AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i094_mgen_mpneu_300.orf -o094_mgen_mpneu_300.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	    0.731542	-76
TCTTTTGAGGAAAAGCAGTTATTATCTGGTTA	1	62	0	AAAAGCTTAT	     0.68878	-51
TTTTTCACTGTAACTTCTTTTGAGGAAAAGCA	1	77	0	TAACTTTTTG	    0.690107	-36
    CAACTTAAAATCATTTTTTCACTGTAAC	1	95	0	AAAATCTTTT	    0.613714	-18
AATTAATGGAAAAAGTTGCCTTCAAA      	4	20	1	AAAAGTCCTT	    0.914293	-16
GTGGCAATTTAAAAGTTACTTTAAACACCACC	5	25	1	AAAAGTCTTT	     0.94198	-66
GAGCTATGTAAAAATCGGTCTTTTCAAAACAC	5	59	0	AAAATCTCTT	    0.806415	-32
tgtaactcaaaaacgtaatttggattgcggta	6	46	0	aaacgttttg	    0.770615	-255
ccgaatactgaaactttgttttgatggtcgac	6	174	1	aaactttttt	    0.949239	-127
acgttctaaaaaacgtgtttttcgaccgcgtt	6	220	0	aaacgttttt	    0.946417	-81
caacttgtgtaaaattcactttaaagaatcca	6	256	1	aaaattcttt	     0.92453	-45
caatttattccaaattctcttgttc       	6	286	1	caaattcttg	    0.858262	-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

GTTATTATCTGGTTATTCCAAAATACTTTG	1	47	0	GGTTATTCCA	    0.988617	-66
          AGTTATTCCAATGCCTAATA	3	15	0	AGTTATTCCA	    0.987724	-10
TTTGAAGGCAACTTTTTCCATTAATTAAAC	4	16	0	ACTTTTTCCA	    0.908189	-20
aaagtgcttgtgttattgcgctatgtcgtg	6	17	0	tgttattgcg	    0.882952	-284
tagtgtgtctttttgttcgatggttgacga	6	132	0	ttttgttcga	    0.865604	-169
cactaacaacggttgttccgaatactgaaa	6	157	1	ggttgttccg	    0.976073	-144
ctaaaaaacgtgtttttcgaccgcgttaag	6	217	0	tgtttttcga	    0.938512	-84
aaagaatccaatttattccaaattctcttg	6	278	1	atttattcca	    0.956443	-23
          **********

Masking position 6
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

TTCCATTAATTAAACACCAC          	4	1	0	TAAACACCAC	    0.992514	-35
AAAGTTACTTTAAACACCACCTGGTGTTTT	5	36	1	TAAACACCAC	    0.992514	-55
CGGTCTTTTCAAAACACCAGGTGGTGTTTA	5	46	0	AAAACACCAG	    0.992514	-45
acatagcgcaataacacaagcactttaccg	6	21	1	ataacacaag	    0.929615	-280
          **********

Masking position 6
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

ATGACTGAAGCACTATCCCAAAG        	1	3	0	CACATCCCAA	    0.985963	-110
TCATTAGCAAAACAATGCAAAGTATTTTGGA	1	30	1	AACATGCAAA	    0.941981	-83
        AAGACTATGACAATGTGGCAATT	5	3	1	GACATGACAA	    0.947562	-88
agcactttaccgcaatccaaattacgttttt	6	39	1	cgcatccaaa	    0.968731	-262
ttcgatggttgacgaaccaaaaggttacgta	6	116	0	gacaaccaaa	    0.968201	-185
gatctcggtcgaccatcaaaacaaagtttca	6	182	0	gacatcaaaa	    0.976582	-119
          *** *******

Masking position 5
Map Score:   2.92759

Number of sites scoring better than the average of aligned sites = 39
Number in coding regions = 38
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