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

Motif number 1

TGTTGCATGCAAACAACATATGCTCTTTTA	1	12	1	AAACAACATA	    0.966398	-289
AAAATTCCAAAAACAACTAAAAGAGCATAT	1	29	0	AAACAACTAA	    0.995618	-272
CCTAGTCCAATTAGAACTAATAAAATTCCA	1	50	0	TTAGAACTAA	    0.764852	-251
AATTTCACTTAAAGAACAAAAGAAAGGTCA	1	101	1	AAAGAACAAA	    0.977569	-200
AAGAAAGGTCAAATTACTAATGATTTGACT	1	120	1	AAATTACTAA	    0.906944	-181
GATGAAAAAGAAACAACAAATTAGTTTTAT	1	190	1	AAACAACAAA	    0.990427	-111
GCAAGCAAAAATAAAACTAATTTGTTGTTT	1	200	0	ATAAAACTAA	    0.945353	-101
CCTAGCATTAAAAAAACTATTGCAAGCAAA	1	221	0	AAAAAACTAT	    0.897497	-80
TTTATTAACCAAACAGCTTAGGAAGGGAAA	1	265	0	AAACAGCTTA	    0.929799	-36
      TTTAAAACTACTAAATTTTATTAA	1	287	0	AAACTACTAA	     0.98375	-14
          **********

Masking position 3
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

TTGTTTTTGGAATTTTATTAGTTCTAATTG	1	43	1	AATTTTATTA	    0.948015	-258
TATTAGTTCTAATTGGACTAGGATTTTTAT	1	58	1	AATTGGACTA	      0.9099	-243
TTGGACTAGGATTTTTATTTTGAGCTTTAA	1	70	1	ATTTTTATTT	    0.916573	-231
GAGCTTTAAAAATTTCACTTAAAGAACAAA	1	91	1	AATTTCACTT	    0.981114	-210
AATCATTAGTAATTTGACCTTTCTTTTGTT	1	115	0	AATTTGACCT	    0.950668	-186
AATTACTAATGATTTGACTTCCAATAACTC	1	131	1	GATTTGACTT	    0.950666	-170
TCCCTCTAGGAACTTCATTTTTAAGTGAGT	1	157	0	AACTTCATTT	    0.869359	-144
AATTAGTTTTATTTTTGCTTGCAATAGTTT	1	208	1	ATTTTTGCTT	    0.834543	-93
AAAACTACTAAATTTTATTAACCAAACAGC	1	278	0	AATTTTATTA	    0.948015	-23
          **********

Masking position 4
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

         ATGTTGCATGCAAACAACATA	1	2	1	TGTTGCATGC	    0.983007	-299
TTAAGTGAGTTATTGGAAGTCAAATCATTA	1	137	0	TATTGGAAGT	    0.958129	-164
TTAAAAAAACTATTGCAAGCAAAAATAAAA	1	214	0	TATTGCAAGC	    0.991517	-87
CAAGTCCACCTATTCCTAGCATTAAAAAAA	1	235	0	TATTCCTAGC	     0.97392	-66
          **********

Masking position 4
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