AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i004_4_1_1_21_mjan_reg_300.orf -o004_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	RMJ15216	108	M_jannaschii_chromosome

Motif number 1

ATCCCTCCTGATATTTTATAGCTTACTCTATAA	1	14	1	AATTTTAACT	    0.966592	-95
AATCAAAACCATAATTTATTTATAATTAGTTTT	1	45	1	AAATTTATAT	    0.844058	-64
TTTATGTAAGAGATTTTAAAACTAATTATAAAT	1	62	0	AATTTTAACT	    0.607259	-47
CTCTTACATAAAAATTTAGACCTTTTTGGTGAA	1	83	1	AAATTTAACT	    0.994109	-26
          * ****** * **

Masking position 7
Map Score:   5.02632

Number of sites scoring better than the average of aligned sites = 77
Number in coding regions = 59
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 2

ATTATAGAGTAAGCTATAAAATATCAGGAG	1	18	0	AAGCTATAAA	    0.958763	-91
TTTATAGCTTACTCTATAATCAAAACCATA	1	28	1	ACTCTATAAT	    0.960818	-81
TCTATAATCAAAACCATAATTTATTTATAA	1	40	1	AAACCATAAT	     0.98237	-69
ATTTTAAAACTAATTATAAATAAATTATGG	1	53	0	TAATTATAAA	    0.903324	-56
AAAATCTCTTACATAAAAATTTAGACCTTT	1	78	1	ACATAAAAAT	    0.853295	-31
      CTTTTCACCAAAAAGGTCTAAATT	1	95	0	TCACCAAAAA	    0.961785	-14
          **********

Masking position 6
Map Score:   2.68583

Number of sites scoring better than the average of aligned sites = 1593
Number in coding regions = 1267
Number in noncoding regions = 326
Number of orfs with sites within 600 bp upstream = 314
Fraction of orfs with sites within 600 bp upstream = 0.0504337


Motif number 3

          **********

No masking
Map Score:   1.37435e-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 4

          **********

No masking
Map Score:   1.37435e-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:   1.37435e-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