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

Motif number 1

TTAGGTGTTGTTATTGCTTCTTCTCTAAGT	1	22	0	TTATTGCTTC	    0.988495	-279
GGTTTAGTAATTAATACTTACCTTGATATA	1	71	0	TTAATACTTA	    0.947925	-230
AACTATAAAATTTTTGCTAATGTACGTTAG	1	116	0	TTTTTGCTAA	    0.985231	-185
TATCTAATCTTTATTGCTAAGAATCTAAAA	1	174	1	TTATTGCTAA	    0.988436	-127
CAAGTCTAATTTTTTGCTTAATTTAGCAAA	1	231	0	TTTTTGCTTA	    0.992119	-70
TTTTATAAAATTATTACTTACTGTATTCAA	1	258	0	TTATTACTTA	    0.983897	-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

TGTACGTTAGATTATTCTATATATAGGTTTA	1	95	0	ATTATTTATA	    0.834337	-206
TACATTAGCAAAAATTTTATAGTTTTAATCT	1	122	1	AAAATTTATA	    0.982342	-179
CTTAGCAATAAAGATTAGATATACTTATTTA	1	164	0	AAGATTGATA	    0.973533	-137
CTTTATTGCTAAGAATCTAAAAAGCTTCTTT	1	182	1	AAGAATTAAA	    0.772201	-119
AATTAAGCAAAAAATTAGACTTGAATACAGT	1	238	1	AAAATTGACT	    0.868294	-63
ACAGTAAGTAATAATTTTATAAAAAATAGAT	1	264	1	ATAATTTATA	    0.953303	-37
TAATTTTATAAAAAATAGATAAAAATTGTAC	1	275	1	AAAAATGATA	     0.95241	-26
AAAATAGATAAAAATTGTACAATTT      	1	286	1	AAAATTTACA	    0.974048	-15
          ****** ****

Masking position 4
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

TTATTGCTTCTTCTCTAAGTACATTTAGAG	1	12	0	TTCTCTAAGT	    0.891338	-289
AAACAATTTCTTTGATATATCAAGGTAAGT	1	56	1	TTTGATATAT	     0.95776	-245
CGTTAGATTATTCTATATATAGGTTTAGTA	1	92	0	TTCTATATAT	    0.936059	-209
ATCTTAATCTTATGATAAATAAGTATATCT	1	149	1	TATGATAAAT	    0.899196	-152
AAAGCTGTAATATTCTCTGTTAAAGAAGCT	1	204	0	TATTCTCTGT	    0.750222	-97
ATATTACAGCTTTGCTAAATTAAGCAAAAA	1	221	1	TTTGCTAAAT	    0.958137	-80
TAAGTAATAATTTTATAAAAAATAGATAAA	1	268	1	TTTTATAAAA	    0.484491	-33
ATTGTACAATTTTTATCTATTTTTTATAAA	1	279	0	TTTTATCTAT	    0.928899	-22
          **********

Masking position 6
Map Score:   4.54606

Number of sites scoring better than the average of aligned sites = 763
Number in coding regions = 539
Number in noncoding regions = 224
Number of orfs with sites within 600 bp upstream = 131
Fraction of orfs with sites within 600 bp upstream = 0.0210408


Motif number 4

AGAAGAAGCAATAACAACACCTAACTTGAAACA	1	28	1	ATAAACACTA	    0.948087	-273
GTAAGTATTAATTACTAAACCTATATATAGAAT	1	80	1	ATATAAACTA	    0.978819	-221
TCATAAGATTAAGATTAAAACTATAAAATTTTT	1	131	0	AAATAAACTA	    0.957771	-170
CTTATGATAAATAAGTATATCTAATCTTTATTG	1	157	1	ATATATACTA	    0.978819	-144
AGTATATCTAATCTTTATTGCTAAGAATCTAAA	1	170	1	ATTTATTCTA	    0.860983	-131
ATTGCTAAGAATCTAAAAAGCTTCTTTAACAGA	1	186	1	ATTAAAACTT	    0.794259	-115
TTTAACAGAGAATATTACAGCTTTGCTAAATTA	1	210	1	AAATACACTT	    0.950907	-91
TATTTTTTATAAAATTATTACTTACTGTATTCA	1	259	0	AAATATTCTT	    0.866165	-42
          ** * **** ***

Masking position 7
Map Score:   4.83089

Number of sites scoring better than the average of aligned sites = 675
Number in coding regions = 448
Number in noncoding regions = 227
Number of orfs with sites within 600 bp upstream = 103
Fraction of orfs with sites within 600 bp upstream = 0.0165435


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