AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i232_formulase_pyro_reg_100.orf -o232_pyro_100.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -x5 -e 
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 =  	0.42
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RPH00277	70	Pyrococcus_OT3
#2	RPH00276	300	Pyrococcus_OT3

Motif number 1

CTCAACAATAAAAAATAGAGATAGA      	1	5	0	AAAAATAGGA	    0.933886	-66
AATCTCTTTTAAATTCAACGTTTTATCTCAA	1	31	0	AAATTCAAGT	    0.918334	-40
        CGAAATATAATCCCTTAAAAATC	1	58	0	AAATATAACC	    0.855199	-13
CTTTCGACGAAAATTCCAAGACTGAAAGAAA	2	58	1	AAATTCCAGA	    0.881269	-243
AAGACTGAAAGAAAATAAAGACAAACTGATA	2	75	1	GAAAATAAGA	    0.872627	-226
TAACCCTAAGAAAAATAAGGTAGCTCTTTTC	2	104	1	AAAAATAAGT	    0.912134	-197
CTAGAAGCTTAAATTCAAGGATATTAAGTAG	2	154	0	AAATTCAAGA	     0.97267	-147
AGGATTTGTAAAATTTAGTCAGGCAACTTAA	2	195	0	AAATTTAGCA	    0.905315	-106
CAAATATGTCAAAAACAAACATTTATATTGA	2	252	1	AAAAACAACA	    0.960146	-49
TTTTCACGGTAAAATTAATCAATATAAATGT	2	270	0	AAAATTAACA	    0.956964	-31
          ******** **

Masking position 3
Map Score:   7.93478

Number of sites scoring better than the average of aligned sites = 618
Number in coding regions = 523
Number in noncoding regions = 95
Number of orfs with sites within 600 bp upstream = 94
Fraction of orfs with sites within 600 bp upstream = 0.015098


Motif number 2

AACAATAAAAAATAGAGATAGA        	1	3	0	AATAGAGATA	    0.975671	-68
TATTTTTTATTGTTGAGATAAAACGTTGAA	1	19	1	TGTTGAGATA	    0.830543	-52
CGTTGAATTTAAAAGAGATTTTTAAGGGAT	1	42	1	AAAAGAGATT	    0.939544	-29
AATTCCTACGTAAAGAGATATGAGGGTATA	2	12	1	TAAAGAGATA	    0.982899	-289
GAGCTAGTGGAAAAGAGCTACCTTATTTTT	2	114	0	AAAAGAGCTA	    0.989059	-187
GTAGCCACACAACTGAGCTAGTGGAAAAGA	2	128	0	AACTGAGCTA	    0.946569	-173
GTCAGGCAACTTAAGAGCTAGGGGCTAGAA	2	179	0	TTAAGAGCTA	    0.944835	-122
          **********

Masking position 6
Map Score:   7.76733

Number of sites scoring better than the average of aligned sites = 275
Number in coding regions = 248
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 3

TTGTTGAGATAAAACGTTGAATTTAAAAGAG	1	28	1	AAAACGTGAA	    0.918614	-43
  CGAAATATAATCCCTTAAAAATCTCTTTT	1	52	0	AATCCCTAAA	    0.943984	-19
CTCATATCTCTTTACGTAGGAATTA      	2	5	0	TTTACGTGGA	    0.770239	-296
ATTTTATCTTATACCCTCATATCTCTTTACG	2	20	0	ATACCCTATA	    0.891541	-281
AGTCTTGGAATTTTCGTCGAAAGATAAGTTA	2	50	0	TTTTCGTGAA	    0.894515	-251
GACAAACTGATAACCCTAAGAAAAATAAGGT	2	94	1	TAACCCTAGA	    0.936592	-207
TGGCTACTTAATATCCTTGAATTTAAGCTTC	2	151	1	ATATCCTGAA	    0.961061	-150
TAAATTTTACAAATCCTCAAATGATGAGCCT	2	209	1	AAATCCTAAA	    0.939616	-92
TTGATTAATTTTACCGTGAAAATGGTGATAT	2	279	1	TTACCGTAAA	    0.962237	-22
          ******* ***

Masking position 7
Map Score:   3.97804

Number of sites scoring better than the average of aligned sites = 914
Number in coding regions = 747
Number in noncoding regions = 167
Number of orfs with sites within 600 bp upstream = 81
Fraction of orfs with sites within 600 bp upstream = 0.01301


Motif number 4

CTAAGAAAAATAAGGTAGCTCTTTTCCACT	2	109	1	TAAGGTAGCT	    0.965471	-192
TTCAAGGATATTAAGTAGCCACACAACTGA	2	142	0	TTAAGTAGCC	    0.993789	-159
CCCCTAGCTCTTAAGTTGCCTGACTAAATT	2	185	1	TTAAGTTGCC	    0.989099	-116
          **********

Masking position 3
Map Score:   0.220967

Number of sites scoring better than the average of aligned sites = 24
Number in coding regions = 21
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 5

          **********

No masking
Map Score:   -1.25466e-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:   -1.25466e-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:   -1.25466e-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