AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -icpxR9_pyro_opreg_100.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	31	277aa long hypothetical methyl-accepting chemotaxis protein
#2	PH0481	263	280aa long hypothetical chemotaxis protein methyltransferase

Motif number 1

     CGTTGAAGACCTCGATAAGGAAATAAA	1	6	1	AAGCCTCATA	    0.956816	-26
GAGCAAAATGAAGAGTTCATAAGTCTTCCTGG	2	12	0	AAGGTTCTAA	    0.842876	-252
CTACCAATTATGACCTTCGTTAAAATATGTAA	2	45	1	TGACTTCTTA	     0.95751	-219
AGAAGAGACGAAAACTTTTTTACATATTTTAA	2	64	0	AAACTTTTTA	    0.869117	-200
GTAAAACTACTAGGCTTCATTAAAAGAAGAGA	2	88	0	TAGCTTCTTA	     0.99308	-176
GTAGATTTTCTAAACTTCAAAAATGGAGATGT	2	118	0	TAACTTCAAA	    0.949472	-146
ATACAATGATAAACCTTCCTTAATAAAAATAT	2	180	0	AAACTTCTTA	     0.98345	-84
CATGATATTTTCGGCTTCTATACAATGATAAA	2	199	0	TCGCTTCATA	     0.98511	-65
AATATCATGATCGTCTTAGATATGCAACAAAA	2	222	1	TCGCTTAATA	    0.880781	-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

          CTCCTTTATTTCCTTATCGA	1	22	0	CTCCTTTATT	    0.978964	-10
GACTTATGAACTCTTCATTTTGCTCACTAC	2	19	1	CTCTTCATTT	    0.978964	-245
AAGTTTTCGTCTCTTCTTTTAATGAAGCCT	2	79	1	CTCTTCTTTT	    0.991567	-185
AGTTTTACATCTCCATTTTTGAAGTTTAGA	2	112	1	CTCCATTTTT	    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

CTTTTAATGAAGCCTAGTAGTTTTACATCT	2	94	1	AGCCTAGTAG	    0.978395	-170
CCATTTTTGAAGTTTAGAAAATCTACAAAG	2	124	1	AGTTTAGAAA	    0.876045	-140
TTGTGTAGGTAGCTTTGTAGATTTTCTAAA	2	136	0	AGCTTTGTAG	    0.985957	-128
TTATGCACGTAGTTGTGTAGGTAGCTTTGT	2	148	0	AGTTGTGTAG	    0.985957	-116
ACAAAATCCAAGTTGAGGGGTGGATT    	2	248	1	AGTTGAGGGG	    0.963746	-16
          **********

Masking position 1
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

CTTTTTTACATATTTTAACGAAGGTCATAA	2	52	0	TATTTTAACG	    0.984632	-212
TTTCGTCTCTTCTTTTAATGAAGCCTAGTA	2	83	1	TCTTTTAATG	    0.984632	-181
TTAATAAAAATATTTTTATGCACGTAGTTG	2	163	0	TATTTTTATG	    0.977781	-101
          **********

Masking position 8
Map Score:   0.926525

Number of sites scoring better than the average of aligned sites = 33
Number in coding regions = 26
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 5

          **********

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 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