAACTTTAA	1	96	1	AAAAATCTTA	    0.946013	-93
AAAAATCTTATAAACTTTAAATCAAAGATT	1	106	1	TAAACTTTAA	    0.799134	-83
AGGCTAAAATTAAAATCTTTGATTTAAAGT	1	119	0	TAAAATCTTT	    0.637117	-70
AAAAGCTAATAAAAGGCTAAAATTAAAATC	1	132	0	AAAAGGCTAA	    0.990018	-57
GAAACTTTATAAAAAGCTAATAAAAGGCTA	1	143	0	AAAAAGCTAA	    0.983116	-46
TAGCTTTTTATAAAGTTTCAAATTAAATTG	1	154	1	TAAAGTTTCA	    0.913412	-35
          **********

Masking position 4
Map Score:   15.0915

Number of sites scoring better than the average of aligned sites = 1717
Number in coding regions = 1477
Number in noncoding regions = 240
Number of orfs with sites within 600 bp upstream = 179
Fraction of orfs with sites within 600 bp upstream = 0.0287504


Motif number 2

TAAATTCTAATTATTTTAGCATAAGCCTTT	1	31	1	TTATTTTAGC	    0.990933	-158
AACTTTAAACCTAATTGAGCGTATTTTTAT	1	67	1	CTAATTGAGC	    0.973746	-122
TCAAAGATTTTAATTTTAGCCTTTTATTAG	1	127	1	TAATTTTAGC	    0.987058	-62
AATTTTAGCCTTTTATTAGCTTTTTATAAA	1	138	1	TTTTATTAGC	    0.909871	-51
AGTTTCAAATTAAATTGAGGTATGAATCTC	1	167	1	TAAATTGAGG	    0.942259	-22
          **********

Masking position 6
Map Score:   3.78537

Number of sites scoring better than the average of aligned sites = 560
Number in coding regions = 504
Number in noncoding regions = 56
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 3

GCATAAGCCTTTTATAAAAACTTTAAACCT	1	49	1	TTTATAAAAA	     0.67388	-140
TTATAAAAACTTTAAACCTAATTGAGCGTA	1	60	1	TTTAAACCTA	    0.967194	-129
TCTTATAAACTTTAAATCAAAGATTTTAAT	1	111	1	TTTAAATCAA	    0.862053	-78
AATCAAAGATTTTAATTTTAGCCTTTTATT	1	125	1	TTTAATTTTA	    0.711525	-64
AATTTGAAACTTTATAAAAAGCTAATAAAA	1	148	0	TTTATAAAAA	     0.67388	-41
TTTATAAAGTTTCAAATTAAATTGAGGTAT	1	160	1	TTCAAATTAA	    0.897133	-29
    GGGAGATTCATACCTCAATTTAATTT	1	173	0	TTCATACCTC	    0.825365	-16
          **********

Masking position 4
Map Score:   2.0443

Number of sites scoring better than the average of aligned sites = 1274
Number in coding regions = 975
Number in noncoding regions = 299
Number of orfs with sites within 600 bp upstream = 206
Fraction of orfs with sites within 600 bp upstream = 0.0330871


Motif number 4

          **********

No masking
Map Score:   6.63809e-14

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:   6.63809e-14

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:   6.63809e-14

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