AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i223_Pseudouridylate_Synthase_mgen_reg_100.orf -o223_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	RMG01475	200	Mycoplasma

Motif number 1

       CTACTTGTATATTCAGTTAAAAT	1	4	1	CTTGTATATT	    0.936034	-197
ATAATTTTTGTTAGTTAATTAGTGAATTTT	1	29	0	TTAGTTAATT	    0.940157	-172
AGTTTAAAAACTAGTAAAAAAGTGTTAATA	1	66	0	CTAGTAAAAA	    0.988097	-135
CTTAAAAAAGTTAGTTTAAAAACTAGTAAA	1	78	0	TTAGTTTAAA	    0.970386	-123
AAGTGTAATCCTAGTTTAATTTCTGGTAGT	1	105	1	CTAGTTTAAT	    0.970102	-96
CAAGTAGCTATTAGTAAAGAAAACTACCAG	1	127	0	TTAGTAAAGA	    0.959498	-74
CTAATAGCTACTTGTAAAAAATTAAAAGTT	1	143	1	CTTGTAAAAA	    0.966513	-58
ATGGCACTATTTAGTATATAGATATCAGGC	1	180	1	TTAGTATATA	     0.97582	-21
          **********

Masking position 8
Map Score:   12.976

Number of sites scoring better than the average of aligned sites = 141
Number in coding regions = 117
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 2

          CTACTTGTATATTCAGTTAA	1	1	1	CTACTTGTAT	    0.871847	-200
TTTTGTTAGTTAATTAGTGAATTTTAACTG	1	24	0	TAATTAGTGA	    0.862628	-177
TAACTAACAAAAATTATTAAGGAGTATTAA	1	42	1	AAATTATTAA	    0.888576	-159
GTTAGTTTAAAAACTAGTAAAAAAGTGTTA	1	69	0	AAACTAGTAA	    0.718841	-132
ACCAGAAATTAAACTAGGATTACACTTAAA	1	102	0	AAACTAGGAT	    0.869982	-99
TTACAAGTAGCTATTAGTAAAGAAAACTAC	1	130	0	CTATTAGTAA	    0.920634	-71
TTACTAATAGCTACTTGTAAAAAATTAAAA	1	140	1	CTACTTGTAA	    0.920687	-61
CCATTAATTCTAACTTTTAATTTTTTACAA	1	154	0	TAACTTTTAA	    0.897269	-47
          **********

Masking position 3
Map Score:   7.43624

Number of sites scoring better than the average of aligned sites = 468
Number in coding regions = 430
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 3

TAGTGAATTTTAACTGAATATACAAGTAG 	1	10	0	TAACTGAATA	    0.820607	-191
TATTCAGTTAAAATTCACTAATTAACTAAC	1	20	1	AAATTCACTA	    0.885416	-181
ATTCACTAATTAACTAACAAAAATTATTAA	1	32	1	TAACTAACAA	    0.947564	-169
ACTAGTTTTTAAACTAACTTTTTTAAGTGT	1	81	1	AAACTAACTT	    0.970913	-120
AAACTACCAGAAATTAAACTAGGATTACAC	1	107	0	AAATTAAACT	    0.792326	-94
TTAGTAAAGAAAACTACCAGAAATTAAACT	1	117	0	AAACTACCAG	    0.915924	-84
TACTTGTAAAAAATTAAAAGTTAGAATTAA	1	151	1	AAATTAAAAG	    0.909791	-50
TGATATCTATATACTAAATAGTGCCATTAA	1	177	0	ATACTAAATA	    0.878964	-24
          **********

Masking position 3
Map Score:   2.09441

Number of sites scoring better than the average of aligned sites = 1095
Number in coding regions = 985
Number in noncoding regions = 110
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 4

          **********

No masking
Map Score:   -2.39152e-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:   -2.39152e-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:   -2.39152e-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