AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i100_mgen_mpneu_300.orf -o100_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:
RMG03444	167	Mycoplasma

Input sequences:
#1	RMG01751	167	Mycoplasma
#2	RMP00381	34	Mycoplasma_pneumoniae
#3	RMP00382	34	Mycoplasma_pneumoniae

Motif number 1

AAAATTCGTTGGGTAATAGTCTCACCTCAGC	1	57	1	GGGTAATATC	    0.976577	-111
ACTCACCACTTGGTTAAAAAAAATTGGCTGA	1	83	0	TGGTTAAAAA	    0.962935	-85
CAAAACCAGATGGTAAAACTCACCACTTGGT	1	100	0	TGGTAAAATC	    0.994949	-68
      ACCTTGGTAAAATTATATTTGATAG	1	153	0	TGGTAAAATA	    0.996355	-15
      atgctggtaaaattatatttatatt	3	5	1	tggtaaaata	    0.996355	-30
          ******** **

Masking position 6
Map Score:   8.45751

Number of sites scoring better than the average of aligned sites = 15
Number in coding regions = 13
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

        AAATAACAGCAAACTTCCAAACA	1	3	1	ATAACAGAAA	    0.980502	-165
AGCAAACTTCCAAACAAGATGCAATAGATAT	1	18	1	CAAACAAATG	    0.942456	-150
AATAGATATAAAAACAAAAAATTCGTTGGGT	1	40	1	AAAACAAAAA	    0.982875	-128
ACAAGAAGACAAAACCAGATGGTAAAACTCA	1	109	0	AAAACCAATG	    0.942457	-59
CGTTCTTTTAATGACAAGAAGACAAAACCAG	1	122	0	ATGACAAAAG	      0.9838	-46
taatataaatataacagtaaatg        	2	3	0	ataacagaaa	    0.980482	-32
      gtaaatgacaatataaatataattt	3	20	0	atgacaaata	    0.974761	-15
          ******* ***

Masking position 4
Map Score:   8.02699

Number of sites scoring better than the average of aligned sites = 224
Number in coding regions = 206
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 3

CAAGATGCAATAGATATAAAAACAAAAAAT	1	32	1	TAGATATAAA	    0.960839	-136
ACCACTTGGTTAAAAAAAATTGGCTGAGGT	1	80	0	TAAAAAAAAT	    0.890796	-88
AGAACGCTATCAAATATAATTTTACCAAGG	1	147	1	CAAATATAAT	    0.975433	-21
tacgaccattttaatataaatataacagta	2	15	0	ttaatataaa	    0.885035	-20
aatgacaatataaatataattttaccagca	3	12	0	taaatataat	    0.988475	-23
          **********

Masking position 6
Map Score:   4.06613

Number of sites scoring better than the average of aligned sites = 69
Number in coding regions = 60
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 4

    AAATAACAGCAAACTTCCAAACAAGA	1	7	1	CAGCAAACTT	    0.980288	-161
GACTATTACCCAACGAATTTTTTGTTTTTA	1	48	0	CAACGAATTT	    0.987834	-120
AGTCTCACCTCAGCCAATTTTTTTTAACCA	1	74	1	CAGCCAATTT	    0.995689	-94
        tacgaccattttaatataaata	2	23	0	cgaccatttt	    0.972008	-12
          **********

Masking position 6
Map Score:   2.61273

Number of sites scoring better than the average of aligned sites = 29
Number in coding regions = 28
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:   -4.52315e-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:   -4.52315e-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:   -4.52315e-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