AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i223_Pseudouridylate_Synthase_mgen_reg_300.orf -o223_mgen_300.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	    0.938705	-197
ATAATTTTTGTTAGTTAATTAGTGAATTTT	1	29	0	TTAGTTAATT	    0.942666	-172
AGTTTAAAAACTAGTAAAAAAGTGTTAATA	1	66	0	CTAGTAAAAA	    0.988614	-135
CTTAAAAAAGTTAGTTTAAAAACTAGTAAA	1	78	0	TTAGTTTAAA	    0.971662	-123
AAGTGTAATCCTAGTTTAATTTCTGGTAGT	1	105	1	CTAGTTTAAT	    0.971394	-96
CAAGTAGCTATTAGTAAAGAAAACTACCAG	1	127	0	TTAGTAAAGA	    0.961226	-74
CTAATAGCTACTTGTAAAAAATTAAAAGTT	1	143	1	CTTGTAAAAA	    0.967793	-58
ATGGCACTATTTAGTATATAGATATCAGGC	1	180	1	TTAGTATATA	    0.976867	-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

TTAACTGAATATACAAGTAG          	1	1	0	ATACAAGTAG	    0.874268	-200
CAGTTAAAATTCACTAATTAACTAACAAAA	1	24	1	TCACTAATTA	      0.8488	-177
TTAATACTCCTTAATAATTTTTGTTAGTTA	1	42	0	TTAATAATTT	    0.876383	-159
TAACACTTTTTTACTAGTTTTTAAACTAAC	1	69	1	TTACTAGTTT	    0.732456	-132
TTTAAGTGTAATCCTAGTTTAATTTCTGGT	1	102	1	ATCCTAGTTT	    0.861682	-99
GTAGTTTTCTTTACTAATAGCTACTTGTAA	1	130	1	TTACTAATAG	     0.92253	-71
TTTTAATTTTTTACAAGTAGCTATTAGTAA	1	140	0	TTACAAGTAG	    0.924703	-61
TTGTAAAAAATTAAAAGTTAGAATTAATGG	1	154	1	TTAAAAGTTA	    0.886228	-47
          **********

Masking position 6
Map Score:   7.43624

Number of sites scoring better than the average of aligned sites = 475
Number in coding regions = 436
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 3

TGTATATTCAGTTAAAATTCACTAATTAAC	1	16	1	GTTAAAATTC	    0.984069	-185
GTAAAAAAGTGTTAATACTCCTTAATAATT	1	53	0	GTTAATACTC	     0.95715	-148
ACTTAAAAAAGTTAGTTTAAAAACTAGTAA	1	79	0	GTTAGTTTAA	    0.890326	-122
TGTAATCCTAGTTTAATTTCTGGTAGTTTT	1	108	1	GTTTAATTTC	    0.938411	-93
TTTAATTTCTGGTAGTTTTCTTTACTAATA	1	119	1	GGTAGTTTTC	    0.972658	-82
AAAATTAAAAGTTAGAATTAATGGCACTAT	1	160	1	GTTAGAATTA	    0.970539	-41
          **********

Masking position 3
Map Score:   4.46913

Number of sites scoring better than the average of aligned sites = 161
Number in coding regions = 143
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


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