AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -iphoB_mgen_opreg_300.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	MG289	300	high affinity transport system protein P37

Motif number 1

 AAGTTACAAACGAAATTGAATTTGTTTAAAACT	1	10	1	AAATTGAATT	    0.997427	-291
GAGTTAGAATATAATGTTAAATTTTCCCTGTCTG	1	48	0	AATTTAAATT	    0.912564	-253
AATTCAAAAAAGTAATTCGGATCTTAAAAAATAT	1	111	1	AAATCGGATT	    0.973475	-190
ATTAATTGCCAGCAACTTGAATCTAAGTAATAAA	1	157	1	AAATTGAATT	    0.997426	-144
GAATCTAAGTAATAAAGTGAATATTTATTTTTAT	1	175	1	AAAGTGAATT	    0.991685	-126
AAAATAGACTACAAATTTGAATATAAGTTTTTAA	1	208	0	AAATTGAATT	    0.997425	-93
AACTAATATAAAAAAGTTGAATATTTAAAAACAA	1	243	1	AAATTGAATT	    0.997426	-58
          *  ** ****** *

Masking position 4
Map Score:   14.3838

Number of sites scoring better than the average of aligned sites = 20
Number in coding regions = 13
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

TTCAATTTCGTTTGTAACTT          	1	1	0	TTTGTAACTT	     0.84206	-300
TCTGTTTTAGTTTTAAACAAATTCAATTTC	1	22	0	TTTTAAACAA	    0.931388	-279
CGAATTACTTTTTTGAATTAAAGCTATTCT	1	100	0	TTTTGAATTA	    0.922962	-201
TAAAAAATATTTTTTAAGATCCGAATTACT	1	121	0	TTTTTAAGAT	    0.930137	-180
TAAAAAATATTTTTTAATAAAGATTAATTG	1	135	1	TTTTTAATAA	    0.750189	-166
TGAATATAAGTTTTTAATAAAAATAAATAT	1	195	0	TTTTTAATAA	    0.750189	-106
TTGTAGTCTATTTTTAACTAATATAAAAAA	1	228	1	TTTTTAACTA	    0.970816	-73
AATATTCAACTTTTTTATATTAGTTAAAAA	1	238	0	TTTTTTATAT	    0.860852	-63
AATTAATTGTTTTTAAATATTCAACTTTTT	1	253	0	TTTTAAATAT	    0.932999	-48
TAATCCTGGATTATTAATTATCAAAATTAA	1	277	0	TTATTAATTA	    0.713291	-24
          **********

Masking position 7
Map Score:   14.6372

Number of sites scoring better than the average of aligned sites = 673
Number in coding regions = 586
Number in noncoding regions = 87
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 3

TGAATTTGTTTAAAACTAAAACAGACAGGG	1	27	1	TAAAACTAAA	    0.958882	-274
TCTGAATAGCAAAAAATATAAGAATAGCTT	1	80	1	AAAAAATATA	    0.945935	-221
TTTTTTGAATTAAAGCTATTCTTATATTTT	1	92	0	TAAAGCTATT	    0.823522	-209
CTTTAATTCAAAAAAGTAATTCGGATCTTA	1	107	1	AAAAAGTAAT	    0.797411	-194
TTCGGATCTTAAAAAATATTTTTTAATAAA	1	126	1	AAAAAATATT	      0.9231	-175
TATTTTTTAATAAAGATTAATTGCCAGCAA	1	142	1	TAAAGATTAA	    0.846368	-159
AAGTTTTTAATAAAAATAAATATTCACTTT	1	188	0	TAAAAATAAA	    0.979542	-113
TTATTTTTATTAAAAACTTATATTCAAATT	1	199	1	TAAAAACTTA	    0.822543	-102
TTATATTAGTTAAAAATAGACTACAAATTT	1	224	0	TAAAAATAGA	    0.945991	-77
GTTGAATATTTAAAAACAATTAATTTTGAT	1	258	1	TAAAAACAAT	    0.933655	-43
          **********

Masking position 4
Map Score:   9.61817

Number of sites scoring better than the average of aligned sites = 776
Number in coding regions = 663
Number in noncoding regions = 113
Number of orfs with sites within 600 bp upstream = 57
Fraction of orfs with sites within 600 bp upstream = 0.00915516


Motif number 4

AGTTTTAAACAAATTCAATTTCGTTTGTAA	1	14	0	AAATTCAATT	     0.97613	-287
TTTATTACTTAGATTCAAGTTGCTGGCAAT	1	161	0	AGATTCAAGT	     0.98097	-140
ATAAAAATAAATATTCACTTTATTACTTAG	1	179	0	ATATTCACTT	    0.979083	-122
TTAAAAACTTATATTCAAATTTGTAGTCTA	1	208	1	ATATTCAAAT	    0.982953	-93
TTGTTTTTAAATATTCAACTTTTTTATATT	1	247	0	ATATTCAACT	    0.988483	-54
          **********

Masking position 5
Map Score:   6.14826

Number of sites scoring better than the average of aligned sites = 29
Number in coding regions = 27
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


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


Motif number 7

          **********

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