AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i094_mgen_mpneu_100.orf -o094_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

Purged sequences:
RMP00575	16	Mycoplasma_pneumoniae

Input sequences:
#1	RMG00209	112	Mycoplasma
#2	RMG02317	20	Mycoplasma
#3	RMG02322	24	Mycoplasma
#4	RMG02325	35	Mycoplasma
#5	RMG02326	90	Mycoplasma
#6	RMP00579	300	Mycoplasma_pneumoniae

Motif number 1

CAAAACAATGCAAAGTATTTTGGAATAACCAG	1	37	1	CAAAGTTTTG	    0.715365	-76
TCTTTTGAGGAAAAGCAGTTATTATCTGGTTA	1	62	0	AAAAGCTTAT	    0.731175	-51
TTTTTCACTGTAACTTCTTTTGAGGAAAAGCA	1	77	0	TAACTTTTTG	    0.741184	-36
    CAACTTAAAATCATTTTTTCACTGTAAC	1	95	0	AAAATCTTTT	    0.598917	-18
AATTAATGGAAAAAGTTGCCTTCAAA      	4	20	1	AAAAGTCCTT	    0.932043	-16
GTGGCAATTTAAAAGTTACTTTAAACACCACC	5	25	1	AAAAGTCTTT	    0.941495	-66
GAGCTATGTAAAAATCGGTCTTTTCAAAACAC	5	59	0	AAAATCTCTT	    0.836539	-32
tgtaactcaaaaacgtaatttggattgcggta	6	46	0	aaacgttttg	    0.747334	-255
ccgaatactgaaactttgttttgatggtcgac	6	174	1	aaactttttt	    0.959396	-127
acgttctaaaaaacgtgtttttcgaccgcgtt	6	220	0	aaacgttttt	     0.94708	-81
caacttgtgtaaaattcactttaaagaatcca	6	256	1	aaaattcttt	    0.927789	-45
caatttattccaaattctcttgttc       	6	286	1	caaattcttg	    0.886005	-15
          ******  ****

Masking position 3
Map Score:   10.3423

Number of sites scoring better than the average of aligned sites = 462
Number in coding regions = 418
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 2

CAAAGTATTTTGGAATAACCAGATAATAAC	1	47	1	TGGAATAACC	    0.984116	-66
TATTAGGCATTGGAATAACT          	3	15	1	TGGAATAACT	    0.982875	-10
GTTTAATTAATGGAAAAAGTTGCCTTCAAA	4	16	1	TGGAAAAAGT	    0.875852	-20
cacgacatagcgcaataacacaagcacttt	6	17	1	cgcaataaca	    0.843265	-284
tcgtcaaccatcgaacaaaaagacacacta	6	132	1	tcgaacaaaa	    0.821221	-169
tttcagtattcggaacaaccgttgttagtg	6	157	0	cggaacaacc	    0.966771	-144
cttaacgcggtcgaaaaacacgttttttag	6	217	1	tcgaaaaaca	    0.915867	-84
caagagaatttggaataaattggattcttt	6	278	0	tggaataaat	    0.939979	-23
          **********

Masking position 5
Map Score:   6.01372

Number of sites scoring better than the average of aligned sites = 59
Number in coding regions = 53
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

          GTGGTGTTTAATTAATGGAA	4	1	1	GTGGTGTTTA	      0.9921	-35
AAAACACCAGGTGGTGTTTAAAGTAACTTT	5	36	0	GTGGTGTTTA	      0.9921	-55
TAAACACCACCTGGTGTTTTGAAAAGACCG	5	46	1	CTGGTGTTTT	      0.9921	-45
cggtaaagtgcttgtgttattgcgctatgt	6	21	0	cttgtgttat	    0.925981	-280
          **********

Masking position 5
Map Score:   3.43124

Number of sites scoring better than the average of aligned sites = 21
Number in coding regions = 19
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 4

        CTTTGGGATAGTGCTTCAGTCAT	1	3	1	TTGGGATGTG	    0.986438	-110
TCCAAAATACTTTGCATTGTTTTGCTAATGA	1	30	0	TTTGCATGTT	    0.943859	-83
AATTGCCACATTGTCATAGTCTT        	5	3	0	TTGTCATGTC	    0.949269	-88
aaaaacgtaatttggattgcggtaaagtgct	6	39	0	tttggatgcg	     0.96977	-262
tacgtaaccttttggttcgtcaaccatcgaa	6	116	1	tttggttgtc	    0.969257	-185
tgaaactttgttttgatggtcgaccgagatc	6	182	1	ttttgatgtc	    0.977367	-119
          ******* ***

Masking position 7
Map Score:   2.92759

Number of sites scoring better than the average of aligned sites = 36
Number in coding regions = 35
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 5

          **********

No masking
Map Score:   7.69818e-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:   7.69818e-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:   7.69818e-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