AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i340_weak11_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	HI0701	108	conserved hypothetical protein
#2	HI1354	300	glutaminyl-tRNA synthetase (glnS)

Motif number 1

AGAACAAAAGTGCGGTTATTTTAGTGGATA	1	28	1	TGCGGTTATT	    0.900588	-81
CGAAATTCTATGCGACTTTTCGTGATTTAT	1	55	0	TGCGACTTTT	    0.929812	-54
   AGTTAAGGGCTCTTTTTTATCGAAAAT	1	92	0	GGCTCTTTTT	    0.960178	-17
TAGGAAATTTTGCTGTTTTTGCCTGCATTC	2	56	0	TGCTGTTTTT	    0.965307	-245
AATGGGAGCTGGCTGGGTTTGGTAAGCTAA	2	89	1	GGCTGGGTTT	    0.976005	-212
CACAAAGTGCGGTAAGTTTTTTGAATGTTT	2	117	0	GGTAAGTTTT	    0.782104	-184
AAATTATCGTGGCGATGTATAAATGCACAA	2	142	0	GGCGATGTAT	    0.894938	-159
ATAATTTCGTGGCGGTTTTTTATGGCAAGT	2	165	1	GGCGGTTTTT	    0.994329	-136
GGTTTTTTATGGCAAGTTTTTACAATCTTT	2	178	1	GGCAAGTTTT	    0.973413	-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

CACTAAAATAACCGCACTTTTGTTCTTGTT	1	24	0	ACCGCACTTT	     0.99703	-85
     AGTTAAGGGCTCTTTTTTATCGAAA	1	94	0	AGGGCTCTTT	    0.979265	-15
TCACGGCGATACCGCTTTTTAATGTGATGT	2	28	0	ACCGCTTTTT	    0.988448	-273
CAAAAAACTTACCGCACTTTGTGCATTTAT	2	124	1	ACCGCACTTT	     0.99703	-177
          **********

Masking position 8
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	    0.993907	-263
GCATTTATACATCGCCACGATAATTTCGTG	2	146	1	ATCGCCACGA	    0.998115	-155
GCCATAAAAAACCGCCACGAAATTATCGTG	2	161	0	ACCGCCACGA	    0.997757	-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	    0.907708	-71
 ATACGCCTCCCTCCACTACATCACATTAA	2	10	1	CCTCCACTAC	    0.970149	-291
AAAAGCGGTATCGCCGTGAATGCAGGCAAA	2	39	1	TCGCCGTGAA	    0.957431	-262
CATTTATACATCGCCACGATAATTTCGTGG	2	147	1	TCGCCACGAT	    0.990396	-154
CCATAAAAAACCGCCACGAAATTATCGTGG	2	160	0	CCGCCACGAA	    0.996457	-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

AGAATTTCGCACAATTATTTTCGATAAAAA	1	76	1	ACAATTATTT	    0.908692	-33
GTTTTTACAATCTTTTATTTAAATCTAGTA	2	193	1	TCTTTTATTT	    0.981001	-108
TTTATTTAAATCTAGTATTTCTATGGCAAG	2	206	1	TCTAGTATTT	    0.941972	-95
CAGGAGATGAACCTTTATTTTCCCTTAGAT	2	238	1	ACCTTTATTT	    0.954819	-63
AGCCGAATATTTTTTTATTTTAACGAGAGA	2	279	1	TTTTTTATTT	    0.908209	-22
          **********

Masking position 6
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