AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -icpxR_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
#3	PH1410	117	332aa long hypothetical dipeptide transport system permease protein dppB
#4	PH1414	26	129aa long hypothetical protein
#5	PH1415	93	343aa long hypothetical 5' nuclease

Motif number 1

GGTAGTGAGCAAAATGAAGAGTTCATAAGTCTTCC	2	15	0	AAAGAAGGTA	    0.935637	-249
GCTTCATTAAAAGAAGAGACGAAAACTTTTTTACA	2	72	0	AAGGAGAGAA	    0.992338	-192
TAAACTTCAAAAATGGAGATGTAAAACTACTAGGC	2	105	0	AAAGAGAGAA	    0.985527	-159
CATTGTATAGAAGCCGAAAATATCATGATCGTCTT	2	204	1	AAGGAAATTA	    0.610131	-60
AACAAAATCCAAGTTGAGGGGTGGATT        	2	247	1	AAGGAGGGGA	    0.988004	-17
GCAATAAAGAAAAGAGAGAAGAAAGATTA      	3	5	0	AAAGAGAGAG	    0.963146	-113
ACAAGAATGTACAAGGAGGGGCAAAT         	3	102	1	ACAGAGGGAA	    0.974781	-16
CAAAAATTGAAAAAAGAAGAGGATAT         	4	2	0	AAAGAAGGAA	    0.981237	-25
CATCACCTTTCAGGTGAGGGGAAGGTTCATCATCA	5	41	0	CAGGAGGGAG	    0.962233	-53
CCTCACCTGAAAGGTGATGAGCACACCGGTAGGCT	5	57	1	AAGGATGGAA	    0.975226	-37
GCACACCGGTAGGCTGAGGGTGATAAT        	5	77	1	AGGGAGGTAA	    0.918869	-17
          ***  **** * * *

Masking position 7
Map Score:   12.0523

Number of sites scoring better than the average of aligned sites = 913
Number in coding regions = 832
Number in noncoding regions = 81
Number of orfs with sites within 600 bp upstream = 91
Fraction of orfs with sites within 600 bp upstream = 0.0146161


Motif number 2

CCAGGAAGACTTATGAACTCTTCATTTTGCT	2	12	1	TATGAACTCT	    0.980491	-252
TTAAAATATGTAAAAAAGTTTTCGTCTCTTC	2	64	1	TAAAAAGTTT	    0.851098	-200
TCTCTTCTTTTAATGAAGCCTAGTAGTTTTA	2	88	1	TATGAAGCCT	    0.978817	-176
ACATCTCCATTTTTGAAGTTTAGAAAATCTA	2	118	1	TTTGAAGTTT	    0.921907	-146
TTCTATACAATGATAAACCTTCCTTAATAAA	2	185	0	TATAAACCTT	    0.977614	-79
      ATTGTTATAAACTTTCAGAGATATC	5	5	1	TATAAACTTT	    0.973091	-89
TCAAGTCTGATGATGAACCTTCCCCTCACCT	5	34	1	TATGAACCTT	    0.989034	-60
          * *********

Masking position 6
Map Score:   6.62698

Number of sites scoring better than the average of aligned sites = 167
Number in coding regions = 138
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 3

TTGAAGACCTCGATAAGGAAATAAAGGAG  	1	13	1	CGATAAGGAA	      0.8317	-19
TTATGACCTTCGTTAAAATATGTAAAAAAGT	2	52	1	CGTTAAAAAT	    0.782803	-212
TACTAGGCTTCATTAAAAGAAGAGACGAAAA	2	82	0	CATTAAAAAA	    0.922883	-182
TTCTAAACTTCAAAAATGGAGATGTAAAACT	2	112	0	CAAAAATGAG	    0.744548	-152
CAACTACGTGCATAAAAATATTTTTATTAAG	2	163	1	CATAAAAAAT	    0.736804	-101
GATAAACCTTCCTTAATAAAAATATTTTTAT	2	174	0	CCTTAATAAA	    0.843529	-90
GTATAGAAGCCGAAAATATCATGATCGTCTT	2	208	1	CGAAAATACA	    0.781341	-56
TAAATAAGGGCAATAAAGAAAAGAGAGAAGA	3	18	0	CAATAAAGAA	    0.910116	-100
TATATTATCGCATAAATAAAAATTTTGGTGT	3	50	0	CATAAATAAA	    0.936483	-68
TTTATTTATGCGATAATATAATTCTCAAACG	3	61	1	CGATAATAAA	    0.957529	-57
          CAAAAATTGAAAAAAGAAGAG	4	16	0	CAAAAATTAA	    0.758443	-11
          ******** **

Masking position 6
Map Score:   3.40961

Number of sites scoring better than the average of aligned sites = 345
Number in coding regions = 286
Number in noncoding regions = 59
Number of orfs with sites within 600 bp upstream = 62
Fraction of orfs with sites within 600 bp upstream = 0.00995824


Motif number 4

          **********

No masking
Map Score:   -3.6705e-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:   -3.6705e-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:   -3.6705e-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