AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i224_Holliday_Junction_enzyme_mgen_reg_100.orf -o224_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	RMG01870	300	Mycoplasma

Motif number 1

GTGCATTCTATATGCTTGTCTTTT          	1	1	0	TATTTGTTTT	    0.976936	-300
GTGAGAAACTAATAAATTTGATTTTTCAAATTGG	1	55	1	AATATTTTTT	    0.938581	-246
TATTGAAACTTATCATACTACTTTAATAAGATTC	1	95	1	TATTACTTTT	    0.939417	-206
TGCCCTCCATTATTTTTTTGATTTGATCCCTTGC	1	153	0	TATTTTTTTT	    0.992788	-148
AGATAGATGTAATCATTTTTATTTGCCCTCCATT	1	176	0	AATTTTTTTT	    0.988467	-125
TGTGCTCAACAATTATTTTTCTTTTGCCTACAAA	1	224	0	AATTTTTTTT	    0.988467	-77
CACAACTGGATTTCATATTGATTTAATACAAAAG	1	254	1	TTTTATTTTT	    0.900311	-47
TTTTCAAATTTATGGTTTTCTTTTGTATTAAATC	1	273	0	TATTTTTTTT	    0.992788	-28
          ***  ****  ***

Masking position 9
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	    0.950281	-235
ATTGGTGATGCTATTGAAACTTATCATACT	1	84	1	CTATTGAAAC	    0.940619	-217
ATGCTTGGGAATTTTGAATCTTATTAAAGT	1	114	0	ATTTTGAATC	    0.950001	-187
TTACATCTATCTTTGGAAAAGTTACTTTTG	1	198	1	CTTTGGAAAA	     0.95459	-103
TATTAAATCAATATGAAATCCAGTTGTGCT	1	252	0	ATATGAAATC	    0.962692	-49
GTTTTCTTTTGTATTAAATCAATATGAAAT	1	263	0	GTATTAAATC	    0.835252	-38
AAAACCATAAATTTGAAAAAAAT       	1	288	1	ATTTGAAAAA	    0.950281	-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	     0.93294	-286
CAAGCATTGTTTGAATGCAAGGGATCAAAT	1	137	1	TTGAATGCAA	    0.793302	-164
AAAAAAATAATGGAGGGCAAATAAAAATGA	1	168	1	TGGAGGGCAA	    0.980119	-133
AAAGTTACTTTTGTAGGCAAAAGAAAAATA	1	215	1	TTGTAGGCAA	    0.843291	-86
AAAATAATTGTTGAGCACAACTGGATTTCA	1	239	1	TTGAGCACAA	    0.681453	-62
TTCATATTGATTTAATACAAAAGAAAACCA	1	265	1	TTTAATACAA	     0.83426	-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	    0.982257	-270
CCTTGCATTCAAACAATGCTTGGGAATTTTGAAT	1	125	0	AAAAATTTGG	    0.994009	-176
GATCAAATCAAAAAAATAATGGAGGGCAAATAAA	1	159	1	AAAAATTGGG	    0.996104	-142
GGCAAAAGAAAAATAATTGTTGAGCACAACTGGA	1	230	1	AAAAATTTGG	    0.994011	-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