AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i193_dna_polymerase_mpneu_reg_100.orf -o193_mpneu_100.ace -a/home/amcguire/alignace/lib/ORF_mpneu.txt -z/skink1/amcguire/genomes/mpneu.fna -g0.40 -x5 -e 
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 =  	0.4
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RMP00460	300	Mycoplasma_pneumoniae

Motif number 1

tctttgatcttctcaacttttttcttaacc	1	195	1	tctcaacttt	    0.996136	-106
tcaacttttttcttaaccttttgtggaaac	1	207	1	tcttaacctt	    0.996136	-94
cggtgcatggtcttaactttaatttgcact	1	238	1	tcttaacttt	    0.994036	-63
cactttagtttctcaaccttgcatttgatt	1	264	1	tctcaacctt	    0.997499	-37
          **********

Masking position 5
Map Score:   9.76688

Number of sites scoring better than the average of aligned sites = 1
Number in coding regions = 1
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 2

ctaaacgcgtcaagagtctctaaattatctt   	1	8	0	caagagttaa	    0.932605	-293
agactcttgacgcgtttagaaataattttaatcg	1	23	1	cgcgtttaaa	    0.952309	-278
gttgtgtcagcgagattatgtacagtttcctatt	1	63	1	cgagatttaa	    0.989348	-238
ccaagttcgacaagttggaataaaaaaaatagga	1	90	0	caagttgtaa	    0.985828	-211
tcgaatcaggcgagtttttccagatgaccaagtt	1	117	0	cgagtttcaa	    0.994382	-184
tacagtagatcaagttgtagtaaattttgaaccc	1	159	0	caagttgtaa	    0.985828	-142
gaccatgcaccgagtttccacaaaaggttaagaa	1	216	0	cgagtttcaa	    0.994378	-85
          *******   ** *

Masking position 12
Map Score:   7.73662

Number of sites scoring better than the average of aligned sites = 35
Number in coding regions = 30
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 3

gacacaacttcagtcgattaaaattatttct	1	40	0	cagcgattaa	    0.982617	-261
cgagtttttccagatgaccaagttcgacaag	1	110	0	cagtgaccaa	     0.98889	-191
tttgaacccacaggagatcgaatcaggcgag	1	137	0	cagagatcga	    0.995603	-164
caaagaactacagtagatcaagttgtagtaa	1	170	0	cagagatcaa	    0.998015	-131
gaaaaaagttgagaagatcaaagaactacag	1	188	0	gagagatcaa	    0.993042	-113
          *** *******

Masking position 7
Map Score:   7.3893

Number of sites scoring better than the average of aligned sites = 7
Number in coding regions = 6
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

ctcgctgacacaacttcagtcgattaaaat	1	47	0	caacttcagt	    0.977692	-254
gaagatcaaagaactacagtagatcaagtt	1	177	0	gaactacagt	     0.99105	-124
actaaagtgcaaattaaagttaagaccatg	1	243	0	aaattaaagt	    0.955088	-58
caaggttgagaaactaaagtgcaaattaaa	1	255	0	aaactaaagt	    0.988348	-46
          **********

Masking position 5
Map Score:   2.74331

Number of sites scoring better than the average of aligned sites = 26
Number in coding regions = 24
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

aattatttctaaacgcgtcaagagtctcta	1	20	0	aaacgcgtca	    0.920531	-281
aactgtacataatctcgctgacacaacttc	1	60	0	aatctcgctg	    0.974787	-241
ttttttattccaacttgtcgaacttggtca	1	97	1	caacttgtcg	    0.938416	-204
tcatctggaaaaactcgcctgattcgatct	1	124	1	aaactcgcct	    0.985496	-177
ccttttgtggaaactcggtgcatggtctta	1	223	1	aaactcggtg	    0.972598	-78
          **********

Masking position 2
Map Score:   1.2128

Number of sites scoring better than the average of aligned sites = 49
Number in coding regions = 42
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


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


Motif number 8

          **********

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