AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i225_mgen_mpneu_100.orf -o225_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

Input sequences:
#1	RMG01274	119	Mycoplasma
#2	RMP00596	197	Mycoplasma_pneumoniae

Motif number 1

AATGGCACTAGGTTTTTTATCAAGTATCGCC	1	39	0	GGTTTTTTTC	     0.90843	-81
TGCCATTAACGATGTTTTAACATCAATTAAT	1	63	1	GATGTTTTAC	    0.809318	-57
  gacaaaaccatttcaaaacagaaattaag	2	9	1	catttcaaac	    0.945979	-189
tactttttacgatttcgaaacaaacaactta	2	36	0	gatttcgaac	    0.951647	-162
ttttagtattctttttattactttttacgat	2	54	0	ctttttatac	    0.891532	-144
atgagtttgtcttttcgtgtcgctcgtcaga	2	96	1	cttttcgttc	    0.978662	-102
agaaatgtaacatttcttttctgacgagcga	2	115	0	catttctttc	    0.988676	-83
agaaatgttacatttcttgacgtttcgacga	2	129	1	catttcttac	    0.990789	-69
aaaatctcaacgtttcgtttcaggttt    	2	181	1	cgtttcgttc	    0.986101	-17
          ******** **

Masking position 5
Map Score:   9.76646

Number of sites scoring better than the average of aligned sites = 93
Number in coding regions = 86
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 2

   TTGTGCGATCAAATATTTTAAGTCTCA	1	8	1	ATCAAATATT	    0.949726	-112
TAGGTTTTTTATCAAGTATCGCCCTGAGAC	1	32	0	ATCAAGTATC	    0.974228	-88
ATGTTTTAACATCAATTAATGCAAAGATAG	1	74	1	ATCAATTAAT	     0.93217	-46
AACTGAATAAATCAAGTAATTTTTTA    	1	104	1	ATCAAGTAAT	    0.991008	-16
acgatttcgaaacaaacaacttaatttctg	2	29	0	aacaaacaac	    0.824679	-169
tcgaaatcgtaaaaagtaataaaaagaata	2	49	1	aaaaagtaat	    0.879555	-149
tcgtcgaaacgtcaagaaatgtaacatttc	2	130	0	gtcaagaaat	    0.907993	-68
          **********

Masking position 5
Map Score:   4.89486

Number of sites scoring better than the average of aligned sites = 226
Number in coding regions = 207
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

ATCGCCCTGAGACTTAAAATATTTGATCGC	1	15	0	GACTTAAAAT	    0.801631	-105
AAAACCTAGTGCCATTAACGATGTTTTAAC	1	54	1	GCCATTAACG	    0.930525	-66
accatttcaaaacagaaattaagttgtttg	2	17	1	aacagaaatt	    0.810503	-181
cgtgtcgctcgtcagaaaagaaatgttaca	2	111	1	gtcagaaaag	    0.963159	-87
cgacgaatttgacagaaacgttcgaacaaa	2	154	1	gacagaaacg	    0.993326	-44
        aaacctgaaacgaaacgttgag	2	186	0	acctgaaacg	    0.966775	-12
          **********

Masking position 7
Map Score:   1.45812

Number of sites scoring better than the average of aligned sites = 40
Number in coding regions = 36
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

CGATACTTGATAAAAAACCTAGTGCCATTA	1	41	1	TAAAAAACCT	     0.86851	-79
AGATAGAACTGAATAAATCAAGTAATTTTT	1	98	1	GAATAAATCA	    0.936296	-22
          gacaaaaccatttcaaaaca	2	1	1	gacaaaacca	    0.990208	-197
ttacgatttcgaaacaaacaacttaatttc	2	31	0	gaaacaaaca	    0.896065	-167
gacacgaaaagacaaactcatgttcgcctt	2	87	0	gacaaactca	    0.971634	-111
gaaacgttcgaacaaaatctcaacgtttcg	2	168	1	aacaaaatct	    0.905848	-30
          **********

Masking position 6
Map Score:   1.84257

Number of sites scoring better than the average of aligned sites = 234
Number in coding regions = 219
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 5

          TTGTGCGATCAAATATTTTA	1	1	1	TTGTGCGATC	    0.989503	-119
TTTTAAGTCTCAGGGCGATACTTGATAAAA	1	26	1	CAGGGCGATA	    0.958364	-94
ATAAAAAACCTAGTGCCATTAACGATGTTT	1	50	1	TAGTGCCATT	    0.905323	-70
TTGATTTATTCAGTTCTATCTTTGCATTAA	1	89	0	CAGTTCTATC	    0.904288	-31
atactaaaaataaggcgaacatgagtttgt	2	76	1	taaggcgaac	    0.923612	-122
cgttgagattttgttcgaacgtttctgtca	2	163	0	ttgttcgaac	    0.944702	-35
          **********

Masking position 8
Map Score:   0.587682

Number of sites scoring better than the average of aligned sites = 36
Number in coding regions = 34
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:   2.51122e-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:   2.51122e-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:   2.51122e-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