AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i301_mixed16_mjan_reg_300.orf -o301_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	RMJ12630	135	M_jannaschii_chromosome

Motif number 1

GAATTTTAATAACTTTTGCAAAAAACTAAA	1	26	0	AACTTTTGCA	    0.992277	-110
ATTCATAATGAAAAATTGAACGCCTTCCCA	1	52	1	AAAAATTGAA	    0.954076	-84
GTACATAAGGAACTTATGAACGCCTTCCTT	1	82	0	AACTTATGAA	    0.985291	-54
TTTTTTGCAAAACATTTGAAGTACATAAGG	1	102	0	AACATTTGAA	    0.990475	-34
TTTTGCAAAAAACTATTGGTGATATT    	1	120	1	AACTATTGGT	    0.955412	-16
          **********

Masking position 7
Map Score:   6.44562

Number of sites scoring better than the average of aligned sites = 378
Number in coding regions = 343
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 2

CCTTCCTTTGGGAAGGCGTTCAATTTTTCA	1	60	0	GGAAGGCGTT	     0.99954	-76
CCTTCCCAAAGGAAGGCGTTCATAAGTTCC	1	74	1	GGAAGGCGTT	     0.99954	-62
          **********

Masking position 4
Map Score:   4.48877

Number of sites scoring better than the average of aligned sites = 19
Number in coding regions = 2
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 3

ACCTTAATTTAGTTTTTTGCAAAAGTTATT	1	19	1	AGTTTTTTGC	    0.998234	-117
TATCACCAATAGTTTTTTGCAAAACATTTG	1	114	0	AGTTTTTTGC	    0.998234	-22
          **********

Masking position 5
Map Score:   3.30835

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

GTTATTAAAATTCATAATGAAAAATTGAAC	1	43	1	TTCATAATGA	     0.97349	-93
TTGAACGCCTTCCCAAAGGAAGGCGTTCAT	1	67	1	TCCCAAAGGA	    0.805146	-69
ACATTTGAAGTACATAAGGAACTTATGAAC	1	91	0	TACATAAGGA	    0.856164	-45
          **********

Masking position 6
Map Score:   1.16665

Number of sites scoring better than the average of aligned sites = 94
Number in coding regions = 86
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 5

          **********

No masking
Map Score:   -1.11255e-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:   -1.11255e-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:   -1.11255e-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