AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -icspA_rpxx_opreg_300.orf -g0.290 -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 =  	0.29
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	RP206	300	DNA GYRASE SUBUNIT A  (gyrA)

Motif number 1

TTTTCAACATAATGGAATGCTTCTAACATTTA	1	11	0	AATGAATGCT	    0.988592	-290
TTATGTTGAAAATGAAATTTGTTAATTTTTAA	1	31	1	AATGAATTTT	    0.989601	-270
ATTTTTAAATTATGTAATTGCTAAAAACAGTT	1	55	1	TATGAATTGT	     0.95177	-246
AGCAAGCTAAAATTAAATTCCTGCTTTTGCAT	1	165	1	AATTAATTCT	    0.973356	-136
ATTATAAGTACAAGCAATTCTTGAAAGAAATT	1	229	1	CAAGAATTCT	    0.978166	-72
GCAATTCTTGAAAGAAATTTATTATGTCTCTA	1	242	1	AAAGAATTTT	    0.976411	-59
TCTATAATTAAATGTAATTCATTTAATTTAAG	1	270	1	AATGAATTCT	    0.996462	-31
          **** ***** *

Masking position 6
Map Score:   9.74179

Number of sites scoring better than the average of aligned sites = 106
Number in coding regions = 79
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 2

AATGAAATTTGTTAATTTTTAAATTATGTA	1	41	1	GTTAATTTTT	     0.78434	-260
TTAATTTTTAAATTATGTAATTGCTAAAAA	1	52	1	AATTATGTAA	     0.67823	-249
GCTAAAAACAGTTAATGTCATGATTATGTC	1	74	1	GTTAATGTCA	      0.9758	-227
TTAATGTCATGATTATGTCAATTGTGTAAA	1	85	1	GATTATGTCA	    0.975801	-216
TTGTATATTTGTTTATCTCATGCCAAGGAA	1	122	1	GTTTATCTCA	    0.933817	-179
AAAGCAGGAATTTAATTTTAGCTTGCTTAC	1	162	0	TTTAATTTTA	    0.810685	-139
TATAATCATGTATTATTTCTCAGAGGTCGG	1	205	0	TATTATTTCT	    0.893697	-96
GAAAGAAATTTATTATGTCTCTATAATTAA	1	251	1	TATTATGTCT	    0.930244	-50
ATGTAATTCATTTAATTTAAGGCTAGTATA	1	281	1	TTTAATTTAA	    0.809957	-20
          **********

Masking position 5
Map Score:   5.96126

Number of sites scoring better than the average of aligned sites = 533
Number in coding regions = 377
Number in noncoding regions = 156
Number of orfs with sites within 600 bp upstream = 93
Fraction of orfs with sites within 600 bp upstream = 0.0149374


Motif number 3

          **********

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 4

          **********

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 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