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

GTGTTAAATTTGATACTACAATC        	1	3	0	TGAACTACAA	    0.988812	-298
TAGTTTATTATGTCATTATAACCACTGTTAC	1	66	1	TGTATTATAA	    0.956936	-235
TTATAACCACTGTTACTATAATAAATGTGCT	1	81	1	TGTACTATAA	    0.971183	-220
CTATAATAAATGTGCTTACAAAGTAGTTGCA	1	96	1	TGTCTTACAA	     0.98217	-205
TTATAAGTGTTGTGATTACCAAATATATTCA	1	142	1	TGTATTACCA	    0.962603	-159
CCAAATATATTCAAACTTCAATAATTGGCTA	1	160	1	TCAACTTCAA	    0.913726	-141
TTGGCTAGAATCACCCTACAAATCTGAAGTA	1	184	1	TCACCTACAA	    0.970994	-117
CTAATACTAATCTAATAACAATAAATGAAGA	1	269	0	TCTATAACAA	    0.914638	-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

       GATTGTAGTATCAAATTTAACAC	1	4	1	TGTAGTATCA	    0.944141	-297
TAACAGTGGTTATAATGACATAATAAACTA	1	66	0	TATAATGACA	     0.94531	-235
GCACATTTATTATAGTAACAGTGGTTATAA	1	81	0	TATAGTAACA	    0.968101	-220
GCAACTACTTTGTAAGCACATTTATTATAG	1	96	0	TGTAAGCACA	    0.945192	-205
GAATATATTTGGTAATCACAACACTTATAA	1	142	0	GGTAATCACA	    0.953015	-159
CTAATACTAATCTAATAACAATAAATGAAG	1	270	0	TCTAATAACA	    0.957918	-31
          **********

Masking position 4
Map Score:   4.56517

Number of sites scoring better than the average of aligned sites = 113
Number in coding regions = 66
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


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