AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i118_SecDF_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HI0240	69	protein-export membrane protein (secD)
#2	HI0241	107	conserved hypothetical protein

Motif number 1

AATGCGTGGCTCTGGAAAATAATTTAATGT	1	16	0	TCTGGAAAAT	    0.941752	-54
TTAGAAAAGAAAAGGAAAACT         	1	59	1	AAAGGAAAAC	    0.980953	-11
TATCCTACGTTATGGCGATTAATT      	2	5	0	TATGGCGATT	    0.911668	-103
AAAGGCGAACTAAGCCCAATATCCTACGTT	2	24	0	TAAGCCCAAT	    0.957434	-84
CTTCATTGGGAAAGGCGAACTAAGCCCAAT	2	34	0	AAAGGCGAAC	    0.980957	-74
TATGGTATTTTACGCAAAATTTTTAACTTA	2	69	1	TACGCAAAAT	    0.949074	-39
CTTAAATTAATAAGGAAAACACA       	2	95	1	TAAGGAAAAC	    0.991624	-13
          **********

Masking position 8
Map Score:   5.66101

Number of sites scoring better than the average of aligned sites = 798
Number in coding regions = 649
Number in noncoding regions = 149
Number of orfs with sites within 600 bp upstream = 131
Fraction of orfs with sites within 600 bp upstream = 0.0210408


Motif number 2

     GAATAACATTAAATTATTTTCCAGA	1	6	1	ACATTAAATT	    0.936863	-64
TGCGTAAAATACCATAAATTGCTTCATTGG	2	55	0	ACCATAAATT	    0.986155	-53
CAAAATTTTTAACTTAAATTAATAAGGAAA	2	83	1	AACTTAAATT	    0.718655	-25
          **********

Masking position 6
Map Score:   2.62838

Number of sites scoring better than the average of aligned sites = 28
Number in coding regions = 17
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 3

AATTATTTTCCAGAGCCACGCATTGTGGCT	1	22	1	CAGAGCCACG	    0.997102	-48
TTCTAACGCACAGAGCCACAATGCGTGGCT	1	35	0	CAGAGCCACA	    0.998742	-35
          **********

Masking position 4
Map Score:   2.56658

Number of sites scoring better than the average of aligned sites = 1
Number in coding regions = 0
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

GTGGCTCTGTGCGTTAGAAAAGAAAAGGAA	1	46	1	GCGTTAGAAA	    0.990619	-24
AATCGCCATAACGTAGGATATTGGGCTTAG	2	15	1	ACGTAGGATA	    0.975637	-93
TAAAAATTTTGCGTAAAATACCATAAATTG	2	64	0	GCGTAAAATA	     0.98556	-44
TTATTAATTTAAGTTAAAAATTTTGCGTAA	2	78	0	AAGTTAAAAA	     0.91734	-30
          **********

Masking position 4
Map Score:   1.25282

Number of sites scoring better than the average of aligned sites = 253
Number in coding regions = 216
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 5

          **********

No masking
Map Score:   -1.11255e-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:   -1.11255e-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 7

          **********

No masking
Map Score:   -1.11255e-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