AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -intrC_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

TTGATGGTAAAAAGAAAGCGAAAGCCTAAG	1	18	1	AAAGAAAGCG	      0.9175	-238
AATATTACGCGAATTAAGCTTAGGCTTTCG	1	36	0	GAATTAAGCT	    0.915883	-220
AAAGATTGTTAAAACAATCTGGATAGTTAA	1	66	0	AAAACAATCT	    0.837657	-190
AAAAAGATCATACTAAAGATTGTTAAAACA	1	80	0	TACTAAAGAT	    0.827597	-176
AGCAAAGTAAGAAAAAAGATCATACTAAAG	1	92	0	GAAAAAAGAT	    0.964015	-164
TGCAAACTCAAAAACAAGATTAAAGATAGC	1	119	0	AAAACAAGAT	    0.964014	-137
TTCTGTTTTCAACTAAAGCTGTAGCTAAAT	1	154	0	AACTAAAGCT	    0.978089	-102
TTGAAAACAGAAATAAAGCTGTGGAACTTG	1	172	1	AAATAAAGCT	    0.989319	-84
CAGTTCTTTTAAAAAAAGACAATGTTATCT	1	203	0	AAAAAAAGAC	    0.926282	-53
          **********

Masking position 6
Map Score:   9.54382

Number of sites scoring better than the average of aligned sites = 583
Number in coding regions = 529
Number in noncoding regions = 54
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 2

TTCGCTTTCTTTTTACCATCAAATATTAA 	1	10	0	TTTTACCATC	    0.975463	-246
AAGCTTAGGCTTTCGCTTTCTTTTTACCAT	1	21	0	TTTCGCTTTC	    0.908821	-235
CGCGTAATATTTTAACTATCCAGATTGTTT	1	55	1	TTTAACTATC	    0.985428	-201
TCCAGATTGTTTTAACAATCTTTAGTATGA	1	73	1	TTTAACAATC	    0.985428	-183
TTTTTTCTTACTTTGCTATCTTTAATCTTG	1	105	1	CTTTGCTATC	    0.981079	-151
AGCTAAATTACTTTGCAAACTCAAAAACAA	1	132	0	CTTTGCAAAC	    0.896724	-124
CAGAGACAAATTTAAAAATCAGTTCTTTTA	1	222	0	TTTAAAAATC	    0.897873	-34
          **********

Masking position 3
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

AGAAAGCGAAAGCCTAAGCTTAATTCGCGT	1	30	1	AGCCTAAGCT	    0.570568	-226
AAAGTAATTTAGCTACAGCTTTAGTTGAAA	1	148	1	AGCTACAGCT	    0.611202	-108
TATCTACAAGTTCCACAGCTTTATTTCTGT	1	178	0	TTCCACAGCT	    0.987096	-78
          **********

Masking position 7
Map Score:   0.106154

Number of sites scoring better than the average of aligned sites = 9
Number in coding regions = 5
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


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