AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i096_Nitrogen_Transport_mjan_reg_300.orf -o096_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 =  	0.31
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RMJ02835	287	M_jannaschii_chromosome

Motif number 1

ATTGATGTTTTCTTTTTTATGTGGGCAGCA	1	26	0	TCTTTTTTAT	    0.922082	-262
GTAGGTAAGATAATTCCTATAAAAGTGTTT	1	77	0	TAATTCCTAT	    0.956882	-211
CCTACTACCCATCTTCCTAATTCCCCTAAT	1	102	1	ATCTTCCTAA	     0.79357	-186
GAAGGAAAATTCTTTCCTTAGTAAGTTATA	1	147	0	TCTTTCCTTA	    0.948086	-141
GAAAGAATTTTCCTTCCTATTATTTAGGAA	1	161	1	TCCTTCCTAT	    0.991662	-127
AAAAGATTCTTTATTCCTAAATAATAGGAA	1	174	0	TTATTCCTAA	    0.967092	-114
TAAAGAATCTTTTTTCCTTTTAGATAAAAA	1	191	1	TTTTTCCTTT	    0.931548	-97
TTGGTAGTAATCATTTTTATTTTTATCTAA	1	210	0	TCATTTTTAT	    0.939058	-78
AATCTCAACCTCATTTTTATAATTTTACAA	1	268	0	TCATTTTTAT	    0.939058	-20
          **********

Masking position 5
Map Score:   10.0421

Number of sites scoring better than the average of aligned sites = 869
Number in coding regions = 785
Number in noncoding regions = 84
Number of orfs with sites within 600 bp upstream = 68
Fraction of orfs with sites within 600 bp upstream = 0.0109219


Motif number 2

TTTCTTTTTTATGTGGGCAGCATCGTTAATAT	1	16	0	ATGGGCAGCA	    0.983497	-272
GAGGTGAAACATATGGATGGTATTGATGTTTT	1	45	0	ATGGATGGTA	    0.983815	-243
GGAATTAGGAAGATGGGTAGTAGGTAAGATAA	1	94	0	ATGGGTAGTA	    0.996605	-194
GATTAATTTGAATTTGGTAGTAATCATTTTTA	1	221	0	ATTGGTAGTA	     0.99239	-67
TAATTTTACAAATTTGGTGGTTTTTAGATTAA	1	247	0	ATTGGTGGTT	    0.977164	-41
          *  *********

Masking position 4
Map Score:   3.85804

Number of sites scoring better than the average of aligned sites = 45
Number in coding regions = 38
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

ACATATGGATGGTATTGATGTTTTCTTTTT	1	39	0	GGTATTGATG	    0.931994	-249
TCCTATAAAAGTGTTTGAGGTGAAACATAT	1	63	0	GTGTTTGAGG	    0.979196	-225
TTAGGAAGATGGGTAGTAGGTAAGATAATT	1	92	0	GGGTAGTAGG	    0.970526	-196
TTTCCATTAGGGGAATTAGGAAGATGGGTA	1	107	0	GGGAATTAGG	    0.989011	-181
TTTCCTTCCTATTATTTAGGAATAAAGAAT	1	169	1	ATTATTTAGG	    0.848151	-119
CAAATTTGGTGGTTTTTAGATTAATTTGAA	1	241	0	GGTTTTTAGA	    0.942957	-47
          **********

Masking position 8
Map Score:   1.8701

Number of sites scoring better than the average of aligned sites = 461
Number in coding regions = 418
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 4

CAGCATCGTTAATATTTTTC          	1	1	0	AATATTTTTC	    0.957979	-287
CTTAGTAAGTTATATATTTAAGCTTTTCCA	1	131	0	TATATATTTA	     0.85555	-157
TTACTAAGGAAAGAATTTTCCTTCCTATTA	1	153	1	AAGAATTTTC	     0.89271	-135
AGTAATCATTTTTATTTTTATCTAAAAGGA	1	205	0	TTTATTTTTA	    0.935582	-83
TGGTTTTTAGATTAATTTGAATTTGGTAGT	1	232	0	ATTAATTTGA	    0.843875	-56
ACCTCATTTTTATAATTTTACAAATTTGGT	1	261	0	TATAATTTTA	     0.89926	-27
          **********

Masking position 4
Map Score:   1.39976

Number of sites scoring better than the average of aligned sites = 1217
Number in coding regions = 842
Number in noncoding regions = 375
Number of orfs with sites within 600 bp upstream = 335
Fraction of orfs with sites within 600 bp upstream = 0.0538066


Motif number 5

          **********

No masking
Map Score:   2.93755e-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:   2.93755e-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:   2.93755e-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