AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i248_cell_division_mpneu_reg_300.orf -o248_mpneu_300.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	RMP00416	184	Mycoplasma_pneumoniae

Motif number 1

gtattacaagtactagtttgccaaagacaa	1	69	1	tactagtttg	    0.993232	-116
tgccaaagacaagtggttggtgcaactagt	1	87	1	aagtggttgg	    0.967241	-98
tggttggtgcaactagttgaggggcgctaa	1	100	1	aactagttga	    0.990331	-85
tactagattattctagttggctttaaggaa	1	134	0	ttctagttgg	    0.990149	-51
aatagtgcattactagattattctagttgg	1	144	0	tactagatta	    0.951788	-41
          **********

Masking position 4
Map Score:   5.17002

Number of sites scoring better than the average of aligned sites = 105
Number in coding regions = 93
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

atacttacttacaatctaactatcatgagcg	1	42	0	acaactaact	    0.974377	-143
ctagtacttgtaatacttacttacaatctaa	1	54	0	taatcttact	    0.962477	-131
tgaggggcgctaaacctttccttaaagccaa	1	117	1	taaactttcc	    0.965155	-68
aacctttccttaaagccaactagaataatct	1	129	1	taaaccaact	    0.981979	-56
gcactattgcaaaatctaacctgatttaa  	1	166	1	aaaactaacc	    0.989146	-19
          **** ******

Masking position 3
Map Score:   2.19836

Number of sites scoring better than the average of aligned sites = 98
Number in coding regions = 84
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 3

          **********

No masking
Map Score:   2.227e-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 4

          **********

No masking
Map Score:   2.227e-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:   2.227e-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