AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i173_1_17_4_2_mjan_reg_100.orf -o173_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	RMJ00919	259	M_jannaschii_chromosome

Motif number 1

        AAATATAAATTAATCCTTATCAAT	1	3	1	ATATAAAAAT	    0.918306	-257
CCTTATCAATATTTCAACATAATAAATCAATA	1	25	1	ATTTCAATAA	    0.935218	-235
TCAACATAATAAATCAATATAAATTGCTCTTT	1	38	1	AAATCAATAA	    0.905386	-222
CTCTTTAGTTAAATAAAGGGATTCTTCCATTT	1	64	1	AAATAAAGAT	     0.97077	-196
TTAAAATAGTATATAAATGGAAGAATCCCTTT	1	78	0	ATATAAAGAA	    0.986548	-182
TTTATATACTATTTTAAAAGATTATCGCACTT	1	93	1	ATTTTAAGAT	    0.948103	-167
TATTTAAAATATTTAAGCGGAAATCCATTCCG	1	124	1	ATTTAAGGAA	    0.912651	-136
CAGTAATAACATATAAACCTAACGGAATGGAT	1	146	0	ATATAAATAA	    0.973911	-114
TTATTTGTAGATTTTAATGGATGACTTTATTA	1	207	0	ATTTTAAGAT	    0.948281	-53
AAATAGTAAAAAATAAAATTATTTGTAGATTT	1	225	0	AAATAAATAT	    0.944137	-35
          *******  ***

Masking position 6
Map Score:   11.9424

Number of sites scoring better than the average of aligned sites = 1117
Number in coding regions = 855
Number in noncoding regions = 262
Number of orfs with sites within 600 bp upstream = 223
Fraction of orfs with sites within 600 bp upstream = 0.0358175


Motif number 2

CAATATTTCAACATAATAAATCAATATAAA	1	31	1	ACATAATAAA	    0.955901	-229
TAATCTTTTAAAATAGTATATAAATGGAAG	1	87	0	AAATAGTATA	    0.957668	-173
CACTTATTTAAAATATTTAAGCGGAAATCC	1	120	1	AAATATTTAA	      0.8924	-140
GTTATTACTGAAAAACTAAATACACATTCC	1	168	1	AAAAACTAAA	     0.92477	-92
TTCCTAAGATAAGTAATAAAGTCATCCATT	1	194	1	AAGTAATAAA	    0.955901	-66
ATCACCCAAAAAATAGTAAAAAATAAAATT	1	237	0	AAATAGTAAA	    0.989212	-23
          **********

Masking position 5
Map Score:   4.81482

Number of sites scoring better than the average of aligned sites = 519
Number in coding regions = 335
Number in noncoding regions = 184
Number of orfs with sites within 600 bp upstream = 175
Fraction of orfs with sites within 600 bp upstream = 0.0281079


Motif number 3

  AAATATAAATTAATCCTTATCAATATTT	1	9	1	ATTAATCCTT	    0.958813	-251
TTTCAACATAATAAATCAATATAAATTGCT	1	36	1	ATAAATCAAT	    0.901223	-224
AAATAAAGGGATTCTTCCATTTATATACTA	1	74	1	ATTCTTCCAT	    0.961861	-186
ATATTTAAGCGGAAATCCATTCCGTTAGGT	1	132	1	GGAAATCCAT	    0.963336	-128
TAAGTAATAAAGTCATCCATTAAAATCTAC	1	203	1	AGTCATCCAT	      0.9887	-57
          **********

Masking position 6
Map Score:   2.4373

Number of sites scoring better than the average of aligned sites = 228
Number in coding regions = 200
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 4

          **********

No masking
Map Score:   -3.81261e-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:   -3.81261e-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:   -3.81261e-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