AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00472_mjan_reg_100.orf -o00472_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	MJ1146	66	glyceraldehyde 3-phosphate dehydrogenase
#2	MJ1530	178	ribosomal protein S18 alanine acetyltransferase

Motif number 1

TCCTACAAAAATTTCAAATGGTGAATCT    	1	49	1	ATTTAAATGT	    0.971787	-18
AACACCCCCTTTATGAAAGCGTTCAAAATTCA	2	11	0	TTATAAAGGT	    0.976523	-168
TTTTAAAACATTTTGAAATACTAAGGACCAAT	2	44	0	TTTTAAATCT	    0.994699	-135
TTTCAAAATGTTTTAAAAGACTCTATAAAAAG	2	58	1	TTTTAAAGCT	    0.995606	-121
TTTTAGTATTATTTTAAATTCTTTTTATAGAG	2	78	0	ATTTAAATCT	    0.987897	-101
GTTGTGTAATTTATTAAATTCTATTTTAATTT	2	107	0	TTATAAATCT	    0.987898	-72
TGATTAAAATTATTCAAAGGCTTTACTAAAGG	2	145	1	TATTAAAGCT	    0.979185	-34
          **** **** **

Masking position 6
Map Score:   13.1789

Number of sites scoring better than the average of aligned sites = 297
Number in coding regions = 250
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 2

TTGGCAATATATATTTTTATAAT       	1	4	0	ATATTTTTAT	     0.94588	-63
ATTGCCAAAGTAATTATTATTAATCCTACA	1	26	1	TAATTATTAT	    0.889921	-41
TCACCATTTGAAATTTTTGTAGGATTAATA	1	43	0	AAATTTTTGT	    0.965005	-24
TTATTTTAAATTCTTTTTATAGAGTCTTTT	2	72	0	TTCTTTTTAT	    0.940936	-107
AATTTTAGTATTATTTTAAATTCTTTTTAT	2	82	0	TTATTTTAAA	    0.834484	-97
AATTCTATTTTAATTTTAGTATTATTTTAA	2	93	0	TAATTTTAGT	    0.977895	-86
AGCCTTTGAATAATTTTAATCAATGAATGT	2	137	0	TAATTTTAAT	    0.978324	-42
GTTCTCACTTAACCTTTAGTAAAGCCTTTG	2	159	0	AACCTTTAGT	    0.805735	-20
          **********

Masking position 5
Map Score:   7.33654

Number of sites scoring better than the average of aligned sites = 1390
Number in coding regions = 901
Number in noncoding regions = 489
Number of orfs with sites within 600 bp upstream = 392
Fraction of orfs with sites within 600 bp upstream = 0.0629618


Motif number 3

          **********

No masking
Map Score:   3.64809e-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:   3.64809e-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:   3.64809e-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