AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i340_weak11_hinf_reg_300.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	HI0701	108	conserved hypothetical protein
#2	HI1354	300	glutaminyl-tRNA synthetase (glnS)

Motif number 1

AGAACAAAAGTGCGGTTATTTTAGTGGATA	1	28	1	TGCGGTTATT	    0.893621	-81
CGAAATTCTATGCGACTTTTCGTGATTTAT	1	55	0	TGCGACTTTT	    0.924722	-54
   AGTTAAGGGCTCTTTTTTATCGAAAAT	1	92	0	GGCTCTTTTT	    0.957189	-17
TAGGAAATTTTGCTGTTTTTGCCTGCATTC	2	56	0	TGCTGTTTTT	    0.962688	-245
AATGGGAGCTGGCTGGGTTTGGTAAGCTAA	2	89	1	GGCTGGGTTT	    0.974172	-212
CACAAAGTGCGGTAAGTTTTTTGAATGTTT	2	117	0	GGTAAGTTTT	    0.768964	-184
AAATTATCGTGGCGATGTATAAATGCACAA	2	142	0	GGCGATGTAT	    0.887625	-159
ATAATTTCGTGGCGGTTTTTTATGGCAAGT	2	165	1	GGCGGTTTTT	    0.993887	-136
GGTTTTTTATGGCAAGTTTTTACAATCTTT	2	178	1	GGCAAGTTTT	    0.971388	-123
          **********

Masking position 10
Map Score:   9.46264

Number of sites scoring better than the average of aligned sites = 728
Number in coding regions = 589
Number in noncoding regions = 139
Number of orfs with sites within 600 bp upstream = 94
Fraction of orfs with sites within 600 bp upstream = 0.015098


Motif number 2

AACAAGAACAAAAGTGCGGTTATTTTAGTG	1	24	1	AAAGTGCGGT	    0.997394	-85
TTTCGATAAAAAAGAGCCCTTAACT     	1	94	1	AAAGAGCCCT	    0.981833	-15
ACATCACATTAAAAAGCGGTATCGCCGTGA	2	28	1	AAAAAGCGGT	    0.989895	-273
ATAAATGCACAAAGTGCGGTAAGTTTTTTG	2	124	0	AAAGTGCGGT	    0.997394	-177
          **********

Masking position 3
Map Score:   6.09819

Number of sites scoring better than the average of aligned sites = 1203
Number in coding regions = 761
Number in noncoding regions = 442
Number of orfs with sites within 600 bp upstream = 302
Fraction of orfs with sites within 600 bp upstream = 0.0485063


Motif number 3

AAAAAGCGGTATCGCCGTGAATGCAGGCAA	2	38	1	ATCGCCGTGA	    0.994142	-263
GCATTTATACATCGCCACGATAATTTCGTG	2	146	1	ATCGCCACGA	    0.998187	-155
GCCATAAAAAACCGCCACGAAATTATCGTG	2	161	0	ACCGCCACGA	    0.997844	-140
          **********

Masking position 1
Map Score:   3.57407

Number of sites scoring better than the average of aligned sites = 25
Number in coding regions = 22
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

TTTCGTGATTTATCCACTAAAATAACCGCA	1	38	0	TATCCACTAA	    0.915589	-71
 ATACGCCTCCCTCCACTACATCACATTAA	2	10	1	CCTCCACTAC	    0.972858	-291
AAAAGCGGTATCGCCGTGAATGCAGGCAAA	2	39	1	TCGCCGTGAA	    0.961247	-262
CATTTATACATCGCCACGATAATTTCGTGG	2	147	1	TCGCCACGAT	    0.991284	-154
CCATAAAAAACCGCCACGAAATTATCGTGG	2	160	0	CCGCCACGAA	    0.996787	-141
          **********

Masking position 9
Map Score:   2.07399

Number of sites scoring better than the average of aligned sites = 235
Number in coding regions = 210
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 5

TTTTTATCGAAAATAATTGTGCGAAATTCT	1	76	0	AAATAATTGT	    0.916096	-33
TACTAGATTTAAATAAAAGATTGTAAAAAC	2	193	0	AAATAAAAGA	    0.982653	-108
CTTGCCATAGAAATACTAGATTTAAATAAA	2	206	0	AAATACTAGA	    0.946837	-95
ATCTAAGGGAAAATAAAGGTTCATCTCCTG	2	238	0	AAATAAAGGT	    0.958652	-63
TCTCTCGTTAAAATAAAAAAATATTCGGCT	2	279	0	AAATAAAAAA	     0.91565	-22
          **********

Masking position 5
Map Score:   1.44281

Number of sites scoring better than the average of aligned sites = 287
Number in coding regions = 216
Number in noncoding regions = 71
Number of orfs with sites within 600 bp upstream = 64
Fraction of orfs with sites within 600 bp upstream = 0.0102795


Motif number 6

          **********

No masking
Map Score:   -1.75204e-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:   -1.75204e-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 8

          **********

No masking
Map Score:   -1.75204e-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