AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i190_ribonucleoside_diphos___mgen_reg_300.orf -o190_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	RMG00426	270	Mycoplasma
#2	RMG01505	45	Mycoplasma
#3	RMG02531	69	Mycoplasma
#4	RMG00446	18	Mycoplasma

Motif number 1

GATTAATAGACAAAAGGAGTTAT       	1	4	0	CAAAAGGAGT	    0.944095	-267
CATCATAGCTCAATAGGACAGAGTATCAGC	1	79	1	CAATAGGACA	    0.973637	-192
ATGGCGTCACCAACAGGAATCGAACCTGTA	1	125	0	CAACAGGAAT	    0.944095	-146
AACTACAAAACAATAAAAAAGCCTACCAGT	1	182	0	CAATAAAAAA	    0.888682	-89
TCTTTTTGTCCAAAATGAAATGACTACAAC	1	230	0	CAAAATGAAA	    0.982454	-41
TCATTTTGGACAAAAAGAAATTTTTATGCT	1	242	1	CAAAAAGAAA	     0.98769	-29
ATTAAAAAAACAAAATAAAAAGCGGTTTTA	3	18	1	CAAAATAAAA	    0.927573	-52
TATAACCTGTCTAAAAGACAATTTC     	3	55	1	CTAAAAGACA	    0.906325	-15
          **********

Masking position 5
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	    0.763795	-259
CAAAGTTTTATAATTGATCAACTGTCATCATAG	1	54	1	TAATATCACT	    0.789795	-217
ACCAGTTATTTAACTGATAGGCAAATAAAGTTA	1	155	0	TAATATAGCA	      0.9787	-116
ATCAGTTAAATAACTGGTAGGCTTTTTTATTGT	1	170	1	TAATGTAGCT	    0.987109	-101
GCTTTTTTATTGTTTTGTAGTTTATCAAGGGTT	1	190	1	TGTTGTAGTT	     0.86747	-81
AGGGTTAATTTAAGTTGTAGTCATTTCATTTTG	1	217	1	TAATGTAGCA	     0.98346	-54
    TTAATTTAATTTATCGTTTAGAATTGCTA	2	7	1	TAATATCGTT	    0.926241	-39
ATTGCTATCTTAAGCAATAGTTT          	2	33	1	TAACATAGTT	    0.857083	-13
     GAAATTGTCTTTTAGACAGGTTATACAT	3	52	0	TGTTTTAGCA	    0.605438	-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

TAATCACATCTAAATCTAAAAGTGCCAAAG	1	29	1	TAAATCTAAA	    0.858334	-242
GACAGTTGATCAATTATAAAACTTTGGCAC	1	50	0	CAATTATAAA	    0.969125	-221
AACTACAAAACAATAAAAAAGCCTACCAGT	1	182	0	CAATAAAAAA	    0.812043	-89
AACCCTTGATAAACTACAAAACAATAAAAA	1	193	0	AAACTACAAA	    0.838797	-78
CTTAAGATAGCAATTCTAAACGATAAATTA	2	17	0	CAATTCTAAA	    0.946741	-29
     AATGTTTATTAAAAAAACAAAATAA	3	6	1	TTATTAAAAA	    0.730383	-64
TTAAAAAAACAAAATAAAAAGCGGTTTTAT	3	19	1	AAAATAAAAA	    0.851511	-51
    AGTGGATAACTATAAATA        	4	3	0	TAACTATAAA	    0.943016	-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

AGTTGATCAATTATAAAACTTTGGCACTTT	1	47	0	TTATAAAACT	    0.945425	-224
TGCCTATCAGTTAAATAACTGGTAGGCTTT	1	165	1	TTAAATAACT	    0.945423	-106
TGACTACAACTTAAATTAACCCTTGATAAA	1	210	0	TTAAATTAAC	    0.839989	-61
  AATGTTTATTAAAAAAACAAAATAAAAA	3	9	1	TTAAAAAAAC	    0.961256	-61
GTTATACATTGTATAAAACCGCTTTTTATT	3	31	0	GTATAAAACC	    0.946129	-39
          **********

Masking position 5
Map Score:   0.026998

Number of sites scoring better than the average of aligned sites = 345
Number in coding regions = 321
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


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


Motif number 7

          **********

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