AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -icoldbox_hpyl_opreg_100.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

TGCTAAAATAATTAGAATTTAGGGAATAAG	1	22	0	ATTAGAATTT	    0.956123	-167
TAAAGTTTTTATAAAAGGCTTATGCTAAAA	1	44	0	ATAAAAGGCT	    0.978386	-145
GCTCAATTAGGTTTAAAGTTTTTATAAAAG	1	57	0	GTTTAAAGTT	    0.920677	-132
TTTAAAGTTTATAAGATTTTTGAGTATAGC	1	97	0	ATAAGATTTT	    0.796132	-92
AAAATCTTTGATTTAAAGTTTATAAGATTT	1	108	0	ATTTAAAGTT	    0.964277	-81
AAAGGCTAAAATTAAAATCTTTGATTTAAA	1	121	0	ATTAAAATCT	    0.979222	-68
TAAAAAGCTAATAAAAGGCTAAAATTAAAA	1	134	0	ATAAAAGGCT	    0.978386	-55
TTGAAACTTTATAAAAAGCTAATAAAAGGC	1	145	0	ATAAAAAGCT	    0.989316	-44
CCTCAATTTAATTTGAAACTTTATAAAAAG	1	157	0	ATTTGAAACT	    0.913792	-32
TTAAATTGAGGTATGAATCTCCC       	1	176	1	GTATGAATCT	     0.93749	-13
          **********

Masking position 6
Map Score:   15.0762

Number of sites scoring better than the average of aligned sites = 777
Number in coding regions = 654
Number in noncoding regions = 123
Number of orfs with sites within 600 bp upstream = 93
Fraction of orfs with sites within 600 bp upstream = 0.0149374


Motif number 2

TAAATTCTAATTATTTTAGCATAAGCCTTT	1	31	1	TTATTTTAGC	     0.99203	-158
AACTTTAAACCTAATTGAGCGTATTTTTAT	1	67	1	CTAATTGAGC	    0.976874	-122
TCAAAGATTTTAATTTTAGCCTTTTATTAG	1	127	1	TAATTTTAGC	    0.988619	-62
AATTTTAGCCTTTTATTAGCTTTTTATAAA	1	138	1	TTTTATTAGC	    0.919985	-51
AGTTTCAAATTAAATTGAGGTATGAATCTC	1	167	1	TAAATTGAGG	    0.948943	-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	    0.873846	-140
ACTCAAAAATCTTATAAACTTTAAATCAAA	1	102	1	CTTATAAACT	    0.981315	-87
ATTTTAGCCTTTTATTAGCTTTTTATAAAG	1	139	1	TTTATTAGCT	    0.954347	-50
TTATTAGCTTTTTATAAAGTTTCAAATTAA	1	150	1	TTTATAAAGT	    0.979527	-39
          **********

Masking position 5
Map Score:   0.8502

Number of sites scoring better than the average of aligned sites = 104
Number in coding regions = 86
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


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