AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i225_Glutamyl_tRNA_synthase_mgen_reg_100.orf -o225_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	RMG01274	119	Mycoplasma

Motif number 1

TGAGACTTAAAATATTTGATCGCACAA   	1	8	0	AATATTTGAT	    0.988558	-112
GTCTCAGGGCGATACTTGATAAAAAACCTA	1	32	1	GATACTTGAT	    0.993761	-88
CTATCTTTGCATTAATTGATGTTAAAACAT	1	74	0	ATTAATTGAT	    0.793342	-46
    TAAAAAATTACTTGATTTATTCAGTT	1	104	0	ATTACTTGAT	    0.973747	-16
          **********

Masking position 6
Map Score:   8.37625

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

TAAAATATTTGATCGCACAA          	1	1	0	GATCGCACAA	    0.992544	-119
TTTTATCAAGTATCGCCCTGAGACTTAAAA	1	26	0	TATCGCCCTG	    0.986404	-94
AAACATCGTTAATGGCACTAGGTTTTTTAT	1	50	0	AATGGCACTA	    0.982654	-70
TTAATGCAAAGATAGAACTGAATAAATCAA	1	89	1	GATAGAACTG	    0.979677	-31
          **********

Masking position 3
Map Score:   2.16235

Number of sites scoring better than the average of aligned sites = 19
Number in coding regions = 18
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 3

CCCTGAGACTTAAAATATTTGATCGCACAA	1	11	0	TAAAATATTT	    0.927598	-109
CGATACTTGATAAAAAACCTAGTGCCATTA	1	41	1	TAAAAAACCT	    0.979536	-79
TAATTGATGTTAAAACATCGTTAATGGCAC	1	62	0	TAAAACATCG	    0.981194	-58
AGATAGAACTGAATAAATCAAGTAATTTTT	1	98	1	GAATAAATCA	    0.933285	-22
          TAAAAAATTACTTGATTTAT	1	110	0	TAAAAAATTA	    0.961015	-10
          **********

Masking position 5
Map Score:   2.97353

Number of sites scoring better than the average of aligned sites = 302
Number in coding regions = 275
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 4

          **********

No masking
Map Score:   9.48026e-14

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:   9.48026e-14

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:   9.48026e-14

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