AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -inagC_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	MG069	300	PTS system, glucose-specific IIABC component (ptsG)

Motif number 1

TAAAAGAGCATATGTTGTTTGCATGCAACA	1	12	0	TATGTTGTTT	    0.965423	-289
ATATGCTCTTTTAGTTGTTTTTGGAATTTT	1	29	1	TTAGTTGTTT	    0.995488	-272
TGGAATTTTATTAGTTCTAATTGGACTAGG	1	50	1	TTAGTTCTAA	    0.760756	-251
TGACCTTTCTTTTGTTCTTTAAGTGAAATT	1	101	0	TTTGTTCTTT	    0.976912	-200
AGTCAAATCATTAGTAATTTGACCTTTCTT	1	120	0	TTAGTAATTT	    0.904451	-181
ATAAAACTAATTTGTTGTTTCTTTTTCATC	1	190	0	TTTGTTGTTT	    0.990142	-111
AAACAACAAATTAGTTTTATTTTTGCTTGC	1	200	1	TTAGTTTTAT	    0.943806	-101
TTTGCTTGCAATAGTTTTTTTAATGCTAGG	1	221	1	ATAGTTTTTT	    0.894748	-80
TTTCCCTTCCTAAGCTGTTTGGTTAATAAA	1	265	1	TAAGCTGTTT	    0.927841	-36
TTAATAAAATTTAGTAGTTTTAAA      	1	287	1	TTAGTAGTTT	    0.983313	-14
          **********

Masking position 8
Map Score:   16.9949

Number of sites scoring better than the average of aligned sites = 421
Number in coding regions = 376
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 2

CAATTAGAACTAATAAAATTCCAAAAACAA	1	43	0	TAATAAAATT	     0.94065	-258
ATAAAAATCCTAGTCCAATTAGAACTAATA	1	58	0	TAGTCCAATT	    0.897739	-243
TTAAAGCTCAAAATAAAAATCCTAGTCCAA	1	70	0	AAATAAAAAT	    0.905197	-231
TTTGTTCTTTAAGTGAAATTTTTAAAGCTC	1	91	0	AAGTGAAATT	    0.978756	-210
AACAAAAGAAAGGTCAAATTACTAATGATT	1	115	1	AGGTCAAATT	    0.943656	-186
GAGTTATTGGAAGTCAAATCATTAGTAATT	1	131	0	AAGTCAAATC	    0.943655	-170
ACTCACTTAAAAATGAAGTTCCTAGAGGGA	1	157	1	AAATGAAGTT	    0.852923	-144
AAACTATTGCAAGCAAAAATAAAACTAATT	1	208	0	AAGCAAAAAT	    0.814244	-93
GCTGTTTGGTTAATAAAATTTAGTAGTTTT	1	278	1	TAATAAAATT	     0.94065	-23
          **********

Masking position 7
Map Score:   7.26547

Number of sites scoring better than the average of aligned sites = 353
Number in coding regions = 312
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 3

TATGTTGTTTGCATGCAACAT         	1	2	0	GCATGCAACA	    0.982607	-299
TAATGATTTGACTTCCAATAACTCACTTAA	1	137	1	ACTTCCAATA	     0.95721	-164
TTTTATTTTTGCTTGCAATAGTTTTTTTAA	1	214	1	GCTTGCAATA	     0.99153	-87
TTTTTTTAATGCTAGGAATAGGTGGACTTG	1	235	1	GCTAGGAATA	    0.973293	-66
          **********

Masking position 7
Map Score:   1.84858

Number of sites scoring better than the average of aligned sites = 26
Number in coding regions = 21
Number in noncoding regions = 5
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:   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