AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i228_6_1_1_17_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	HI0274	300	glutamyl-tRNA synthetase (gltX)

Motif number 1

TTGACCAAGCGGGCGATTAGC         	1	2	0	GGGCGATTAG	    0.996664	-299
GAGAAGTGGTGGGCGATACCGGTCTCGAAC	1	59	1	GGGCGATACC	    0.987205	-242
TAGCTCAGTTGGGAGAGCACCTCCCTTACA	1	104	0	GGGAGAGCAC	    0.973904	-197
ACAACATTAAGGGCGATTAGCTCAGTTGGG	1	121	0	GGGCGATTAG	    0.996664	-180
TGGCATTATAGGGAGAATGCATTTTCAGTC	1	155	1	GGGAGAATGC	    0.978184	-146
          **********

Masking position 6
Map Score:   5.95413

Number of sites scoring better than the average of aligned sites = 94
Number in coding regions = 71
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 2

TTGGTCAAACTTAGTAAAATTAAGAAAACT	1	24	1	TTAGTAAAAT	    0.957514	-277
TAAACAAAATTTAATAAAAAGGTATTGACT	1	181	0	TTAATAAAAA	     0.96341	-120
TTACGACAATTAAACAAAATTTAATAAAAA	1	191	0	TAAACAAAAT	    0.969973	-110
GTCGTAAAAATAAGCATAAAATCCGCTTTT	1	214	1	TAAGCATAAA	    0.868534	-87
GTTTGACTTCTAAATAAAAAAGCGGATTTT	1	231	0	TAAATAAAAA	    0.974922	-70
TAACCTATCTTCAATAAAATATTAGTCGTT	1	276	0	TCAATAAAAT	    0.958079	-25
          **********

Masking position 6
Map Score:   5.18349

Number of sites scoring better than the average of aligned sites = 553
Number in coding regions = 359
Number in noncoding regions = 194
Number of orfs with sites within 600 bp upstream = 163
Fraction of orfs with sites within 600 bp upstream = 0.0261805


Motif number 3

CTTTTTAGAGAAGTGGTGGGCGATACCGGT	1	52	1	AAGTGGTGGG	    0.994829	-249
CCTCCCTTACAAGGAGGGGGTCACTGGTTC	1	85	0	AAGGAGGGGG	    0.994205	-216
CCCTCCTTGTAAGGGAGGTGCTCTCCCAAC	1	97	1	AAGGGAGGTG	     0.95757	-204
GCGATTAGCTCAGTTGGGAGAGCACCTCCC	1	109	0	CAGTTGGGAG	    0.969486	-192
ATCGCCCTTAATGTTGTGGGTTGGCATTAT	1	134	1	ATGTTGTGGG	    0.974228	-167
          **********

Masking position 3
Map Score:   2.42297

Number of sites scoring better than the average of aligned sites = 77
Number in coding regions = 49
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

CCACCACTTCTCTAAAAAGTTTTCTTAATT	1	41	0	TCTAAAAAGT	    0.971029	-260
GATACCGGTCTCGAACCAGTGACCCCCTCC	1	73	1	TCGAACCAGT	    0.978054	-228
TGTTTAATTGTCGTAAAAATAAGCATAAAA	1	205	1	TCGTAAAAAT	    0.925164	-96
TATTTAGAAGTCAAACAAGTCGTAGTAGAA	1	245	1	TCAAACAAGT	    0.984605	-56
TAACCTATCTTCAATAAAATATTAGTCGTT	1	276	0	TCAATAAAAT	    0.888794	-25
          **********

Masking position 8
Map Score:   1.82403

Number of sites scoring better than the average of aligned sites = 121
Number in coding regions = 96
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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