AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -idnaA_mjan_opreg_300.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

TATAAAATCAATAAATCTTTTAAAAGATGGT	1	12	1	ATAATCTTTT	    0.878213	-289
GAGAGTTGATTTATATTGTTCCATATCACTT	1	44	1	TTAATTGTTC	    0.850376	-257
ATTGTTCCATATCACTTTTTTTATAACACAT	1	58	1	ATCCTTTTTT	    0.968979	-243
ATGTTGTCTCTTACAATTTTTGCATATGTGT	1	83	0	TTAAATTTTT	    0.959478	-218
CAATAATTATTTCCAATTTTCCATGTTTTAG	1	115	0	TTCAATTTTC	    0.948066	-186
TGTTTCAGGATTTTCATTTTTAAATAGCCTA	1	159	0	TTTCATTTTT	    0.871891	-142
TGTGGTTAAATTCTCCTTTTTTAAACTTAAA	1	196	0	TTCCCTTTTT	    0.941175	-105
TTCTAATAACATCAATTTTTTCAGATTTGTG	1	223	0	ATCATTTTTT	    0.951064	-78
ATTGATGTTATTAGAATTATCTCAAAAAAAG	1	238	1	TTAAATTATC	    0.693339	-63
CTCTTTTAATTTAACTTTTTTTGAGATAATT	1	252	0	TTACTTTTTT	    0.984704	-49
GCTTTTTCTTTTATCTCTTTTAATTTAACTT	1	266	0	TTACTCTTTT	    0.957125	-35
TAACACATTAATAGCTTTTTCTTTTATCTCT	1	279	0	ATACTTTTTC	    0.964891	-22
          *** *******

Masking position 2
Map Score:   14.7342

Number of sites scoring better than the average of aligned sites = 2271
Number in coding regions = 1848
Number in noncoding regions = 423
Number of orfs with sites within 600 bp upstream = 336
Fraction of orfs with sites within 600 bp upstream = 0.0539672


Motif number 2

AAAAAAGTGATATGGAACAATATAAATCAAC	1	48	0	TATGAACAAT	    0.991174	-253
TTATAACACATATGCAAAAATTGTAAGAGAC	1	78	1	TATGAAAAAT	    0.992684	-223
CATTCTAAAACATGGAAAATTGGAAATAATT	1	111	1	CATGAAAATT	    0.965194	-190
GAAGTTAGGCTATTTAAAAATGAAAATCCTG	1	154	1	TATTAAAAAT	    0.954478	-147
AAATGAAAATCCTGAAACAATAATATTTAAG	1	171	1	CCTGAACAAT	    0.987231	-130
TAACCACAAATCTGAAAAAATTGATGTTATT	1	219	1	TCTGAAAAAT	    0.991191	-82
          **** ******

Masking position 6
Map Score:   9.06338

Number of sites scoring better than the average of aligned sites = 158
Number in coding regions = 137
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

ACTCTCCACCATCTTTTAAAAGATTTATTG	1	20	0	ATCTTTTAAA	    0.952889	-281
TTCCATATCACTTTTTTTATAACACATATG	1	62	1	CTTTTTTTAT	    0.944213	-239
CCAATTTTCCATGTTTTAGAATGTTGTCTC	1	104	0	ATGTTTTAGA	    0.880891	-197
TCAGGATTTTCATTTTTAAATAGCCTAACT	1	156	0	CATTTTTAAA	    0.948894	-145
TTAAATTCTCCTTTTTTAAACTTAAATATT	1	192	0	CTTTTTTAAA	    0.988942	-109
TTTAATTTAACTTTTTTTGAGATAATTCTA	1	249	0	CTTTTTTTGA	    0.963209	-52
TTTCTTTTATCTCTTTTAATTTAACTTTTT	1	263	0	CTCTTTTAAT	    0.969929	-38
          **********

Masking position 5
Map Score:   8.16539

Number of sites scoring better than the average of aligned sites = 1177
Number in coding regions = 1014
Number in noncoding regions = 163
Number of orfs with sites within 600 bp upstream = 147
Fraction of orfs with sites within 600 bp upstream = 0.0236107


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