AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i173_mjan_pyro_100.orf -o173_mjan_pyro_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 =  	0.37
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RMJ00919	259	M_jannaschii_chromosome
#2	RPH01018	214	Pyrococcus_OT3

Motif number 1

ATATTGATTTATTATGTTGAAATATTGATAAGGA	1	24	0	ATATTAAATA	    0.949964	-236
AGAATCCCTTTATTTAACTAAAGAGCAATTTATA	1	55	0	TTTTAAAAGA	    0.629878	-205
CCATTTATATACTATTTTAAAAGATTATCGCACT	1	90	1	ATATTAAAGA	    0.855423	-170
AGATTATCGCACTTATTTAAAATATTTAAGCGGA	1	111	1	ATTATAAATA	    0.887649	-149
ATGTTATTACTGAAAAACTAAATACACATTCCTA	1	166	1	TAAAAAAATA	     0.60854	-94
GTCATCCATTAAAATCTACAAATAATTTTATTTT	1	214	1	AAATTAAATA	    0.859536	-46
TCACCCAAAAAATAGTAAAAAATAAAATTATTTG	1	232	0	ATAGAAAATA	    0.982146	-28
TAAAGCGAAAAGTTGAACAAAATATCAA      	2	5	0	ATTGAAAATA	     0.98462	-210
AGACGGATACATTATTATCAAATAGATGAAAGTA	2	45	0	ATATAAAATA	     0.97608	-170
TGTATCCGTCTTATGTACAAAATATAACTGCAAT	2	68	1	TATGAAAATA	    0.868443	-147
AATTTTTAGAATTTTGACTAAATATTATTGGATA	2	99	1	ATTTAAAATA	    0.979159	-116
AGGGCTTGAGAATTGGATAAAATATCCAATAATA	2	121	0	ATTGAAAATA	    0.976578	-94
GCTATCTCCAAGTTGGACAAAATATCCAAGAGGT	2	185	1	ATTGAAAATA	     0.98462	-30
          * *** *  *****

Masking position 10
Map Score:   17.5707

Number of sites scoring better than the average of aligned sites = 1101
Number in coding regions = 875
Number in noncoding regions = 226
Number of orfs with sites within 600 bp upstream = 204
Fraction of orfs with sites within 600 bp upstream = 0.0327658


Motif number 2

        AAATATAAATTAATCCTTATCAA	1	3	1	ATATAAATTA	    0.938742	-257
AGAGCAATTTATATTGATTTATTATGTTGAA	1	37	0	ATATTGATTA	    0.941088	-223
TTAAAATAGTATATAAATGGAAGAATCCCTT	1	79	0	ATATAAATGA	    0.981922	-181
GGTTTATATGTTATTACTGAAAAACTAAATA	1	159	1	TTATTACTGA	     0.91529	-101
TTATTTGTAGATTTTAATGGATGACTTTATT	1	208	0	ATTTTAATGA	    0.917962	-52
ACTTTTCGCTTTATTGATTTACTTTCATCTA	2	26	1	TTATTGATTA	    0.816078	-189
CATTATTATCAAATAGATGAAAGTAAATCAA	2	39	0	AAATAGATGA	    0.844762	-176
CATCTATTTGATAATAATGTATCCGTCTTAT	2	51	1	ATAATAATGA	    0.917957	-164
TATGTACAAAATATAACTGCAATTTTTAGAA	2	79	1	ATATAACTGA	    0.963703	-136
TTTTGACTAAATATTATTGGATATTTTATCC	2	110	1	ATATTATTGA	     0.93443	-105
          ********* *

Masking position 8
Map Score:   9.3824

Number of sites scoring better than the average of aligned sites = 833
Number in coding regions = 716
Number in noncoding regions = 117
Number of orfs with sites within 600 bp upstream = 110
Fraction of orfs with sites within 600 bp upstream = 0.0176678


Motif number 3

CAATATTTCAACATAATAAATCAATATAAA	1	31	1	ACATAATAAA	    0.900413	-229
TAATCTTTTAAAATAGTATATAAATGGAAG	1	87	0	AAATAGTATA	     0.90418	-173
GTTATTACTGAAAAACTAAATACACATTCC	1	168	1	AAAAACTAAA	     0.93218	-92
TTCCTAAGATAAGTAATAAAGTCATCCATT	1	194	1	AAGTAATAAA	    0.900413	-66
ATCACCCAAAAAATAGTAAAAAATAAAATT	1	237	0	AAATAGTAAA	    0.978473	-23
TATTTAGTCAAAATTCTAAAAATTGCAGTT	2	93	0	AAATTCTAAA	    0.942308	-122
CTCATGCCATAAATCCTAAAAGCCTTGAAT	2	153	1	AAATCCTAAA	     0.96033	-62
          **********

Masking position 8
Map Score:   5.48149

Number of sites scoring better than the average of aligned sites = 669
Number in coding regions = 463
Number in noncoding regions = 206
Number of orfs with sites within 600 bp upstream = 174
Fraction of orfs with sites within 600 bp upstream = 0.0279473


Motif number 4

TGGATTTCCGCTTAAATATTTTAAATAAGT	1	121	0	CTTAAATATT	    0.915861	-139
TATTACTTATCTTAGGAATGTGTATTTAGT	1	182	0	CTTAGGAATG	    0.870504	-78
ACTAAATATTATTGGATATTTTATCCAATT	2	115	1	ATTGGATATT	    0.914464	-100
GGCATGAGGGCTTGAGAATTGGATAAAATA	2	131	0	CTTGAGAATT	    0.935035	-84
TCCTAAAAGCCTTGAATCTGCTATCTCCAA	2	166	1	CTTGAATCTG	    0.910556	-49
TTTTGTCCAACTTGGAGATAGCAGATTCAA	2	177	0	CTTGGAGATA	    0.918603	-38
ACTTTCACCTCTTGGATATTTTGTCCAACT	2	195	0	CTTGGATATT	    0.988012	-20
          **********

Masking position 3
Map Score:   2.1818

Number of sites scoring better than the average of aligned sites = 424
Number in coding regions = 384
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 5

          **********

No masking
Map Score:   -5.51791e-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:   -5.51791e-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:   -5.51791e-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