AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -irpoE_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	RP123	143	HFLC PROTEIN  (hflC)
#2	RP124	30	PROBABLE PERIPLASMIC SERINE PROTEASE DO-LIKE PRECURSOR (htrA)
#3	RP303	89	RNA POLYMERASE SIGMA-32 FACTOR (rpoH)

Motif number 1

AACATCGTAGTACTTTAGCATGATATATCTAATT  	1	9	0	TTTTAATAAT	    0.994531	-135
GATGTTCACATCATTTAGGATAAGATTTTATCTCAT	1	39	1	TTTTAATAAT	    0.994531	-105
GGATCTTTGCTCTTTTTGAAGTTGATCTTCTTACAA	1	76	1	TTTTTAGTAT	    0.974258	-68
CTTACAAGGCTTTTTTAGTATGATATTATAAAATAA	1	105	1	TTTTAATAAT	    0.994531	-39
    TTAATATTCCTTATTATTTTATAATATCATAC	1	122	0	TCTTAATTAT	    0.957059	-22
TTTTCTATAATTTTTTTAAATAAAATCAAACA    	3	7	0	TTTTTATAAT	    0.993041	-83
TAGAAAAAGTTTATTTTAGATCATATATATGTTAGT	3	36	1	TTTTTATAAT	    0.993263	-54
AAAACTATTTTCGTTTATACTAACATATATATGATC	3	54	0	TTTTACTAAT	    0.977005	-36
TAAACGAAAATAGTTTTTCAGGTTATT         	3	73	1	TTTTTAGTAT	    0.974258	-17
          *  ****  ** * **

Masking position 6
Map Score:   19.3345

Number of sites scoring better than the average of aligned sites = 267
Number in coding regions = 163
Number in noncoding regions = 104
Number of orfs with sites within 600 bp upstream = 69
Fraction of orfs with sites within 600 bp upstream = 0.0110826


Motif number 2

TTTAGCATGATATATCTAATT         	1	2	0	TATATCTAAT	    0.950317	-142
CATTTAGGATAAGATTTTATCTCATTGGAT	1	50	1	AAGATTTTAT	    0.968613	-94
AAAAAGAGCAAAGATCCAATGAGATAAAAT	1	63	0	AAGATCCAAT	    0.903753	-81
CTTTTTGAAGTTGATCTTCTTACAAGGCTT	1	87	1	TTGATCTTCT	    0.965184	-57
AATATTCCTTATTATTTTATAATATCATAC	1	122	0	ATTATTTTAT	    0.881601	-22
          TATATTTACTGTCGTCTTTA	2	1	1	TATATTTACT	    0.872316	-30
       TGTTTGATTTTATTTAAAAAAAT	3	4	1	TTGATTTTAT	    0.968614	-86
AAGTTTATTTTAGATCATATATATGTTAGT	3	42	1	TAGATCATAT	    0.942213	-48
          **********

Masking position 4
Map Score:   6.95047

Number of sites scoring better than the average of aligned sites = 730
Number in coding regions = 511
Number in noncoding regions = 219
Number of orfs with sites within 600 bp upstream = 107
Fraction of orfs with sites within 600 bp upstream = 0.017186


Motif number 3

  AATTAGATATATCATGCTAAAGTACTAC	1	9	1	ATATCATGCT	    0.978353	-135
AATGATGTGAACATCGTAGTACTTTAGCAT	1	24	0	ACATCGTAGT	    0.973066	-120
TTATTTTATAATATCATACTAAAAAAGCCT	1	111	0	ATATCATACT	    0.987187	-33
TAGATCATATATATGTTAGTATAAACGAAA	3	52	1	ATATGTTAGT	    0.942198	-38
          **********

Masking position 4
Map Score:   0.37009

Number of sites scoring better than the average of aligned sites = 59
Number in coding regions = 42
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

          **********

No masking
Map Score:   -1.1836e-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:   -1.1836e-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:   -1.1836e-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