AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i318_mixed31_hpyl_reg_300.orf -o318_hpyl_300.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	RHP00617	40	AE000511
#2	RHP00618	65	AE000511

Motif number 1

      ATGGTGTATAATTAAAGAATTTCT	1	5	1	TGTATAATTA	    0.953715	-36
      TGCCTTTACCCTTTAAAGAAATTC	1	27	0	TTTACCCTTT	    0.959602	-14
         GTTTATCCTTAGTTTTTAAAA	2	2	1	TTTATCCTTA	    0.986924	-64
ATCCTTAGTTTTTAAAATAAGGTTATGTTA	2	15	1	TTTAAAATAA	      0.9589	-51
ATCAAATCATTGTAACATAACCTTATTTTA	2	27	0	TGTAACATAA	    0.983056	-39
AACATTCCTATTTATCAAATCATTGTAACA	2	40	0	TTTATCAAAT	    0.905572	-26
       TCCTTAAACATTCCTATTTATCA	2	53	0	TTAAACATTC	    0.913052	-13
          **********

Masking position 4
Map Score:   6.10719

Number of sites scoring better than the average of aligned sites = 961
Number in coding regions = 763
Number in noncoding regions = 198
Number of orfs with sites within 600 bp upstream = 175
Fraction of orfs with sites within 600 bp upstream = 0.0281079


Motif number 2

TTTAAAGAAATTCTTTAATTATACACCAT 	1	10	0	TTCTTTAATT	    0.989162	-31
ATTAAAGAATTTCTTTAAAGGGTAAAGGCA	1	21	1	TTCTTTAAAG	    0.989143	-20
TTATCCTTAGTTTTTAAAATAAGGTTATGT	2	13	1	TTTTTAAAAT	    0.747373	-53
          **********

Masking position 7
Map Score:   2.15726

Number of sites scoring better than the average of aligned sites = 288
Number in coding regions = 253
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 3

          **********

No masking
Map Score:   -4.73059e-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 4

          **********

No masking
Map Score:   -4.73059e-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:   -4.73059e-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