AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i190_ribonucleoside_diphos___mgen_reg_100.orf -o190_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	RMG00426	270	Mycoplasma
#2	RMG01505	45	Mycoplasma
#3	RMG02531	69	Mycoplasma
#4	RMG00446	18	Mycoplasma

Motif number 1

       ATAACTCCTTTTGTCTATTAATC	1	4	1	ACTCCTTTTG	    0.943092	-267
GCTGATACTCTGTCCTATTGAGCTATGATG	1	79	0	TGTCCTATTG	    0.973149	-192
TACAGGTTCGATTCCTGTTGGTGACGCCAT	1	125	1	ATTCCTGTTG	    0.943092	-146
ACTGGTAGGCTTTTTTATTGTTTTGTAGTT	1	182	1	TTTTTTATTG	    0.886804	-89
GTTGTAGTCATTTCATTTTGGACAAAAAGA	1	230	1	TTTCATTTTG	    0.982126	-41
AGCATAAAAATTTCTTTTTGTCCAAAATGA	1	242	0	TTTCTTTTTG	    0.987458	-29
TAAAACCGCTTTTTATTTTGTTTTTTTAAT	3	18	0	TTTTATTTTG	    0.926297	-52
     GAAATTGTCTTTTAGACAGGTTATA	3	55	0	TGTCTTTTAG	    0.904713	-15
          **********

Masking position 6
Map Score:   8.56049

Number of sites scoring better than the average of aligned sites = 231
Number in coding regions = 204
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

GATTTAGATGTGATTAATAGACAAAAGGAGTTA	1	12	0	TGATATAGCA	    0.754203	-259
CAAAGTTTTATAATTGATCAACTGTCATCATAG	1	54	1	TAATATCACT	    0.804144	-217
ACCAGTTATTTAACTGATAGGCAAATAAAGTTA	1	155	0	TAATATAGCA	    0.979452	-116
ATCAGTTAAATAACTGGTAGGCTTTTTTATTGT	1	170	1	TAATGTAGCT	    0.988182	-101
GCTTTTTTATTGTTTTGTAGTTTATCAAGGGTT	1	190	1	TGTTGTAGTT	    0.877282	-81
AGGGTTAATTTAAGTTGTAGTCATTTCATTTTG	1	217	1	TAATGTAGCA	    0.984708	-54
    TTAATTTAATTTATCGTTTAGAATTGCTA	2	7	1	TAATATCGTT	    0.932074	-39
ATTGCTATCTTAAGCAATAGTTT          	2	33	1	TAACATAGTT	    0.867585	-13
     GAAATTGTCTTTTAGACAGGTTATACAT	3	52	0	TGTTTTAGCA	    0.606641	-18
          *** * **** **

Masking position 8
Map Score:   4.83102

Number of sites scoring better than the average of aligned sites = 49
Number in coding regions = 41
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

CTTTGGCACTTTTAGATTTAGATGTGATTA	1	29	0	TTTAGATTTA	    0.878357	-242
GTGCCAAAGTTTTATAATTGATCAACTGTC	1	50	1	TTTATAATTG	    0.973963	-221
ACTGGTAGGCTTTTTTATTGTTTTGTAGTT	1	182	1	TTTTTTATTG	    0.837371	-89
TTTTTATTGTTTTGTAGTTTATCAAGGGTT	1	193	1	TTTGTAGTTT	    0.861136	-78
TAATTTATCGTTTAGAATTGCTATCTTAAG	2	17	1	TTTAGAATTG	    0.954925	-29
TTATTTTGTTTTTTTAATAAACATT     	3	6	0	TTTTTAATAA	    0.762602	-64
ATAAAACCGCTTTTTATTTTGTTTTTTTAA	3	19	0	TTTTTATTTT	    0.872354	-51
        TATTTATAGTTATCCACT    	4	3	1	TTTATAGTTA	    0.951741	-16
          **********

Masking position 3
Map Score:   3.34753

Number of sites scoring better than the average of aligned sites = 496
Number in coding regions = 404
Number in noncoding regions = 92
Number of orfs with sites within 600 bp upstream = 59
Fraction of orfs with sites within 600 bp upstream = 0.00947639


Motif number 4

          **********

No masking
Map Score:   -1.32571e-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:   -1.32571e-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:   -1.32571e-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