AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -icspA_rpxx_opreg_100.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

TAAATGTTAGAAGCATTCCATTATGTTGAAAA	1	11	1	AGCATTCATT	    0.987291	-290
TTAAAAATTAACAAATTTCATTTTCAACATAA	1	31	0	AAAATTCATT	    0.988413	-270
AACTGTTTTTAGCAATTACATAATTTAAAAAT	1	55	0	ACAATTCATA	    0.946494	-246
ATGCAAAAGCAGGAATTTAATTTTAGCTTGCT	1	165	0	AGAATTAATT	    0.970368	-136
AATTTCTTTCAAGAATTGCTTGTACTTATAAT	1	229	0	AGAATTCTTG	    0.975704	-72
TAGAGACATAATAAATTTCTTTCAAGAATTGC	1	242	0	AAAATTCTTT	    0.973757	-59
CTTAAATTAAATGAATTACATTTAATTATAGA	1	270	0	AGAATTCATT	    0.996055	-31
          * ***** ****

Masking position 5
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

TTTGTTAATTTTTAAATTATGTAATTGCTAA	1	48	1	TTTAATTATG	    0.973717	-253
CTAAAAACAGTTAATGTCATGATTATGTCAA	1	75	1	TTAATTCATG	    0.948279	-226
TGTATATTTGTTTATCTCATGCCAAGGAAAG	1	123	1	TTTATTCATG	    0.980422	-178
AAAGCAGGAATTTAATTTTAGCTTGCTTACC	1	161	0	TTTAATTTAG	    0.923159	-140
TTGCTTGTACTTATAATCATGTATTATTTCT	1	215	0	TTATATCATG	    0.859274	-86
ACATAATAAATTTCTTTCAAGAATTGCTTGT	1	238	0	TTTCTTCAAG	    0.939058	-63
ATGAATTACATTTAATTATAGAGACATAATA	1	261	0	TTTAATATAG	    0.847152	-40
ATGTAATTCATTTAATTTAAGGCTAGTATA 	1	281	1	TTTAATTAAG	    0.944211	-20
          ***** *****

Masking position 7
Map Score:   7.79303

Number of sites scoring better than the average of aligned sites = 383
Number in coding regions = 278
Number in noncoding regions = 105
Number of orfs with sites within 600 bp upstream = 65
Fraction of orfs with sites within 600 bp upstream = 0.0104401


Motif number 3

GAAGCATTCCATTATGTTGAAAATGAAATT	1	20	1	ATTATGTTGA	    0.965772	-281
TAATTTTTAAATTATGTAATTGCTAAAAAC	1	53	1	ATTATGTAAT	    0.895528	-248
TAATGTCATGATTATGTCAATTGTGTAAAG	1	86	1	ATTATGTCAA	    0.976205	-215
TTGTGTAAAGATTTTGTTGTATATTTGTTT	1	106	1	ATTTTGTTGT	    0.874392	-195
ATAATCATGTATTATTTCTCAGAGGTCGGT	1	204	0	ATTATTTCTC	     0.90771	-97
AAAGAAATTTATTATGTCTCTATAATTAAA	1	252	1	ATTATGTCTC	    0.984513	-49
          **********

Masking position 5
Map Score:   3.43668

Number of sites scoring better than the average of aligned sites = 153
Number in coding regions = 102
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


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


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