AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i327_not_clear2_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	HI0016	167	GTP-binding membrane protein (lepA)

Motif number 1

CCGAATAACTTCGGGGTTTCTTTTTTCATT	1	21	0	TCGGGGTTTC	    0.991475	-147
CCGAAGTTATTCGGGGTTTTGTTTTATCTA	1	37	1	TCGGGGTTTT	    0.996141	-131
GGTCAAATTTTCAAACTTTTTAGATAAAAC	1	57	0	TCAAACTTTT	    0.921397	-111
GAAAATTTGACCGCACTTTTCCCTTTCATC	1	75	1	CCGCACTTTT	     0.99448	-93
CTAGCGATTTCCGCGCTTTTCAGGTACAAT	1	106	1	CCGCGCTTTT	    0.997541	-62
          **********

Masking position 7
Map Score:   6.97952

Number of sites scoring better than the average of aligned sites = 756
Number in coding regions = 469
Number in noncoding regions = 287
Number of orfs with sites within 600 bp upstream = 219
Fraction of orfs with sites within 600 bp upstream = 0.0351751


Motif number 2

TCTTTTTTCATTCAAACTGAAA          	1	1	0	TTAACTGAAA	    0.982991	-167
CGGGGTTTTGTTTTATCTAAAAAGTTTGAAAA	1	48	1	TTTACTAAAA	    0.533492	-120
AACTGGCGGATTGTACCTGAAAAGCGCGGAAA	1	113	0	TTTACTGAAA	    0.955439	-55
AAAAGATTGTTTTTCTCAAAAATCATTAAATT	1	146	0	TTTCCAAAAA	    0.921218	-22
          ** ** ******

Masking position 10
Map Score:   2.71481

Number of sites scoring better than the average of aligned sites = 75
Number in coding regions = 49
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 3

TTTCTTTTTTCATTCAAACTGAAA      	1	5	0	CATTCAAACT	    0.973066	-163
GGGAAAAGTGCGGTCAAATTTTCAAACTTT	1	68	0	CGGTCAAATT	    0.993641	-100
TACAATCCGCCAGTTAAATTTAATGATTTT	1	130	1	CAGTTAAATT	    0.972773	-38
          **********

Masking position 6
Map Score:   1.44963

Number of sites scoring better than the average of aligned sites = 59
Number in coding regions = 39
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 4

CAGTTTGAATGAAAAAAGAAACCCCGAAGT	1	14	1	GAAAAAAGAA	    0.988191	-154
AAACTTTTTAGATAAAACAAAACCCCGAAT	1	45	0	GATAAAACAA	    0.988679	-123
ATGATTTTTGAGAAAAACAATCTTTT    	1	152	1	AGAAAAACAA	    0.979362	-16
          **********

Masking position 5
Map Score:   0.619952

Number of sites scoring better than the average of aligned sites = 205
Number in coding regions = 166
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


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