AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i099_Phosphate_Transport_1_mpneu_reg_100.orf -o099_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

Input sequences:
#1	RMP00232	241	Mycoplasma_pneumoniae

Motif number 1

tcaacatctggttagttttagcactagt    	1	7	0	gttgttttac	     0.98613	-235
agatgttgacctgatctttatcagcgattgct	1	30	1	ctgtctttac	    0.955001	-212
ttgctggagtgttagctttaggtgccacggcc	1	57	1	gttgctttag	    0.979252	-185
agaggctgcttttcttttaatcattcaaccaa	1	90	0	tttttttaac	    0.895534	-152
cctttgctaatttctttttacgagaggctgct	1	112	0	ttttttttag	    0.965546	-130
tttctggcgtttattctttgccaattgtttcc	1	142	0	ttatctttgc	    0.876786	-100
ccagaaaatcgttgtttttaactacttaaagc	1	167	1	gtttttttac	    0.988529	-75
catttcttagttgtgctttaagtagttaaaaa	1	181	0	ttggctttag	    0.952439	-61
     tttcggtactttttaaccaacttttaa	1	225	0	gtatttttac	    0.974041	-17
          *** ****** *

Masking position 7
Map Score:   9.88069

Number of sites scoring better than the average of aligned sites = 363
Number in coding regions = 313
Number in noncoding regions = 50
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 2

gctaaaactaaccagatgttgacctgatctt	1	17	1	accaatgttg	    0.966672	-225
aggtgccacggccattggttgaatgattaaa	1	76	1	gccatggttg	    0.989324	-166
atttctttttacgagaggctgcttttctttt	1	104	0	acgaaggctg	    0.965123	-138
tgtttcctttgctaatttctttttacgagag	1	118	0	gctatttctt	    0.904329	-124
tttattctttgccaattgtttcctttgctaa	1	134	0	gccattgttt	    0.985223	-108
gttaaaaacaacgattttctggcgtttattc	1	158	0	acgatttctg	     0.96264	-84
actaagaaatgcaacttgcttaattaaaagt	1	202	1	gcaattgctt	    0.971949	-40
          **** ******

Masking position 4
Map Score:   4.94701

Number of sites scoring better than the average of aligned sites = 253
Number in coding regions = 227
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 3

gaatgattaaaagaaaagcagcctctcgta	1	96	1	aagaaaagca	    0.992338	-146
attggcaaagaataaacgccagaaaatcgt	1	149	1	aataaacgcc	    0.976347	-93
gtttttaactacttaaagcacaactaagaa	1	180	1	acttaaagca	    0.951068	-62
aagcacaactaagaaatgcaacttgcttaa	1	195	1	aagaaatgca	    0.986567	-47
          **********

Masking position 5
Map Score:   1.76487

Number of sites scoring better than the average of aligned sites = 58
Number in coding regions = 43
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

          **********

No masking
Map Score:   2.58227e-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:   2.58227e-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:   2.58227e-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