AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i321_mixed6_hpyl_reg_100.orf -o321_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	RHP00864	26	AE000511
#2	RHP00871	104	AE000511
#3	RHP00951	74	AE000511

Motif number 1

 GACTTTTCTTTTTTCATGGCTTGTCT         	1	2	0	TTTTTTGTGC	    0.949837	-25
        GGTTTTTGAAGGCTTGATTTTTAAAAGT	2	3	1	TTTTTAGTGT	    0.986166	-102
AAGGCTTGATTTTTAAAAGTTAGGCTTAATCTTTTA	2	19	1	TTTTAATAGT	    0.989505	-86
AATCTCAGAATTTTAACATAAAAGATTAAGCCTAAC	2	37	0	TTTTAAAAGT	    0.973806	-68
ATTTTATATATTTTATATTTATCGTTAGGTTTTAGG	2	70	1	TTTTATTTGT	    0.989505	-35
TATCGTTAGGTTTTAGGTTTAAAGTT          	2	89	1	TTTTATTAGT	    0.989505	-16
ATTCTCCTTATGTTAGAATGTTTGATTATTGTAACA	3	22	1	TGTTAAGTGT	    0.981028	-53
TATCCTATGGTTTTATTTAGTATGTTACAATAATCA	3	44	0	TTTTATGAGT	    0.994891	-31
          *****  * * * * *

Masking position 4
Map Score:   11.3236

Number of sites scoring better than the average of aligned sites = 603
Number in coding regions = 497
Number in noncoding regions = 106
Number of orfs with sites within 600 bp upstream = 94
Fraction of orfs with sites within 600 bp upstream = 0.015098


Motif number 2

          AGACAAGCCATGAAAAAAGAA	1	1	1	AGACAAGCAT	    0.977652	-26
AACTTTTAAAAATCAAGCCTTCAAAAACC  	2	9	0	AATCAAGCTT	    0.975529	-96
TAAAAGATTAAGCCTAACTTTTAAAAATCAA	2	24	0	AGCCTAACTT	    0.983299	-81
TTAAACCTAAAACCTAACGATAAATATAAAA	2	80	0	AACCTAACAT	    0.984462	-25
TAACATAAGGAGAATAACAATCAATT     	3	6	0	AGAATAACAT	     0.93159	-69
ATGTTACAATAATCAAACATTCTAACATAAG	3	28	0	AATCAAACTT	    0.983294	-47
TAACATACTAAATAAAACCATAGGATAAAAG	3	53	1	AATAAAACAT	    0.954635	-22
          ******** **

Masking position 6
Map Score:   9.02916

Number of sites scoring better than the average of aligned sites = 481
Number in coding regions = 397
Number in noncoding regions = 84
Number of orfs with sites within 600 bp upstream = 57
Fraction of orfs with sites within 600 bp upstream = 0.00915516


Motif number 3

AAGCCATGAAAAAAGAAAAGTC        	1	15	1	AAAAGAAAAG	    0.953687	-12
TCAGAATTTTAACATAAAAGATTAAGCCTA	2	39	0	AACATAAAAG	    0.985452	-66
CCTAACGATAAATATAAAATATATAAAATC	2	69	0	AATATAAAAT	    0.896775	-36
GTTAGGTTTTAGGTTTAAAGTT        	2	93	1	AGGTTTAAAG	    0.925561	-12
ATAAAACCATAGGATAAAAGC         	3	64	1	AGGATAAAAG	    0.992622	-11
          **********

Masking position 7
Map Score:   2.60367

Number of sites scoring better than the average of aligned sites = 353
Number in coding regions = 288
Number in noncoding regions = 65
Number of orfs with sites within 600 bp upstream = 52
Fraction of orfs with sites within 600 bp upstream = 0.00835207


Motif number 4

          **********

No masking
Map Score:   -1.60993e-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:   -1.60993e-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:   -1.60993e-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