AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -irpoN_mgen_opreg_100.orf -g0.317 -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 =  	0.317
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	MG064	255	conserved hypothetical protein

Motif number 1

CGAAAGCCTAAGCTTAATTCGCGTAATATT	1	36	1	AGCTTAATTC	    0.978881	-220
TGTTTTAACAATCTTTAGTATGATCTTTTT	1	80	1	ATCTTTAGTA	    0.959877	-176
CTTTAGTATGATCTTTTTTCTTACTTTGCT	1	92	1	ATCTTTTTTC	    0.967227	-164
TTACTTTGCTATCTTTAATCTTGTTTTTGA	1	112	1	ATCTTTAATC	    0.952094	-144
CTAAAGCTGTAGCTAAATTACTTTGCAAAC	1	142	0	AGCTAAATTA	    0.788218	-114
ATTTAGCTACAGCTTTAGTTGAAAACAGAA	1	154	1	AGCTTTAGTT	    0.976163	-102
CAAGTTCCACAGCTTTATTTCTGTTTTCAA	1	172	0	AGCTTTATTT	    0.987714	-84
AGATAACATTGTCTTTTTTTAAAAGAACTG	1	203	1	GTCTTTTTTT	     0.83292	-53
          **********

Masking position 4
Map Score:   9.49278

Number of sites scoring better than the average of aligned sites = 313
Number in coding regions = 282
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 2

 TTAATATTTGATGGTAAAAAGAAAGCGAA	1	10	1	GATGGTAAAA	    0.978432	-246
ATGGTAAAAAGAAAGCGAAAGCCTAAGCTT	1	21	1	GAAAGCGAAA	     0.91919	-235
AAACAATCTGGATAGTTAAAATATTACGCG	1	55	0	GATAGTTAAA	    0.987199	-201
TCATACTAAAGATTGTTAAAACAATCTGGA	1	73	0	GATTGTTAAA	    0.987199	-183
CAAGATTAAAGATAGCAAAGTAAGAAAAAA	1	105	0	GATAGCAAAG	    0.983094	-151
TTGTTTTTGAGTTTGCAAAGTAATTTAGCT	1	132	1	GTTTGCAAAG	    0.902661	-124
TAAAAGAACTGATTTTTAAATTTGTCTCTG	1	222	1	GATTTTTAAA	    0.909364	-34
          **********

Masking position 8
Map Score:   7.37595

Number of sites scoring better than the average of aligned sites = 155
Number in coding regions = 138
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

TACTAAAGATTGTTAAAACAATCTGGATAGT	1	69	0	TGTAAAACAA	    0.913284	-187
AAGATAGCAAAGTAAGAAAAAAGATCATACT	1	96	0	AGTAGAAAAA	    0.967835	-160
TACTTTGCAAACTCAAAAACAAGATTAAAGA	1	123	0	ACTAAAAACA	    0.954899	-133
CTACAGCTTTAGTTGAAAACAGAAATAAAGC	1	160	1	AGTGAAAACA	    0.983676	-96
CTGTGGAACTTGTAGATAACATTGTCTTTTT	1	190	1	TGTGATAACA	    0.899475	-66
AAATCAGTTCTTTTAAAAAAAGACAATGTTA	1	206	0	TTTAAAAAAA	    0.838515	-50
CTAATAAATTAGTCAGAGACAAATTTAAAAA	1	234	0	AGTAGAGACA	    0.949706	-22
          *** *******

Masking position 11
Map Score:   2.41292

Number of sites scoring better than the average of aligned sites = 419
Number in coding regions = 381
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 4

          **********

No masking
Map Score:   -2.59896e-14

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:   -2.59896e-14

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:   -2.59896e-14

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