AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i194_dna_replication_mgen_reg_100.orf -o194_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	RMG03264	97	Mycoplasma
#2	RMG03260	188	Mycoplasma

Motif number 1

CAAAAAGAGATATTTTCTTTAGCATGTACCT	1	42	0	TATTTTTTTA	    0.976261	-56
AGAAAATATCTCTTTTTGATAATCTAGAACA	1	55	1	TCTTTTGATA	     0.92984	-43
ATGGCTTTGTTAATTTGTTTAGATGTATAGA	2	18	1	TAATTTTTTA	    0.937431	-171
ATTCTCTCGATATTTTCGATATTTAAATCTA	2	45	0	TATTTTGATA	    0.975507	-144
ATATAGTTTTTATTTTTATTAATAAATTCTC	2	70	0	TATTTTATTA	    0.973417	-119
AAATAAAAACTATATTTATTATAAGTAATAA	2	86	1	TATATTATTA	     0.95559	-103
AGCCGTTTTCTAATTTTGTTATAATTCAACG	2	155	1	TAATTTGTTA	    0.975507	-34
ATTCAACGTGTTTATTAATTA          	2	178	1	TTTATTATTA	    0.842458	-11
          ****** ****

Masking position 11
Map Score:   10.6662

Number of sites scoring better than the average of aligned sites = 186
Number in coding regions = 155
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 2

GTACCTTTCAAATTTTAATTGCTAATCTTT	1	18	0	AATTTTAATT	    0.853401	-80
GTTAAATGGCTTTGTTAATTTGTTTAGATG	2	13	1	TTTGTTAATT	    0.965806	-176
ATATAGTTTTTATTTTTATTAATAAATTCT	2	71	0	TATTTTTATT	    0.916149	-118
AAATAAAAACTATATTTATTATAAGTAATA	2	86	1	TATATTTATT	    0.934513	-103
CTCCTACTTACTTATTACTTATAATAAATA	2	98	0	CTTATTACTT	    0.916143	-91
AGTAGGAGAATTTATTACTTCTAACCTTGG	2	120	1	TTTATTACTT	    0.972607	-69
CAATGAGCCGTTTTCTAATTTTGTTATAAT	2	150	1	TTTTCTAATT	     0.92747	-39
ATTCAACGTGTTTATTAATTA         	2	178	1	TTTATTAATT	    0.984297	-11
          **********

Masking position 6
Map Score:   9.29914

Number of sites scoring better than the average of aligned sites = 243
Number in coding regions = 199
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 3

ACATGCTAAAGAAAATATCTCTTTTTGATA	1	46	1	GAAAATATCT	    0.974582	-52
ATCTCTTTTTGATAATCTAGAACAGTGGGT	1	62	1	GATAATCTAG	    0.948194	-36
TTTAAATATCGAAAATATCGAGAGAATTTA	2	49	1	GAAAATATCG	    0.976407	-140
AAAATATCGAGAGAATTTATTAATAAAAAT	2	60	1	GAGAATTTAT	    0.982112	-129
AAGTAAGTAGGAGAATTTATTACTTCTAAC	2	115	1	GAGAATTTAT	    0.982112	-74
          **********

Masking position 5
Map Score:   4.16079

Number of sites scoring better than the average of aligned sites = 17
Number in coding regions = 13
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

          **********

No masking
Map Score:   1.09013e-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:   1.09013e-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:   1.09013e-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