AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i194_dna_replication_mgen_reg_300.orf -o194_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	RMG03264	97	Mycoplasma
#2	RMG03260	188	Mycoplasma

Motif number 1

AGGTACATGCTAAAGAAAATATCTCTTTTTG	1	42	1	TAAAAAAATA	    0.977479	-56
TGTTCTAGATTATCAAAAAGAGATATTTTCT	1	55	0	TATCAAAAGA	    0.936012	-43
TCTATACATCTAAACAAATTAACAAAGCCAT	2	18	0	TAAAAAATTA	    0.940528	-171
TAGATTTAAATATCGAAAATATCGAGAGAAT	2	45	1	TATCAAAATA	    0.977404	-144
GAGAATTTATTAATAAAAATAAAAACTATAT	2	70	1	TAATAAAATA	    0.973272	-119
TTATTACTTATAATAAATATAGTTTTTATTT	2	86	0	TAATAATATA	    0.957825	-103
CGTTGAATTATAACAAAATTAGAAAACGGCT	2	155	0	TAACAAATTA	    0.977404	-34
          TAATTAATAAACACGTTGAAT	2	178	0	TAATAATAAA	    0.853643	-11
          **** ******

Masking position 6
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

AAGATTAGCAATTAAAATTTGAAAGGTACA	1	19	1	ATTAAAATTT	    0.924262	-79
GTACATGCTAAAGAAAATATCTCTTTTTGA	1	44	1	AAGAAAATAT	    0.892887	-54
TATTTTCGATATTTAAATCTATACATCTAA	2	36	0	ATTTAAATCT	    0.940224	-153
TATTTTTATTAATAAATTCTCTCGATATTT	2	61	0	AATAAATTCT	    0.984531	-128
TATTAATAAAAATAAAAACTATATTTATTA	2	77	1	AATAAAAACT	    0.966931	-112
GGTTAGAAGTAATAAATTCTCCTACTTACT	2	116	0	AATAAATTCT	    0.984531	-73
          **********

Masking position 5
Map Score:   5.84869

Number of sites scoring better than the average of aligned sites = 156
Number in coding regions = 130
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

GTTAATTTGTTTAGATGTATAGATTTAAAT	2	26	1	TTAGATGTAT	     0.88081	-163
TCGAGAGAATTTATTAATAAAAATAAAAAC	2	66	1	TTATTAATAA	    0.489972	-123
ACTATATTTATTATAAGTAATAAGTAAGTA	2	94	1	TTATAAGTAA	    0.861066	-95
ATTGCCAAGGTTAGAAGTAATAAATTCTCC	2	124	0	TTAGAAGTAA	    0.951149	-65
TCTAATTTTGTTATAATTCAACGTGTTTAT	2	163	1	TTATAATTCA	    0.890958	-26
          **********

Masking position 3
Map Score:   1.62516

Number of sites scoring better than the average of aligned sites = 99
Number in coding regions = 85
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 4

ACCTTAAAGATTAGCAATTAAAATTTGAAA	1	13	1	TTAGCAATTA	    0.984872	-85
GATATTTTCTTTAGCATGTACCTTTCAAAT	1	35	0	TTAGCATGTA	    0.948015	-63
GTTTTTATTTTTATTAATAAATTCTCTCGA	2	66	0	TTATTAATAA	    0.489273	-123
TTATAAGTAATAAGTAAGTAGGAGAATTTA	2	104	1	TAAGTAAGTA	    0.906306	-85
ACTTCTAACCTTGGCAATGAGCCGTTTTCT	2	136	1	TTGGCAATGA	    0.936223	-53
TTCAACGTGTTTATTAATTA          	2	179	1	TTATTAATTA	    0.604534	-10
          **********

Masking position 6
Map Score:   2.68045

Number of sites scoring better than the average of aligned sites = 265
Number in coding regions = 248
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


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


Motif number 7

          **********

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