AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i286_hypothetical_lipid_degradation_mjan_reg_100.orf -o286_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	RMJ12041	189	M_jannaschii_chromosome

Motif number 1

AAAGTCCTATCTACATAATGCTTATGGGGTGGAAA	1	13	0	CTATAACTAT	    0.992379	-177
AGAAGATAAGCTGCGAAAGTCCTATCTACATAATG	1	28	0	CTGAAACTAT	    0.995247	-162
AATTTAGACACTCAAAAGTGTCAATATGCAATAAA	1	69	1	CTAAAGTAAT	    0.906289	-121
TGTCAATATGCAATAAAACATTTATTCCTGCGAAA	1	87	1	CAAAAATTAT	    0.985041	-103
ACATTTATTCCTGCGAAAGTCCTATAGTAAGAGAT	1	104	1	CTGAAACTAT	    0.995247	-86
TTTATTAAGGCATTAAAATATATATCTCTTACTAT	1	127	0	CAAAAATTAT	    0.985016	-63
ATTTTAATGCCTTAATAAAACTTATTGTAAGCATG	1	143	1	CTATAACTAT	    0.992683	-47
          **  ****  * ***

Masking position 7
Map Score:   9.94516

Number of sites scoring better than the average of aligned sites = 239
Number in coding regions = 182
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 2

AGCTTATCTTCTTACTGGAATTTAGACACT	1	51	1	CTTACTGGAA	    0.971808	-139
TGTTTTATTGCATATTGACACTTTTGAGTG	1	77	0	CATATTGACA	    0.935476	-113
CTGCGAAAGTCCTATAGTAAGAGATATATA	1	114	1	CCTATAGTAA	    0.956486	-76
ATTTTAATGCCTTAATAAAACTTATTGTAA	1	143	1	CTTAATAAAA	    0.930422	-47
CTTAATAAAACTTATTGTAAGCATGGTTTT	1	153	1	CTTATTGTAA	    0.989132	-37
AACCTCCCCCCTTATAAAAACCATGCTTAC	1	169	0	CTTATAAAAA	    0.959166	-21
          **********

Masking position 4
Map Score:   4.33206

Number of sites scoring better than the average of aligned sites = 295
Number in coding regions = 253
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 3

          **********

No masking
Map Score:   -3.24418e-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:   -3.24418e-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:   -3.24418e-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