AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00471_rpxx_reg_100.orf -o00471_rpxx_100.ace -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -g0.29 -x5 -e 
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 = 	1

Input sequences:
#1	RP247	182	UDP-N-ACETYLMURAMATE--ALANINE LIGASE (murC)
#2	RP410	149	UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE (murD)

Motif number 1

AATTATAACAAGATCAATTTTGAAACTCTCAAGGAATCCATAAGAT	1	20	1	ATATTAAAGA	    0.996274	-163
TGCATCAATTATTATACTTTATAACATAGGTAATGATCTTTATGAC	1	119	1	AAATTAAAAA	    0.985791	-64
CTTTATGACGAATTCAATTTTAAATTATTAAACTTAA         	1	156	1	ATATTAAACA	    0.987001	-27
AGAATTAATTAGCAAATTTTTAAAGTGCATCAAATATA        	2	3	0	AAATTAAAAA	    0.985791	-147
AAAATTTGCTAATTAATTCTATAAGAACTGGAGGTATTAAGTCACA	2	29	1	ATATTAAAGA	    0.996274	-121
GATGACTTCAAAAAGAATATGAAATTAATACAGTGAAGATAAAAAA	2	76	0	AAATTAAAGA	    0.995153	-74
TAGTCATTGTAGTTTAGTATCTAAGACAAATAGATAGAGATGACTT	2	114	0	ATATTAAAGA	    0.996273	-36
          *  * * * *  **       **  *

Masking position 13
Map Score:   9.2897

Number of sites scoring better than the average of aligned sites = 67
Number in coding regions = 50
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 2

AAAATTGATCTTGTTATAATTATAACGTTT	1	11	0	TTGTTATAAT	    0.835301	-172
AGTATAATAATTGATGCACTACAAATACTA	1	107	0	TTGATGCACT	    0.976278	-76
AGTGCATCAATTATTATACTTTATAACATA	1	117	1	TTATTATACT	     0.95637	-66
CAATTTTAAATTATTAAACTTAA       	1	170	1	TTATTAAACT	    0.938642	-13
     TATATTTGATGCACTTTAAAAATTT	2	6	1	TTGATGCACT	    0.976278	-144
GAATATGAAATTAATACAGTGAAGATAAAA	2	78	0	TTAATACAGT	     0.94239	-72
TTTCATATTCTTTTTGAAGTCATCTCTATC	2	98	1	TTTTTGAAGT	     0.84882	-52
       TAGTCATTGTAGTTTAGTATCTA	2	137	0	TCATTGTAGT	    0.875481	-13
          **********

Masking position 8
Map Score:   5.13624

Number of sites scoring better than the average of aligned sites = 390
Number in coding regions = 247
Number in noncoding regions = 143
Number of orfs with sites within 600 bp upstream = 76
Fraction of orfs with sites within 600 bp upstream = 0.0122069


Motif number 3

TTTTGCTTACTTATTAAGTATATGCCTTATC	1	63	0	TTATTAATAT	    0.958437	-120
CAAAATTATAGTATTACATAGTATTTGTAGT	1	89	1	GTATTACTAG	    0.952827	-94
TATTTGTAGTGCATCAATTATTATACTTTAT	1	110	1	GCATCAATAT	    0.975137	-73
ATTACCTATGTTATAAAGTATAATAATTGAT	1	122	0	TTATAAATAT	    0.852163	-61
GTCATAAAGATCATTACCTATGTTATAAAGT	1	134	0	TCATTACTAT	    0.972986	-49
TTTTTAAAGTGCATCAAATATA         	2	2	0	GCATCAATAT	    0.975107	-148
AGTTCTTATAGAATTAATTAGCAAATTTTTA	2	27	0	GAATTAATAG	    0.936079	-123
TTCACTGTATTAATTTCATATTCTTTTTGAA	2	85	1	TAATTTCTAT	    0.741124	-65
          ******* ***

Masking position 3
Map Score:   5.75493

Number of sites scoring better than the average of aligned sites = 443
Number in coding regions = 304
Number in noncoding regions = 139
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 4

TAAGATAAGGCATATACTTAATAAGTAAGC	1	60	1	CATATACTTA	    0.863615	-123
TAAGCAAAATTATAGTATTACATAGTATTT	1	85	1	TATAGTATTA	    0.950417	-98
TATAGTATTACATAGTATTTGTAGTGCATC	1	95	1	CATAGTATTT	    0.968452	-88
AATTCAATTTTAAATTATTAAACTTAA   	1	166	1	TAAATTATTA	    0.804128	-17
AATTAATTAGCAAATTTTTAAAGTGCATCA	2	17	0	CAAATTTTTA	    0.847586	-133
CTCCAGTTCTTATAGAATTAATTAGCAAAT	2	32	0	TATAGAATTA	    0.858022	-118
GGTATTAAGTCACAGTTTTTTATCTTCACT	2	61	1	CACAGTTTTT	    0.899863	-89
TTTTTATCTTCACTGTATTAATTTCATATT	2	77	1	CACTGTATTA	    0.861259	-73
GTATTAATTTCATATTCTTTTTGAAGTCAT	2	91	1	CATATTCTTT	     0.91315	-59
          **********

Masking position 8
Map Score:   6.70825

Number of sites scoring better than the average of aligned sites = 611
Number in coding regions = 420
Number in noncoding regions = 191
Number of orfs with sites within 600 bp upstream = 105
Fraction of orfs with sites within 600 bp upstream = 0.0168648


Motif number 5

          **********

No masking
Map Score:   -2.46258e-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:   -2.46258e-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:   -2.46258e-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