AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i287_hypothetical_nitrate_reductase_mjan_reg_100.orf -o287_mjan_100.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	RMJ09899	241	M_jannaschii_chromosome

Motif number 1

ATTATAATGATTTAGATTAGAAGAATTTACG	1	14	0	TTTAGATTGA	    0.885942	-228
AATCTAAATCATTATAATATTTATTTTTTAT	1	27	1	ATTATAATTT	    0.791775	-215
ATATTTATTTTTTATGGTTGTATTTTTATAT	1	43	1	TTTATGGTGT	    0.946604	-199
TGGTTGTATTTTTATATTATTAGCTTTACCA	1	57	1	TTTATATTTT	    0.963463	-185
GTAGAAAAGCTTTATATTGGTAAAGCTAATA	1	74	0	TTTATATTGT	    0.992588	-168
AGAACTTTTATTCATATATGTTGAACTATTT	1	112	1	TTCATATAGT	    0.950217	-130
TGTTGAACTATTTATAAATATGTGAGCAAGA	1	130	1	TTTATAAAAT	    0.842781	-112
TAGAAACTTTTTTATATAGGTGTGTGTCTTG	1	156	0	TTTATATAGT	    0.989192	-86
ATACATAGTATTTATAAATGAAAATCATCAA	1	197	1	TTTATAAAGA	    0.930292	-45
TCACATGGACATTATGTTAGTTGATGATTTT	1	217	0	ATTATGTTGT	    0.941155	-25
          ******** **

Masking position 4
Map Score:   11.7777

Number of sites scoring better than the average of aligned sites = 761
Number in coding regions = 581
Number in noncoding regions = 180
Number of orfs with sites within 600 bp upstream = 185
Fraction of orfs with sites within 600 bp upstream = 0.0297141


Motif number 2

TGATTTAGATTAGAAGAATTTACGGTG    	1	7	0	TGAAGAATTT	    0.950296	-235
ATCTAAATCATTATAATATTTATTTTTTATG	1	28	1	TATAATATTT	    0.781599	-214
TTATTTTTTATGGTTGTATTTTTATATTATT	1	47	1	TGTTGTATTT	    0.959729	-195
CTTTACCAATATAAAGCTTTTCTACCAAAAA	1	80	1	AAAAGCTTTT	    0.779935	-162
ATATGAATAAAAGTTCTATTTTTGGTAGAAA	1	98	0	AGTTCTATTT	    0.779366	-144
TTCATATATGTTGAACTATTTATAAATATGT	1	122	1	TGAACTATTT	    0.971507	-120
AAGTTTAAGTAGAAACTTTTTTATATAGGTG	1	165	0	AAAACTTTTT	    0.690365	-77
TAAACTTCATACATAGTATTTATAAATGAAA	1	189	1	AATAGTATTT	    0.745221	-53
ATTATGTTAGTTGATGATTTTCATTTATAAA	1	207	0	TGATGATTTT	    0.849815	-35
          * *********

Masking position 9
Map Score:   4.20873

Number of sites scoring better than the average of aligned sites = 1307
Number in coding regions = 1138
Number in noncoding regions = 169
Number of orfs with sites within 600 bp upstream = 164
Fraction of orfs with sites within 600 bp upstream = 0.0263412


Motif number 3

AAAAGCTTTATATTGGTAAAGCTAATAATA	1	71	0	TATTGGTAAA	    0.973035	-171
AAAGTTCTATTTTTGGTAGAAAAGCTTTAT	1	90	0	TTTTGGTAGA	    0.975522	-152
CTTTTATTCATATATGTTGAACTATTTATA	1	116	1	TATATGTTGA	    0.929067	-126
TATGTTGAACTATTTATAAATATGTGAGCA	1	128	1	TATTTATAAA	    0.894018	-114
ATGTATGAAGTTTAAGTAGAAACTTTTTTA	1	173	0	TTTAAGTAGA	    0.915275	-69
TCATACATAGTATTTATAAATGAAAATCAT	1	195	1	TATTTATAAA	    0.894018	-47
ATGGACATTATGTTAGTTGATGATTTTCAT	1	214	0	TGTTAGTTGA	    0.904577	-28
          **********

Masking position 10
Map Score:   5.11376

Number of sites scoring better than the average of aligned sites = 642
Number in coding regions = 567
Number in noncoding regions = 75
Number of orfs with sites within 600 bp upstream = 73
Fraction of orfs with sites within 600 bp upstream = 0.011725


Motif number 4

          **********

No masking
Map Score:   2.58227e-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:   2.58227e-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:   2.58227e-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