AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i055_mgen_mpneu_100.orf -o055_mgen_mpneu_100.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.36 -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 =  	0.36
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RMP00283	53	Mycoplasma_pneumoniae
#2	RMP00531	247	Mycoplasma_pneumoniae

Motif number 1

caattaaagcaattgttaattatttaaaattaatc	1	21	1	aattttattt	    0.798854	-33
        gtaaattcgattaattttaaataatta	1	37	0	aatgtaattt	    0.867011	-17
gaatatgtttaaatacggttaattgaattttccag	2	25	1	aatgtaattg	    0.959334	-223
catcatttcaaatttcgtctcagttccgatgctgg	2	56	0	aatgtcagtt	    0.858581	-192
ttatcaattaaactcgtcatcatttcaaatttcgt	2	73	0	aatttcattt	    0.929537	-175
gcggtaactaaattttgcgtcatttatggttcaac	2	118	1	aatgtcattt	    0.988179	-130
ccatcttagaaaaaccttgtcattttgttacaaga	2	181	0	aaattcattt	    0.960969	-67
          ** *  *  ******

Masking position 12
Map Score:   8.1156

Number of sites scoring better than the average of aligned sites = 60
Number in coding regions = 50
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

tacggttaattgaattttccagcatcggaac	2	38	1	tgattttcca	    0.974839	-210
accgctccagttaatttatcaattaaactcg	2	92	0	ttatttatca	    0.850932	-156
tgacgcaaaatttagttaccgctccagttaa	2	109	0	ttagttaccg	    0.993431	-139
tttccgtcggtgaagtttccgtgttgcccat	2	218	0	tgagtttccg	    0.995509	-30
      tgggttcagtttccgtcggtgaagt	2	233	0	ttagtttccg	    0.995405	-15
          ** ********

Masking position 6
Map Score:   5.25759

Number of sites scoring better than the average of aligned sites = 11
Number in coding regions = 11
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 3

acaattgctttaattgcgttacttcc    	1	7	0	taattgcgtt	    0.953205	-47
         gtaaattcgattaattttaaa	1	43	0	taaattcgat	    0.974925	-11
tgaatatgtttaaatacggttaattgaatt	2	24	1	taaatacggt	    0.889652	-224
ccgatgctggaaaattcaattaaccgtatt	2	36	0	aaaattcaat	    0.794792	-212
tcatcatttcaaatttcgtctcagttccga	2	62	0	aaatttcgtc	    0.966432	-186
atttatcaattaaactcgtcatcatttcaa	2	80	0	taaactcgtc	     0.93758	-168
aaatgacgcaaaatttagttaccgctccag	2	113	0	aaatttagtt	    0.847249	-135
          **********

Masking position 3
Map Score:   1.96056

Number of sites scoring better than the average of aligned sites = 125
Number in coding regions = 109
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 4

          **********

No masking
Map Score:   -4.80737e-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:   -4.80737e-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:   -4.80737e-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