AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i192_topoisomerase_mpneu_reg_300.orf -o192_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	RMP00033	125	Mycoplasma_pneumoniae
#2	RMP00035	22	Mycoplasma_pneumoniae
#3	RMP00036	300	Mycoplasma_pneumoniae

Motif number 1

gagacaataagccgtggttaataattataaaggag     	1	6	0	gggttaatta	    0.991694	-120
attcaaaatcgtagttgcgaattacattgaaccagtactt	3	14	1	gggcgaatta	     0.99401	-287
agtacttggcgacggaactaaaatccgtgatttcgaaatt	3	47	1	ggactaaata	    0.966147	-254
aagcttagggggtgtggttaaaccacctcacataactaaa	3	107	1	gggttaaata	    0.993605	-194
aatacttaattttgtcgtgaatgtcgttaaggcggtttcg	3	152	1	tggtgaatta	    0.969685	-149
gtgcgtttgtgttggcgtgaaatggattaaccgtcactac	3	210	0	gggtgaaata	    0.996895	-91
ttttaatatggttgagatgaaagaatcttatttgcaatg 	3	272	1	ggatgaaata	    0.988713	-29
          *  *  ******     * *

Masking position 10
Map Score:   6.9514

Number of sites scoring better than the average of aligned sites = 41
Number in coding regions = 34
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

tataattattaaccacggcttattgtctcag	1	17	1	aaccacggtt	     0.77381	-109
ggcttaatcaaatccccgttttgtctaggta	1	70	0	aatccccgtt	    0.940524	-56
tcttaataggaacttcggcttaatcaaatcc	1	86	0	aacttcggtt	    0.966451	-40
tgtaattcgcaactacgattttgaatgtt  	3	9	0	aactacgatt	    0.932811	-292
ttccgtcgccaagtactggttcaatgtaatt	3	33	0	aagtactgtt	    0.821429	-268
ttaatttcgaaatcacggattttagttccgt	3	58	0	aatcacggtt	    0.705763	-243
caaaattaagtattcctgttttagttatgtg	3	135	0	tattcctgtt	    0.813725	-166
          ******** **

Masking position 2
Map Score:   4.23162

Number of sites scoring better than the average of aligned sites = 159
Number in coding regions = 144
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

ttgacaagagactaggaatggtacctagacaa	1	49	1	atggaatggt	    0.994122	-77
          aatcttaatgttatttaatgag	2	1	1	atttaatgtt	     0.94192	-22
cgcaactacgattttgaatgtt          	3	1	0	attgaatgtt	    0.963384	-300
gcttcgttaaattgctaatggtttaatttcga	3	79	0	atctaatggt	    0.976411	-222
cggtttcgatagtgggaacggtctaagtagtg	3	184	1	atggaacggt	    0.993166	-117
gaacggtctaagtagtgacggttaatccattt	3	199	1	atgtgacggt	    0.971278	-102
          * * ********

Masking position 8
Map Score:   3.96536

Number of sites scoring better than the average of aligned sites = 24
Number in coding regions = 23
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 4

tcaagctgagacaataagccgtggttaata	1	23	0	acaataagcc	    0.943667	-103
aacggggatttgattaagccgaagttccta	1	81	1	tgattaagcc	    0.972349	-45
attaagatcaaatttaaacctgcctc    	1	110	1	aatttaaacc	    0.939918	-16
gttgcgaattacattgaaccagtacttggc	3	27	1	acattgaacc	    0.967682	-274
cgtgatttcgaaattaaaccattagcaatt	3	72	1	aaattaaacc	    0.981346	-229
ttagggggtgtggttaaaccacctcacata	3	111	1	tggttaaacc	    0.948134	-190
          **********

Masking position 5
Map Score:   3.24994

Number of sites scoring better than the average of aligned sites = 113
Number in coding regions = 106
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 5

attcctagtctcttgtcaagctgagacaat	1	38	0	tcttgtcaag	     0.97035	-88
caaatccccgttttgtctaggtaccattcc	1	63	0	ttttgtctag	     0.97496	-63
gaatacttaattttgtcgtgaatgtcgtta	3	151	1	ttttgtcgtg	    0.990672	-150
tgtgcgtttgtgttggcgtgaaatggatta	3	221	0	tgttggcgtg	     0.98126	-80
          **********

Masking position 4
Map Score:   0.965275

Number of sites scoring better than the average of aligned sites = 12
Number in coding regions = 10
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 6

          **********

No masking
Map Score:   7.2008e-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:   7.2008e-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 8

          **********

No masking
Map Score:   7.2008e-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