AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00430_mjan_reg_300.orf -o00430_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	MJ0050	109	group II decarboxylase

Motif number 1

AACATTTATTTGAGGTTTAATT        	1	3	0	TGAGGTTTAA	    0.979079	-107
CAAATAAATGTTTAGTATATTGTATTATAT	1	21	1	TTTAGTATAT	    0.974496	-89
TTTAGTATATTGTATTATATTTATACCTAA	1	31	1	TGTATTATAT	    0.940213	-79
TAATGCGTTCTTAGGTATAAATATAATACA	1	41	0	TTAGGTATAA	    0.961165	-69
AACATCATGATTAAATTTATAAGTATTTAA	1	68	0	TTAAATTTAT	    0.743976	-42
AATTTAATCATGATGTTTATCAACTAAAAA	1	81	1	TGATGTTTAT	    0.976294	-29
       CCTTTAATTTTTTTAGTTGATAA	1	97	0	TTAATTTTTT	    0.888931	-13
          **********

Masking position 6
Map Score:   7.75489

Number of sites scoring better than the average of aligned sites = 1278
Number in coding regions = 1035
Number in noncoding regions = 243
Number of orfs with sites within 600 bp upstream = 222
Fraction of orfs with sites within 600 bp upstream = 0.0356569


Motif number 2

ATACTAAACATTTATTTGAGGTTTAATT  	1	9	0	TTTATTTGAG	    0.967106	-101
CAAATAAATGTTTAGTATATTGTATTATAT	1	21	1	TTTAGTATAT	    0.977301	-89
TTTAGTATATTGTATTATATTTATACCTAA	1	31	1	TGTATTATAT	    0.970766	-79
TAAATTTATAAGTATTTAATGCGTTCTTAG	1	57	0	AGTATTTAAT	     0.85227	-53
AACATCATGATTAAATTTATAAGTATTTAA	1	68	0	TTAAATTTAT	    0.804002	-42
CTTTAATTTTTTTAGTTGATAAACATCATG	1	89	0	TTTAGTTGAT	    0.988172	-21
          **********

Masking position 6
Map Score:   4.65994

Number of sites scoring better than the average of aligned sites = 1087
Number in coding regions = 851
Number in noncoding regions = 236
Number of orfs with sites within 600 bp upstream = 222
Fraction of orfs with sites within 600 bp upstream = 0.0356569


Motif number 3

          **********

No masking
Map Score:   1.16119e-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:   1.16119e-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:   1.16119e-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