AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -icpxR9_pyro_opreg_300.orf -g0.419 -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 =  	0.419
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	PH0479_PH0480	31	PH0479: 277aa long hypothetical methyl-accepting chemotaxis protein, PH0480: 110aa long hypothetical protein
#2	PH0481	263	280aa long hypothetical chemotaxis protein methyltransferase

Motif number 1

     CGTTGAAGACCTCGATAAGGAAATAAA	1	6	1	AAGCCTCATA	    0.951514	-26
GAGCAAAATGAAGAGTTCATAAGTCTTCCTGG	2	12	0	AAGGTTCTAA	    0.826127	-252
CTACCAATTATGACCTTCGTTAAAATATGTAA	2	45	1	TGACTTCTTA	    0.952293	-219
AGAAGAGACGAAAACTTTTTTACATATTTTAA	2	64	0	AAACTTTTTA	    0.854684	-200
GTAAAACTACTAGGCTTCATTAAAAGAAGAGA	2	88	0	TAGCTTCTTA	    0.992199	-176
GTAGATTTTCTAAACTTCAAAAATGGAGATGT	2	118	0	TAACTTCAAA	    0.943322	-146
ATACAATGATAAACCTTCCTTAATAAAAATAT	2	180	0	AAACTTCTTA	    0.981357	-84
CATGATATTTTCGGCTTCTATACAATGATAAA	2	199	0	TCGCTTCATA	    0.983221	-65
AATATCATGATCGTCTTAGATATGCAACAAAA	2	222	1	TCGCTTAATA	    0.867437	-42
          *** **** ***

Masking position 7
Map Score:   7.57328

Number of sites scoring better than the average of aligned sites = 869
Number in coding regions = 812
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 2

TCGATAAGGAAATAAAGGAG          	1	22	1	AATAAAGGAG	    0.978964	-10
GTAGTGAGCAAAATGAAGAGTTCATAAGTC	2	19	0	AAATGAAGAG	    0.978964	-245
AGGCTTCATTAAAAGAAGAGACGAAAACTT	2	79	0	AAAAGAAGAG	    0.991567	-185
TCTAAACTTCAAAAATGGAGATGTAAAACT	2	112	0	AAAAATGGAG	    0.978964	-152
          **********

Masking position 2
Map Score:   2.88072

Number of sites scoring better than the average of aligned sites = 164
Number in coding regions = 151
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 3

AGATGTAAAACTACTAGGCTTCATTAAAAG	2	94	0	CTACTAGGCT	    0.979516	-170
CTTTGTAGATTTTCTAAACTTCAAAAATGG	2	124	0	TTTCTAAACT	    0.881843	-140
TTTAGAAAATCTACAAAGCTACCTACACAA	2	136	1	CTACAAAGCT	    0.986692	-128
ACAAAGCTACCTACACAACTACGTGCATAA	2	148	1	CTACACAACT	    0.986692	-116
    AATCCACCCCTCAACTTGGATTTTGT	2	248	0	CCCCTCAACT	    0.965603	-16
          **********

Masking position 10
Map Score:   1.30133

Number of sites scoring better than the average of aligned sites = 292
Number in coding regions = 275
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 4

CTTCGTTAAAATATGTAAAAAAGTTTTCGT	2	59	1	ATATGTAAAA	    0.986159	-205
TCAAAAATGGAGATGTAAAACTACTAGGCT	2	104	0	AGATGTAAAA	    0.983671	-160
ATCGTCTTAGATATGCAACAAAATCCAAGT	2	231	1	ATATGCAACA	     0.97706	-33
          **********

Masking position 7
Map Score:   0.926525

Number of sites scoring better than the average of aligned sites = 23
Number in coding regions = 18
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 5

TTAAAAGAAGAGACGAAAACTTTTTTACAT	2	71	0	AGACGAAAAC	    0.990883	-193
ATTGTATAGAAGCCGAAAATATCATGATCG	2	205	1	AGCCGAAAAT	    0.990883	-59
TGCATATCTAAGACGATCATGATATTTTCG	2	218	0	AGACGATCAT	    0.984034	-46
          **********

Masking position 6
Map Score:   0.577447

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 11
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 6

          **********

No masking
Map Score:   -2.17836e-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:   -2.17836e-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 8

          **********

No masking
Map Score:   -2.17836e-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