AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i348_weak9_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	HI0813	77	carbon storage regulator (csrA)
#2	HI0814	187	alanyl-tRNA synthetase (alaS)

Motif number 1

TATTTCAGATTATTCAAAAAACAATTTCTT	2	16	0	TATTCAAAAA	    0.944365	-172
TTTTTGAATAATCTGAAATAACTTAAATTT	2	26	1	ATCTGAAATA	     0.84109	-162
TTAACCGCACTTCTCAAATAGCGTCGTGAA	2	55	1	TTCTCAAATA	    0.970475	-133
TTTTTGCCAAAACTCCAAAATAAAACCGCA	2	86	0	AACTCCAAAA	    0.937214	-102
TTTTGGAGTTTTGGCAAAAAGCCTTTTTAT	2	96	1	TTGGCAAAAA	    0.953941	-92
CTTTTTATAAATTTCAAAAATATGCAAAAA	2	118	1	ATTTCAAAAA	    0.972596	-70
ATTTCAAAAATATGCAAAAATAGGGCGACT	2	128	1	TATGCAAAAA	    0.963132	-60
          **********

Masking position 7
Map Score:   5.66387

Number of sites scoring better than the average of aligned sites = 792
Number in coding regions = 606
Number in noncoding regions = 186
Number of orfs with sites within 600 bp upstream = 173
Fraction of orfs with sites within 600 bp upstream = 0.0277867


Motif number 2

CTATCAATCAAGGAACGGTTGGCATTCCAC	1	24	0	AGGAACGGTT	    0.990324	-54
GCTATTTGAGAAGTGCGGTTAAAATTTAAG	2	47	0	AAGTGCGGTT	    0.982115	-141
TAGCGTCGTGAAGTGCGGTTTTATTTTGGA	2	73	1	AAGTGCGGTT	    0.982115	-115
          **********

Masking position 1
Map Score:   4.16574

Number of sites scoring better than the average of aligned sites = 492
Number in coding regions = 312
Number in noncoding regions = 180
Number of orfs with sites within 600 bp upstream = 129
Fraction of orfs with sites within 600 bp upstream = 0.0207196


Motif number 3

AATCAAGGAACGGTTGGCATTCCACCAACCA	1	18	0	CGGTTGCATT	    0.983079	-60
TTATCTCCTTAGTTTGCATTTATTAGATATC	1	54	0	AGTTTGATTT	    0.973228	-24
TTGAGAAGTGCGGTTAAAATTTAAGTTATTT	2	41	0	CGGTTAAATT	     0.97902	-147
TCGTGAAGTGCGGTTTTATTTTGGAGTTTTG	2	78	1	CGGTTTATTT	    0.991698	-110
AGGGCGACTTAGTTTTTATTTTTATTATGGG	2	149	1	AGTTTTATTT	    0.959091	-39
          ****** ****

Masking position 5
Map Score:   2.6784

Number of sites scoring better than the average of aligned sites = 294
Number in coding regions = 222
Number in noncoding regions = 72
Number of orfs with sites within 600 bp upstream = 59
Fraction of orfs with sites within 600 bp upstream = 0.00947639


Motif number 4

ATGCCAACCGTTCCTTGATTGATAGGATAT	1	29	1	TTCCTTGATT	    0.891609	-49
CAAAAAACAATTTCTTGTTAA         	2	2	0	TTTCTTGTTA	    0.975311	-186
TTTGGCAAAAAGCCTTTTTATAAATTTCAA	2	105	1	AGCCTTTTTA	    0.935376	-83
CTTAGTTTTTATTTTTATTATGGGTAACAA	2	156	1	ATTTTTATTA	     0.73209	-32
  TAAAAAGAATCCTTGTTACCCATAATAA	2	170	0	ATCCTTGTTA	    0.992226	-18
          **********

Masking position 5
Map Score:   0.208433

Number of sites scoring better than the average of aligned sites = 236
Number in coding regions = 169
Number in noncoding regions = 67
Number of orfs with sites within 600 bp upstream = 58
Fraction of orfs with sites within 600 bp upstream = 0.00931577


Motif number 5

          **********

No masking
Map Score:   -2.59896e-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 6

          **********

No masking
Map Score:   -2.59896e-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 7

          **********

No masking
Map Score:   -2.59896e-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