AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i030_Glycerol_Uptake_mgen_reg_100.orf -o030_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	RMG01136	197	Mycoplasma
#2	RMG05235	158	Mycoplasma

Motif number 1

TTATATCATTAACGTTTAAATAAATATTATTGCT	1	14	1	AACTTATAAA	    0.740135	-184
GATTACTTTAAACTTGTTAGCAAACTTTAATCAT	1	50	1	AACTGACAAA	    0.970101	-148
TAATTTAGCTAAAAAATGATTAAAGTTTGCTAAC	1	65	0	AAAAAATAAA	    0.925886	-133
TAGCTAAATTAAACAACCAGTTAATTAGTAAACA	1	88	1	AAAAAATTAA	    0.925887	-110
TTTAATTCTGGAACTGTTTACTAATTAACTGGTT	1	102	0	GAATGTCTAA	    0.727174	-96
AACAGTTCCAGAATTAAAATCAAATATTAGTTAG	1	118	1	GAATAACAAA	    0.938225	-80
TTGAAAATACAAAATAAAAACTAACTAATATTTG	1	138	0	AAATAACTAA	    0.981246	-60
TTCAGCAAGAAACCATCATCCTAATTGAGTAGAA	1	174	0	AACATTCTAA	    0.795182	-24
TTTTTACTAAAAATAATTAGCTAAAATACCGTCA	2	14	0	AAAAAACTAA	    0.985696	-145
TATTTTTAGTAAAAAGAAATCAAAAGATAAAAAA	2	33	1	AAAAGACAAA	     0.98472	-126
ATCTCTATAAAAAGTAGTATCAAACATTTTTTTA	2	60	0	AAATAACAAA	    0.981246	-99
ACTACTTTTTATAGAGATACCAAAAAGTAAATCA	2	76	1	ATAAGACAAA	    0.863809	-83
AGTAAATCACAACTATAAAACTAATCCTTTTTTG	2	101	1	AACATACTAA	    0.953894	-58
CTTTTTTGCAAAATAACTAACTAAATACTAGAAG	2	127	1	AAAAAACTAA	    0.985695	-32
          *** **  * ****

Masking position 13
Map Score:   19.6029

Number of sites scoring better than the average of aligned sites = 776
Number in coding regions = 698
Number in noncoding regions = 78
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 2

TTAAAGTAATCTTAGCAATAATATTTATTTA	1	30	0	CTTAGCAAAA	    0.989824	-168
GGTTGTTTAATTTAGCTAAAAAATGATTAAA	1	75	0	TTTAGCTAAA	    0.991224	-123
          TTCAGCAAGAAACCATCATCC	1	187	0	TTCAGCAAAA	    0.987417	-11
ACTAAAAATAATTAGCTAAAATACCGTCATA	2	12	0	ATTAGCTAAA	    0.972347	-147
GCTAATTATTTTTAGTAAAAAGAAATCAAAA	2	27	1	TTTAGTAAAA	    0.970729	-132
TAGTTAGTTATTTTGCAAAAAAGGATTAGTT	2	119	0	TTTTGCAAAA	    0.977384	-40
          ******** **

Masking position 8
Map Score:   8.95259

Number of sites scoring better than the average of aligned sites = 73
Number in coding regions = 68
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

TTAGCAATAATATTTATTTAAACGTTAATG	1	20	0	TATTTATTTA	    0.786454	-178
AACAAGTTTAAAGTAATCTTAGCAATAATA	1	38	0	AAGTAATCTT	    0.768673	-160
TAGCAAACTTTAATCATTTTTTAGCTAAAT	1	67	1	TAATCATTTT	    0.910965	-131
TAATATTTGATTTTAATTCTGGAACTGTTT	1	117	0	TTTTAATTCT	    0.723211	-81
TATTAGTTAGTTTTTATTTTGTATTTTCAA	1	142	1	TTTTTATTTT	    0.944732	-56
GTATTTTAGCTAATTATTTTTAGTAAAAAG	2	19	1	TAATTATTTT	    0.937761	-140
ATCAAACATTTTTTTATCTTTTGATTTCTT	2	46	0	TTTTTATCTT	    0.914575	-113
TATAGTTGTGATTTACTTTTTGGTATCTCT	2	88	0	ATTTACTTTT	    0.679595	-71
ACTATAAAACTAATCCTTTTTTGCAAAATA	2	112	1	TAATCCTTTT	    0.797064	-47
AGTATTTAGTTAGTTATTTTGCAAAAAAGG	2	126	0	TAGTTATTTT	    0.942245	-33
         TAATTAATCTTCTAGTATTTA	2	148	0	AATTAATCTT	    0.854448	-11
          **********

Masking position 4
Map Score:   7.07722

Number of sites scoring better than the average of aligned sites = 746
Number in coding regions = 650
Number in noncoding regions = 96
Number of orfs with sites within 600 bp upstream = 61
Fraction of orfs with sites within 600 bp upstream = 0.00979762


Motif number 4

          **********

No masking
Map Score:   -7.43638e-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:   -7.43638e-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:   -7.43638e-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