AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i303_mgen_mpneu_300.orf -o303_mgen_mpneu_300.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	RMG03030	66	Mycoplasma
#2	RMP00236	54	Mycoplasma_pneumoniae

Motif number 1

          ATTAAATAGAAAAATATTGTT	1	1	1	ATTAATAGAA	    0.986971	-66
ATAGAAAAATATTGTTAATAAAATTATTATA	1	16	1	ATTTTAATAA	    0.942769	-51
TTGTTAATAAAATTATTATATGTTTTAAGAT	1	27	1	AATATTATAT	    0.930519	-40
  ATTACTTGAATTAATAGAAATCTTAAAAC	1	48	0	AATAATAGAA	    0.983129	-19
tactgcgaagattgattataaatgaatttaa	2	11	1	attattataa	    0.988527	-44
ttataaatgaatttaatataactggttattt	2	26	1	attaatataa	    0.989088	-29
       aaggatttaaataaccagttatat	2	41	0	gattaaataa	    0.835273	-14
          *** *******

Masking position 8
Map Score:   10.1095

Number of sites scoring better than the average of aligned sites = 189
Number in coding regions = 148
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 2

  ATTAAATAGAAAAATATTGTTAATAAAA	1	9	1	GAAAAATATT	     0.87291	-58
ATATTGTTAATAAAATTATTATATGTTTTA	1	24	1	TAAAATTATT	    0.973608	-43
AATAGAAATCTTAAAACATATAATAATTTT	1	35	0	TTAAAACATA	    0.879205	-32
     ATTACTTGAATTAATAGAAATCTTA	1	52	0	TTGAATTAAT	    0.879391	-15
taaattcatttataatcaatcttcgcagta	2	11	0	tataatcaat	    0.915072	-44
accagttatattaaattcatttataatcaa	2	22	0	ttaaattcat	    0.961247	-33
aactggttatttaaatcctt          	2	45	1	ttaaatcctt	    0.981568	-10
          **********

Masking position 5
Map Score:   6.50676

Number of sites scoring better than the average of aligned sites = 767
Number in coding regions = 684
Number in noncoding regions = 83
Number of orfs with sites within 600 bp upstream = 55
Fraction of orfs with sites within 600 bp upstream = 0.00883392


Motif number 3

          **********

No masking
Map Score:   -1.17788e-14

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 4

          **********

No masking
Map Score:   -1.17788e-14

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:   -1.17788e-14

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