AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i233_protein_modification____mjan_reg_300.orf -o233_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	RMJ13697	22	M_jannaschii_chromosome
#2	RMJ15370	178	M_jannaschii_chromosome

Motif number 1

AACACCCCCTTTATGAAAGCGTTCAAAATTCA	2	11	0	TTATAAAGGT	    0.979979	-168
TTTTAAAACATTTTGAAATACTAAGGACCAAT	2	44	0	TTTTAAATCT	    0.992625	-135
TTTCAAAATGTTTTAAAAGACTCTATAAAAAG	2	58	1	TTTTAAAGCT	    0.996415	-121
TTTTAGTATTATTTTAAATTCTTTTTATAGAG	2	78	0	ATTTAAATCT	    0.965447	-101
GTTGTGTAATTTATTAAATTCTATTTTAATTT	2	107	0	TTATAAATCT	    0.990418	-72
TGATTAAAATTATTCAAAGGCTTTACTAAAGG	2	145	1	TATTAAAGCT	    0.982967	-34
TTCAAAGGCTTTACTAAAGGTTAAGTGAGAAC	2	157	1	TTACAAAGTT	    0.910409	-22
          **** **** **

Masking position 6
Map Score:   11.1775

Number of sites scoring better than the average of aligned sites = 273
Number in coding regions = 237
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 2

AAAAGAATTTAAAATAATACTAAAATTAAA	2	85	1	AAAATAATAC	    0.976179	-94
AAATAATACTAAAATTAAAATAGAATTTAA	2	96	1	AAAATTAAAA	     0.93671	-83
TAGAATTTAATAAATTACACAACATTCATT	2	116	1	TAAATTACAC	    0.971825	-63
TTCATTGATTAAAATTATTCAAAGGCTTTA	2	140	1	AAAATTATTC	    0.976179	-39
          **********

Masking position 5
Map Score:   1.21663

Number of sites scoring better than the average of aligned sites = 157
Number in coding regions = 125
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 3

AAGACTCTATAAAAAGAATTTAAAATAATA	2	74	1	AAAAAGAATT	    0.986749	-105
ACTAAAATTAAAATAGAATTTAATAAATTA	2	103	1	AAATAGAATT	    0.970832	-76
          **********

Masking position 5
Map Score:   0.30181

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:   1.65857e-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:   1.65857e-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:   1.65857e-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