AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -ifadR_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	RP560	300	PROBABLE 3-HYDROXYACYL-COA DEHYDROGENASE B0272.3 (fadB)

Motif number 1

TTTTACTCATAATTATTATACTGTGTGTTAAATTTG	1	22	0	ATTATTATTT	    0.985613	-279
GAGTAAAAAAATTTATTAGTTTATTATGTCATTATA	1	50	1	ATTATTATTA	    0.992005	-251
TTGTAAGCACATTTATTATAGTAACAGTGGTTATAA	1	81	0	ATTATTATAA	    0.942724	-220
TAATCACAACACTTATAAGGGTCTTACCGACTATGC	1	124	0	ATTATAATTA	    0.957044	-177
GATTCTAGCCAATTATTGAAGTTTGAATATATTTGG	1	160	0	ATTATTGTTA	    0.991845	-141
GTACTCTTGTATTAATTATGTTCTGTATAGTGTATT	1	212	1	ATAATTATTT	    0.932767	-89
TGTATAGTGTATTTATTGCTCTTTCTGAAGTTGATC	1	235	1	ATTATTGTTT	    0.985783	-66
GTTGATCTTCATTTATTGTTATTAGATTAGTATTAG	1	264	1	ATTATTGTAA	     0.94697	-37
          * ******   * * *

Masking position 5
Map Score:   11.5666

Number of sites scoring better than the average of aligned sites = 232
Number in coding regions = 131
Number in noncoding regions = 101
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 2

        GATTGTAGTATCAAATTTAACAC	1	3	1	TTGTAGTTCA	     0.98878	-298
GTAACAGTGGTTATAATGACATAATAAACTA	1	66	0	TTATAATACA	    0.956793	-235
AGCACATTTATTATAGTAACAGTGGTTATAA	1	81	0	TTATAGTACA	    0.971094	-220
TGCAACTACTTTGTAAGCACATTTATTATAG	1	96	0	TTGTAAGACA	    0.982109	-205
TGAATATATTTGGTAATCACAACACTTATAA	1	142	0	TGGTAATACA	    0.962478	-159
TAGCCAATTATTGAAGTTTGAATATATTTGG	1	160	0	TTGAAGTTGA	    0.913452	-141
TACTTCAGATTTGTAGGGTGATTCTAGCCAA	1	184	0	TTGTAGGTGA	    0.970896	-117
TCTTCATTTATTGTTATTAGATTAGTATTAG	1	269	1	TTGTTATAGA	    0.914367	-32
          ******* ***

Masking position 11
Map Score:   9.14104

Number of sites scoring better than the average of aligned sites = 209
Number in coding regions = 133
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 3

TGTTAAATTTGATACTACAATC        	1	3	0	GATACTACAA	    0.966805	-298
AGTTTATTATGTCATTATAACCACTGTTAC	1	67	1	GTCATTATAA	    0.947542	-234
TATAACCACTGTTACTATAATAAATGTGCT	1	82	1	GTTACTATAA	    0.948352	-219
TATAATAAATGTGCTTACAAAGTAGTTGCA	1	97	1	GTGCTTACAA	    0.977932	-204
TATAAGTGTTGTGATTACCAAATATATTCA	1	143	1	GTGATTACCA	    0.951328	-158
TGGCTAGAATCACCCTACAAATCTGAAGTA	1	185	1	CACCCTACAA	    0.895437	-116
          **********

Masking position 6
Map Score:   1.99287

Number of sites scoring better than the average of aligned sites = 147
Number in coding regions = 98
Number in noncoding regions = 49
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


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