AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i301_mixed16_mpneu_reg_100.orf -o301_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

Purged sequences:
RMP00371	18	Mycoplasma_pneumoniae

Input sequences:
#1	RMP00126	20	Mycoplasma_pneumoniae
#2	RMP00127	32	Mycoplasma_pneumoniae
#3	RMP00368	300	Mycoplasma_pneumoniae

Motif number 1

agcaaactttgttcgtttaagttttcgtcaaaatc	3	21	0	gttgtaattt	    0.953918	-280
ggcatgagttgcttgagcaaactttgttcgtttaa	3	36	0	gctggaattt	    0.988853	-265
atgttacgggttttgggcatgagttgcttgagcaa	3	51	0	tttggatgtt	    0.984496	-250
ccttgttggttctagggtaatgttacgggttttgg	3	70	0	tctggaatta	    0.909277	-231
aatgttacgttctaggggaactgttattgtttccc	3	103	0	tctggaagtt	    0.993059	-198
acgtagtttctttggcgaattagatcagttagaga	3	143	1	tttggatgat	    0.919224	-158
cttggagttggttagcgaagtggtttaacacatca	3	247	0	gttggaggtt	    0.988326	-54
         tgttagatcaacggtttgcggtttat	3	285	0	gttgtaagtt	    0.981466	-16
          *** * * **  ***

Masking position 9
Map Score:   6.70815

Number of sites scoring better than the average of aligned sites = 192
Number in coding regions = 171
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 2

acgaaaacttaaacgaacaaagtttgctca	3	28	1	aaacgaacaa	    0.983165	-273
cattaccctagaaccaacaagggaaacaat	3	83	1	gaaccaacaa	    0.995709	-218
accaacaagggaaacaataacagttcccct	3	95	1	gaaacaataa	    0.974197	-206
atcagttagagaaagaacaatcaattcgca	3	166	1	gaaagaacaa	    0.993378	-135
          **********

Masking position 6
Map Score:   4.06427

Number of sites scoring better than the average of aligned sites = 24
Number in coding regions = 21
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 3

acaaagtttgctcaagcaactcatgcccaa	3	44	1	ctcaagcaac	    0.945887	-257
gcaactcatgcccaaaacccgtaacattac	3	59	1	cccaaaaccc	    0.975238	-242
cgtaacattaccctagaaccaacaagggaa	3	78	1	ccctagaacc	    0.996869	-223
ataacagttcccctagaacgtaacattgta	3	111	1	ccctagaacg	    0.989061	-190
atctaattcgccaaagaaactacgttctac	3	138	0	ccaaagaaac	    0.974876	-163
          **********

Masking position 5
Map Score:   3.26896

Number of sites scoring better than the average of aligned sites = 78
Number in coding regions = 67
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

tggcttttgaccacaccatatctaccataaa	3	207	0	ccacccatat	    0.991994	-94
ggtcaaaagccaaccccatgttgatgtgtta	3	226	1	caacccatgt	    0.997518	-75
cttcgctaaccaactccaagttcataaaccg	3	262	1	caacccaagt	    0.995636	-39
          **** ******

Masking position 8
Map Score:   1.13593

Number of sites scoring better than the average of aligned sites = 11
Number in coding regions = 9
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

          **********

No masking
Map Score:   -6.15168e-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 6

          **********

No masking
Map Score:   -6.15168e-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 7

          **********

No masking
Map Score:   -6.15168e-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