AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -irpoE_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	RP122	98	HFLK PROTEIN (hflK)
#2	RP123	143	HFLC PROTEIN  (hflC)
#3	RP124	30	PROBABLE PERIPLASMIC SERINE PROTEASE DO-LIKE PRECURSOR (htrA)
#4	RP303	89	RNA POLYMERASE SIGMA-32 FACTOR (rpoH)

Motif number 1

GTGATTATATATATAATAGTATATAACGTCAAGTTA	1	45	0	ATTATTATAA	    0.952675	-54
TAATCTTAAAATAATATAAAAAAGCAA         	1	82	1	ATAATAAAAA	    0.987438	-17
  AATTAGATATATCATGCTAAAGTACTACGATGTT	2	9	1	ATTATTAAAA	    0.993728	-135
ATGAGATAAAATCTTATCCTAAATGATGTGAACATC	2	39	0	ATTATTAAAA	    0.993728	-105
TTGTAAGAAGATCAACTTCAAAAAGAGCAAAGATCC	2	76	0	ATACTAAAAA	    0.967918	-68
TTATTTTATAATATCATACTAAAAAAGCCTTGTAAG	2	105	0	ATTATTAAAA	    0.993728	-39
GTATGATATTATAAAATAATAAGGAATATTAA    	2	122	1	ATAATTAAGA	    0.946212	-22
    TGTTTGATTTTATTTAAAAAAATTATAGAAAA	4	7	1	ATTATAAAAA	    0.992465	-83
ACTAACATATATATGATCTAAAATAAACTTTTTCTA	4	36	0	ATTATAAAAA	    0.992553	-54
GATCATATATATGTTAGTATAAACGAAAATAGTTTT	4	54	1	ATTAGTAAAA	     0.96757	-36
         AATAACCTGAAAAACTATTTTCGTTTA	4	73	0	ATACTAAAAA	    0.967918	-17
          ** * **  ****  *

Masking position 11
Map Score:   24.2673

Number of sites scoring better than the average of aligned sites = 357
Number in coding regions = 215
Number in noncoding regions = 142
Number of orfs with sites within 600 bp upstream = 96
Fraction of orfs with sites within 600 bp upstream = 0.0154192


Motif number 2

AACTTGACGTTATATACTATTATATATATAA	1	46	1	TATATACATT	    0.960145	-53
TATACTATTATATATATAATCACTTAATCTT	1	58	1	TATATATATC	    0.985485	-41
   TTGCTTTTTTATATTATTTTAAGATTAA	1	81	0	TTTATATATT	    0.977048	-18
TTTAGCATGATATATCTAATT          	2	1	0	TATATCTATT	    0.948205	-143
AGGATAAGATTTTATCTCATTGGATCTTTGC	2	55	1	TTTATCTATT	    0.948206	-89
TCCTTATTATTTTATAATATCATACTAAAAA	2	116	0	TTTATAAATC	    0.961186	-28
ATAATTTTTTTAAATAAAATCAAACA     	4	6	0	TAAATAAATC	    0.777652	-84
AAATAAACTTTTTCTATAATTTTTTTAAATA	4	21	0	TTTCTATATT	    0.898777	-69
TATACTAACATATATATGATCTAAAATAAAC	4	44	0	TATATATATC	    0.985479	-46
ACTATTTTCGTTTATACTAACATATATATGA	4	56	0	TTTATACAAC	    0.843989	-34
          ******* ***

Masking position 5
Map Score:   15.3375

Number of sites scoring better than the average of aligned sites = 398
Number in coding regions = 246
Number in noncoding regions = 152
Number of orfs with sites within 600 bp upstream = 84
Fraction of orfs with sites within 600 bp upstream = 0.0134918


Motif number 3

GACGTTATATACTATTATATATATAATCAC	1	51	1	ACTATTATAT	    0.958841	-48
GTAGTACTTTAGCATGATATATCTAATT  	2	9	0	AGCATGATAT	    0.966245	-135
ATGCTAAAGTACTACGATGTTCACATCATT	2	24	1	ACTACGATGT	    0.960384	-120
AGGCTTTTTTAGTATGATATTATAAAATAA	2	111	1	AGTATGATAT	    0.984507	-33
TTTCGTTTATACTAACATATATATGATCTA	4	52	0	ACTAACATAT	    0.931811	-38
          **********

Masking position 4
Map Score:   1.72216

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 33
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

AGCTTTAAAAAGGAAATTTAATT        	1	3	0	AGGAATTTAA	    0.959164	-96
TACCAGCTTAAAGAGCTTTAAAAAGGAAATT	1	16	0	AAGAGTTTAA	    0.917208	-83
TTAATCTTAAAATAATATAAAAAAGCAA   	1	81	1	AATAAATAAA	    0.848009	-18
AAAGCCTTGTAAGAAGATCAACTTCAAAAAG	2	87	0	AAGAAATCAA	     0.97825	-57
TAAAATAATAAGGAATATTAA          	2	133	1	AGGAAATTAA	    0.974284	-11
AATTTTTTTAAATAAAATCAAACA       	4	4	0	AATAAATCAA	    0.938332	-86
GATTTTATTTAAAAAAATTATAGAAAAAGTT	4	16	1	AAAAAATTAT	    0.891877	-74
AAAATTATAGAAAAAGTTTATTTTAGATCAT	4	29	1	AAAAATTTAT	    0.829926	-61
          ***** *****

Masking position 4
Map Score:   5.31676

Number of sites scoring better than the average of aligned sites = 719
Number in coding regions = 490
Number in noncoding regions = 229
Number of orfs with sites within 600 bp upstream = 126
Fraction of orfs with sites within 600 bp upstream = 0.0202377


Motif number 5

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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:   1.3033e-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