AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i096_Nitrogen_Transport_mjan_reg_100.orf -o096_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	RMJ02835	287	M_jannaschii_chromosome

Motif number 1

ATTGATGTTTTCTTTTTTATGTGGGCAGCA	1	26	0	TCTTTTTTAT	    0.919672	-262
GTAGGTAAGATAATTCCTATAAAAGTGTTT	1	77	0	TAATTCCTAT	    0.955497	-211
CCTACTACCCATCTTCCTAATTCCCCTAAT	1	102	1	ATCTTCCTAA	    0.788099	-186
GAAGGAAAATTCTTTCCTTAGTAAGTTATA	1	147	0	TCTTTCCTTA	    0.946434	-141
GAAAGAATTTTCCTTCCTATTATTTAGGAA	1	161	1	TCCTTCCTAT	    0.991384	-127
AAAAGATTCTTTATTCCTAAATAATAGGAA	1	174	0	TTATTCCTAA	    0.966025	-114
TAAAGAATCTTTTTTCCTTTTAGATAAAAA	1	191	1	TTTTTCCTTT	    0.929408	-97
TTGGTAGTAATCATTTTTATTTTTATCTAA	1	210	0	TCATTTTTAT	    0.937137	-78
AATCTCAACCTCATTTTTATAATTTTACAA	1	268	0	TCATTTTTAT	    0.937137	-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

ATATTAACGATGCTGCCCACATAAAAAAGAAA	1	16	1	TGCTGCCCAT	    0.982681	-272
AAAACATCAATACCATCCATATGTTTCACCTC	1	45	1	TACCATCCAT	    0.983014	-243
TTATCTTACCTACTACCCATCTTCCTAATTCC	1	94	1	TACTACCCAT	    0.996435	-194
TAAAAATGATTACTACCAAATTCAAATTAATC	1	221	1	TACTACCAAT	    0.992009	-67
TTAATCTAAAAACCACCAAATTTGTAAAATTA	1	247	1	AACCACCAAT	    0.976041	-41
          *********  *

Masking position 9
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	    0.928983	-249
TCCTATAAAAGTGTTTGAGGTGAAACATAT	1	63	0	GTGTTTGAGG	    0.978227	-225
TTAGGAAGATGGGTAGTAGGTAAGATAATT	1	92	0	GGGTAGTAGG	    0.969164	-196
TTTCCATTAGGGGAATTAGGAAGATGGGTA	1	107	0	GGGAATTAGG	    0.988494	-181
TTTCCTTCCTATTATTTAGGAATAAAGAAT	1	169	1	ATTATTTAGG	    0.842058	-119
CAAATTTGGTGGTTTTTAGATTAATTTGAA	1	241	0	GGTTTTTAGA	      0.9404	-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

          GAAAAATATTAACGATGCTG	1	1	1	GAAAAATATT	    0.956602	-287
TGGAAAAGCTTAAATATATAACTTACTAAG	1	131	1	TAAATATATA	    0.852311	-157
TAATAGGAAGGAAAATTCTTTCCTTAGTAA	1	153	0	GAAAATTCTT	    0.889452	-135
TCCTTTTAGATAAAAATAAAAATGATTACT	1	205	1	TAAAAATAAA	     0.93358	-83
ACTACCAAATTCAAATTAATCTAAAAACCA	1	232	1	TCAAATTAAT	     0.83936	-56
ACCAAATTTGTAAAATTATAAAAATGAGGT	1	261	1	TAAAATTATA	    0.900076	-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