AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i209_rpod_mgen_reg_100.orf -o209_mgen_100.ace -a/home/amcguire/alignace/lib/ORF_mgen.txt -z/skink1/amcguire/genomes/mgen.fna -g0.32 -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 =  	0.32
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RMG04660	44	Mycoplasma
#2	RMG04657	19	Mycoplasma
#3	RMG03599	178	Mycoplasma

Motif number 1

          AAGTTATATAAGCTAAAATT	1	1	1	AAGTTATATA	    0.915272	-44
ATATAAGCTAAAATTATAATGCTAGTCGCA	1	16	1	AAATTATAAT	     0.89774	-29
     TTTTTAAGATTAATTAACA      	2	6	1	AAGATTAATT	    0.781212	-14
        GCAAGTTAAAATATACTAAATA	3	3	1	AAGTTAAAAT	    0.977184	-176
AACCTTGGCAAGGTTATGTTCTACCATTGA	3	57	0	AGGTTATGTT	    0.958236	-122
AACCTTGCCAAGGTTAAGATGCGGGTTCGA	3	72	1	AGGTTAAGAT	      0.9592	-107
TTTTACAAAGAAGTTTTAATTTGGAGCAGA	3	111	0	AAGTTTTAAT	    0.967388	-68
          **********

Masking position 1
Map Score:   6.22061

Number of sites scoring better than the average of aligned sites = 251
Number in coding regions = 224
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 2

GCGACTAGCATTATAATTTTAGCTTATATA	1	15	0	TTATAATTTT	    0.921549	-30
ACTTTAATATTTAGTATATTTTAACTTGC 	3	10	0	TTAGTATATT	    0.948642	-169
TTGATACCAATCAGGATTTTACAAAGAAGT	3	127	0	TCAGGATTTT	    0.994947	-52
ATCAACTAAGTCAGGATTTTTCTTATTTAT	3	152	1	TCAGGATTTT	    0.994947	-27
          **********

Masking position 6
Map Score:   3.12742

Number of sites scoring better than the average of aligned sites = 40
Number in coding regions = 35
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 3

         TTAGCTCAATGCGACTAGCAT	1	34	0	TAGCTCAATG	    0.996686	-11
AACGCAGATATAGaTCAATGGTAGAACATA	3	43	1	TAGaTCAATG	    0.995101	-136
          **********

Masking position 5
Map Score:   0.750581

Number of sites scoring better than the average of aligned sites = 1
Number in coding regions = 0
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

          **********

No masking
Map Score:   4.07441e-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:   4.07441e-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:   4.07441e-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