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

Motif number 1

         GCTAATCGCCCGCTTGGTCAA	1	2	1	CTAATCGCCC	    0.996629	-299
GTTCGAGACCGGTATCGCCCACCACTTCTC	1	59	0	GGTATCGCCC	    0.987134	-242
TGTAAGGGAGGTGCTCTCCCAACTGAGCTA	1	104	1	GTGCTCTCCC	    0.973867	-197
CCCAACTGAGCTAATCGCCCTTAATGTTGT	1	121	1	CTAATCGCCC	    0.996629	-180
GACTGAAAATGCATTCTCCCTATAATGCCA	1	155	0	GCATTCTCCC	     0.97796	-146
          **********

Masking position 5
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

AGTTTTCTTAATTTTACTAAGTTTGACCAA	1	24	0	ATTTTACTAA	    0.956029	-277
AGTCAATACCTTTTTATTAAATTTTGTTTA	1	181	1	TTTTTATTAA	    0.962201	-120
TTTTTATTAAATTTTGTTTAATTGTCGTAA	1	191	1	ATTTTGTTTA	    0.968909	-110
AAAAGCGGATTTTATGCTTATTTTTACGAC	1	214	0	TTTATGCTTA	    0.864377	-87
AAAATCCGCTTTTTTATTTAGAAGTCAAAC	1	231	1	TTTTTATTTA	    0.974033	-70
AACGACTAATATTTTATTGAAGATAGGTTA	1	276	1	ATTTTATTGA	    0.956613	-25
          **********

Masking position 5
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

ACCGGTATCGCCCACCACTTCTCTAAAAAG	1	52	0	CCCACCACTT	    0.994358	-249
GAACCAGTGACCCCCTCCTTGTAAGGGAGG	1	85	1	CCCCCTCCTT	    0.993678	-216
GTTGGGAGAGCACCTCCCTTACAAGGAGGG	1	97	0	CACCTCCCTT	    0.953867	-204
GGGAGGTGCTCTCCCAACTGAGCTAATCGC	1	109	1	CTCCCAACTG	    0.966787	-192
ATAATGCCAACCCACAACATTAAGGGCGAT	1	134	0	CCCACAACAT	    0.971937	-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	    0.975641	-260
GATACCGGTCTCGAACCAGTGACCCCCTCC	1	73	1	TCGAACCAGT	    0.981588	-228
TGTTTAATTGTCGTAAAAATAAGCATAAAA	1	205	1	TCGTAAAAAT	    0.936664	-96
TATTTAGAAGTCAAACAAGTCGTAGTAGAA	1	245	1	TCAAACAAGT	    0.987098	-56
TAACCTATCTTCAATAAAATATTAGTCGTT	1	276	0	TCAATAAAAT	    0.905311	-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