AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i287_hypothetical_nitrate_reductase_mjan_reg_300.orf -o287_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	RMJ09899	241	M_jannaschii_chromosome

Motif number 1

ATTATAATGATTTAGATTAGAAGAATTTACG	1	14	0	TTTAGATTGA	    0.881411	-228
AATCTAAATCATTATAATATTTATTTTTTAT	1	27	1	ATTATAATTT	    0.784563	-215
ATATTTATTTTTTATGGTTGTATTTTTATAT	1	43	1	TTTATGGTGT	    0.944331	-199
TGGTTGTATTTTTATATTATTAGCTTTACCA	1	57	1	TTTATATTTT	     0.96188	-185
GTAGAAAAGCTTTATATTGGTAAAGCTAATA	1	74	0	TTTATATTGT	    0.992257	-168
AGAACTTTTATTCATATATGTTGAACTATTT	1	112	1	TTCATATAGT	     0.94809	-130
TGTTGAACTATTTATAAATATGTGAGCAAGA	1	130	1	TTTATAAAAT	    0.836852	-112
TAGAAACTTTTTTATATAGGTGTGTGTCTTG	1	156	0	TTTATATAGT	     0.98871	-86
ATACATAGTATTTATAAATGAAAATCATCAA	1	197	1	TTTATAAAGA	    0.927378	-45
TCACATGGACATTATGTTAGTTGATGATTTT	1	217	0	ATTATGTTGT	    0.938672	-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	    0.947238	-235
ATCTAAATCATTATAATATTTATTTTTTATG	1	28	1	TATAATATTT	    0.769093	-214
TTATTTTTTATGGTTGTATTTTTATATTATT	1	47	1	TGTTGTATTT	    0.956864	-195
CTTTACCAATATAAAGCTTTTCTACCAAAAA	1	80	1	AAAAGCTTTT	     0.76845	-162
ATATGAATAAAAGTTCTATTTTTGGTAGAAA	1	98	0	AGTTCTATTT	    0.781876	-144
TTCATATATGTTGAACTATTTATAAATATGT	1	122	1	TGAACTATTT	    0.969488	-120
AAGTTTAAGTAGAAACTTTTTTATATAGGTG	1	165	0	AAAACTTTTT	    0.692045	-77
TAAACTTCATACATAGTATTTATAAATGAAA	1	189	1	AATAGTATTT	     0.75075	-53
ATTATGTTAGTTGATGATTTTCATTTATAAA	1	207	0	TGATGATTTT	    0.840367	-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

TATTATTAGCTTTACCAATATAAAGCTTTT	1	71	1	TTTACCAATA	    0.973035	-171
ATAAAGCTTTTCTACCAAAAATAGAACTTT	1	90	1	TCTACCAAAA	    0.975522	-152
TATAAATAGTTCAACATATATGAATAAAAG	1	116	0	TCAACATATA	    0.929067	-126
TGCTCACATATTTATAAATAGTTCAACATA	1	128	0	TTTATAAATA	    0.894018	-114
TAAAAAAGTTTCTACTTAAACTTCATACAT	1	173	1	TCTACTTAAA	    0.915275	-69
ATGATTTTCATTTATAAATACTATGTATGA	1	195	0	TTTATAAATA	    0.894018	-47
ATGAAAATCATCAACTAACATAATGTCCAT	1	214	1	TCAACTAACA	    0.904577	-28
          **********

Masking position 4
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

GAATAAAAGTTCTATTTTTGGTAGAAAAGC	1	95	0	TCTATTTTTG	    0.823415	-147
TAAATAGTTCAACATATATGAATAAAAGTT	1	114	0	AACATATATG	     0.71061	-128
ACTATTTATAAATATGTGAGCAAGACACAC	1	136	1	AATATGTGAG	    0.977277	-106
AACTTTTTTATATAGGTGTGTGTCTTGCTC	1	153	0	TATAGGTGTG	    0.929966	-89
ATTTATAAATACTATGTATGAAGTTTAAGT	1	186	0	ACTATGTATG	    0.975129	-56
TCACATGGACATTATGTTAGTTGATGATTT	1	218	0	ATTATGTTAG	    0.883533	-24
TAACATAATGTCCATGTGAGACG       	1	229	1	TCCATGTGAG	    0.972282	-13
          **********

Masking position 4
Map Score:   2.73354

Number of sites scoring better than the average of aligned sites = 337
Number in coding regions = 292
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


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


Motif number 7

          **********

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