AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -isoxS_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	RP665	300	FUMARATE HYDRATASE (fumC)

Motif number 1

TTAGGTGTTGTTATTGCTTCTTCTCTAAGT	1	22	0	TTATTGCTTC	    0.988096	-279
GGTTTAGTAATTAATACTTACCTTGATATA	1	71	0	TTAATACTTA	    0.946429	-230
AACTATAAAATTTTTGCTAATGTACGTTAG	1	116	0	TTTTTGCTAA	    0.984732	-185
TATCTAATCTTTATTGCTAAGAATCTAAAA	1	174	1	TTATTGCTAA	    0.988287	-127
CAAGTCTAATTTTTTGCTTAATTTAGCAAA	1	231	0	TTTTTGCTTA	    0.991845	-70
TTTTATAAAATTATTACTTACTGTATTCAA	1	258	0	TTATTACTTA	    0.983591	-43
          **********

Masking position 5
Map Score:   11.8079

Number of sites scoring better than the average of aligned sites = 179
Number in coding regions = 132
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 2

TAAACCTATATATAGAATAATCTAACGTACA	1	95	1	TATAAATAAT	    0.847466	-206
AGATTAAAACTATAAAATTTTTGCTAATGTA	1	122	0	TATAAATTTT	    0.983958	-179
TAAATAAGTATATCTAATCTTTATTGCTAAG	1	164	1	TATCAATCTT	    0.975949	-137
AAAGAAGCTTTTTAGATTCTTAGCAATAAAG	1	182	0	TTTAATTCTT	    0.789017	-119
ACTGTATTCAAGTCTAATTTTTTGCTTAATT	1	238	0	AGTCAATTTT	    0.879126	-63
ATCTATTTTTTATAAAATTATTACTTACTGT	1	264	0	TATAAATTAT	    0.957484	-37
GTACAATTTTTATCTATTTTTTATAAAATTA	1	275	0	TATCATTTTT	    0.956669	-26
      AAATTGTACAATTTTTATCTATTTT	1	286	0	TGTAAATTTT	    0.976419	-15
          **** ******

Masking position 6
Map Score:   6.86629

Number of sites scoring better than the average of aligned sites = 691
Number in coding regions = 436
Number in noncoding regions = 255
Number of orfs with sites within 600 bp upstream = 132
Fraction of orfs with sites within 600 bp upstream = 0.0212014


Motif number 3

GAAACAATTTCTTTGATATATCAAGGTAAGTATTA	1	55	1	CTTTAACAAG	    0.981551	-246
ATTAGATATACTTATTTATCATAAGATTAAGATTA	1	147	0	CTTTACTAAG	    0.624112	-154
AATATTACAGCTTTGCTAAATTAAGCAAAAAATTA	1	220	1	CTTTAATAAG	    0.865184	-81
AAAAATTAGACTTGAATACAGTAAGTAATAATTTT	1	247	1	CTTTAATAAG	    0.927301	-54
          ***   ** * ****

Masking position 8
Map Score:   3.02573

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 7
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

AGAAGAAGCAATAACAACACCTAACTTGAAAC	1	28	1	ATACAACACT	    0.939338	-273
GTAAGTATTAATTACTAAACCTATATATAGAA	1	80	1	ATACTAAACT	    0.975779	-221
TCATAAGATTAAGATTAAAACTATAAAATTTT	1	132	0	AAATTAAACT	    0.972816	-169
CTTATGATAAATAAGTATATCTAATCTTTATT	1	157	1	ATAGTATACT	    0.956436	-144
TTTAACAGAGAATATTACAGCTTTGCTAAATT	1	210	1	AAATTACACT	    0.982339	-91
TATTTTTTATAAAATTATTACTTACTGTATTC	1	260	0	AAATTATTCT	    0.900427	-41
          ** ****** **

Masking position 7
Map Score:   1.88535

Number of sites scoring better than the average of aligned sites = 298
Number in coding regions = 212
Number in noncoding regions = 86
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


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