AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i224_Holliday_Junction_enzyme_mgen_reg_300.orf -o224_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	RMG01870	300	Mycoplasma

Motif number 1

          AAAAGACAAGCATATAGAATGCAC	1	1	1	AAAACAAATA	    0.978549	-300
CCAATTTGAAAAATCAAATTTATTAGTTTCTCAC	1	55	0	AAAAAATATT	    0.942667	-246
GAATCTTATTAAAGTAGTATGATAAGTTTCAATA	1	95	0	AAAAGTAATA	    0.943502	-206
GCAAGGGATCAAATCAAAAAAATAATGGAGGGCA	1	153	1	AAAAAAAATA	      0.9933	-148
AATGGAGGGCAAATAAAAATGATTACATCTATCT	1	176	1	AAAAAAAATT	     0.98928	-125
TTTGTAGGCAAAAGAAAAATAATTGTTGAGCACA	1	224	1	AAAAAAAATT	     0.98928	-77
CTTTTGTATTAAATCAATATGAAATCCAGTTGTG	1	254	0	AAAAATAAAA	    0.906771	-47
GATTTAATACAAAAGAAAACCATAAATTTGAAAA	1	273	1	AAAAAAAATA	      0.9933	-28
          ***  ****  ***

Masking position 6
Map Score:   11.8731

Number of sites scoring better than the average of aligned sites = 115
Number in coding regions = 101
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 2

AGCATCACCAATTTGAAAAATCAAATTTAT	1	66	0	ATTTGAAAAA	    0.946912	-235
ATTGGTGATGCTATTGAAACTTATCATACT	1	84	1	CTATTGAAAC	    0.935998	-217
ATGCTTGGGAATTTTGAATCTTATTAAAGT	1	114	0	ATTTTGAATC	    0.946111	-187
TTACATCTATCTTTGGAAAAGTTACTTTTG	1	198	1	CTTTGGAAAA	    0.950869	-103
TATTAAATCAATATGAAATCCAGTTGTGCT	1	252	0	ATATGAAATC	    0.959556	-49
GTTTTCTTTTGTATTAAATCAATATGAAAT	1	263	0	GTATTAAATC	    0.825426	-38
AAAACCATAAATTTGAAAAAAAT       	1	288	1	ATTTGAAAAA	    0.946912	-13
          **********

Masking position 7
Map Score:   4.90457

Number of sites scoring better than the average of aligned sites = 262
Number in coding regions = 242
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 3

GACAAGCATATAGAATGCACTGTCAAAGAC	1	15	1	TAGAATGCAC	    0.933575	-286
CAAGCATTGTTTGAATGCAAGGGATCAAAT	1	137	1	TTGAATGCAA	    0.792122	-164
AAAAAAATAATGGAGGGCAAATAAAAATGA	1	168	1	TGGAGGGCAA	    0.980307	-133
AAAGTTACTTTTGTAGGCAAAAGAAAAATA	1	215	1	TTGTAGGCAA	    0.842557	-86
AAAATAATTGTTGAGCACAACTGGATTTCA	1	239	1	TTGAGCACAA	    0.680558	-62
TTCATATTGATTTAATACAAAAGAAAACCA	1	265	1	TTTAATACAA	    0.835063	-36
          **********

Masking position 9
Map Score:   3.65664

Number of sites scoring better than the average of aligned sites = 79
Number in coding regions = 72
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

GCACTGTCAAAGACAATTTTGGTCGTGAGAAACT	1	31	1	AGAAATTGGC	    0.980552	-270
CCTTGCATTCAAACAATGCTTGGGAATTTTGAAT	1	125	0	AAAAATTTGG	     0.99341	-176
GATCAAATCAAAAAAATAATGGAGGGCAAATAAA	1	159	1	AAAAATTGGG	    0.995717	-142
GGCAAAAGAAAAATAATTGTTGAGCACAACTGGA	1	230	1	AAAAATTTGG	    0.993411	-71
          *** ***  *** *

Masking position 7
Map Score:   0.972355

Number of sites scoring better than the average of aligned sites = 22
Number in coding regions = 19
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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