AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -idnaA_mjan_opreg_100.orf -g0.314 -x5 
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 =  	0.314
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	MJ1328	300	modification methylase, type II R/M system

Motif number 1

AAAAGATTTATTGATTTTATAA          	1	1	0	TTATTTATAA	    0.927058	-300
ATAAAATCAATAAATCTTTTAAAAGATGGTGG	1	13	1	TAATTTTTAA	    0.956833	-288
TTGTTCCATATCACTTTTTTTATAACACATAT	1	59	1	TCCTTTTTTA	    0.959241	-242
ATGTTGTCTCTTACAATTTTTGCATATGTGTT	1	82	0	TTCATTTTTG	     0.85861	-219
TTTCCAATTTTCCATGTTTTAGAATGTTGTCT	1	105	0	TCATTTTTAG	    0.943357	-196
GTTTCAGGATTTTCATTTTTAAATAGCCTAAC	1	157	0	TTCATTTTAA	    0.927488	-144
TTTTTAAACTTAAATATTATTGTTTCAGGATT	1	178	0	TAATTTATTG	    0.837633	-123
TGGTTAAATTCTCCTTTTTTAAACTTAAATAT	1	193	0	CTCTTTTTAA	    0.907602	-108
TCTGAAAAAATTGATGTTATTAGAATTATCTC	1	229	1	TTATTTATTA	    0.902273	-72
TCTTTTAATTTAACTTTTTTTGAGATAATTCT	1	250	0	TACTTTTTTG	    0.958928	-51
CTTTTTCTTTTATCTCTTTTAATTTAACTTTT	1	264	0	TACTTTTTAA	     0.97505	-37
GAAAAAGCTATTAATGTGTTAA          	1	289	1	TTATTGTTAA	    0.859256	-12
          ** ** ******

Masking position 7
Map Score:   13.8658

Number of sites scoring better than the average of aligned sites = 2101
Number in coding regions = 1654
Number in noncoding regions = 447
Number of orfs with sites within 600 bp upstream = 346
Fraction of orfs with sites within 600 bp upstream = 0.0555734


Motif number 2

CTTTTAAAAGATTTATTGATTTTATAA   	1	8	0	ATTTATTGAT	     0.93898	-293
GTTGATTTATATTGTTCCATATCACTTTTT	1	48	1	ATTGTTCCAT	    0.962632	-253
GTCTCTTACAATTTTTGCATATGTGTTATA	1	79	0	ATTTTTGCAT	    0.961603	-222
AATTATTTCCAATTTTCCATGTTTTAGAAT	1	112	0	AATTTTCCAT	    0.944051	-189
AATTGGAAATAATTATTGATTTGGATGAAG	1	128	1	AATTATTGAT	    0.849449	-173
CTTAAATATTATTGTTTCAGGATTTTCATT	1	172	0	ATTGTTTCAG	     0.97437	-129
AATAACATCAATTTTTTCAGATTTGTGGTT	1	220	0	ATTTTTTCAG	    0.985324	-81
TTAATTTAACTTTTTTTGAGATAATTCTAA	1	248	0	TTTTTTTGAG	    0.880886	-53
          **********

Masking position 9
Map Score:   8.88428

Number of sites scoring better than the average of aligned sites = 735
Number in coding regions = 643
Number in noncoding regions = 92
Number of orfs with sites within 600 bp upstream = 85
Fraction of orfs with sites within 600 bp upstream = 0.0136524


Motif number 3

AAAAGATGGTGGAGAGTTGATTTATATTGT	1	33	1	GGAGAGTTGA	    0.981592	-268
ATGTGTTATAAAAAAAGTGATATGGAACAA	1	59	0	AAAAAAGTGA	     0.91983	-242
TCTAAAACATGGAAAATTGGAAATAATTAT	1	114	1	GGAAAATTGG	    0.965948	-187
GTTTAAAAAAGGAGAATTTAACCACAAATC	1	201	1	GGAGAATTTA	    0.924954	-100
CACAAATCTGAAAAAATTGATGTTATTAGA	1	223	1	AAAAAATTGA	    0.969105	-78
ATTATCTCAAAAAAAGTTAAATTAAAAGAG	1	253	1	AAAAAGTTAA	    0.832906	-48
          **********

Masking position 5
Map Score:   1.8199

Number of sites scoring better than the average of aligned sites = 619
Number in coding regions = 557
Number in noncoding regions = 62
Number of orfs with sites within 600 bp upstream = 55
Fraction of orfs with sites within 600 bp upstream = 0.00883392


Motif number 4

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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