AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i228_6_1_1_17_mgen_reg_100.orf -o228_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	RMG05344	25	Mycoplasma
#2	RMG04236	300	Mycoplasma

Motif number 1

AATCACCTGATTAATTGTTTC         	1	15	1	TTAATTGTTT	    0.811032	-11
AAGAGTTTATCTTTTTCATTAACATCGCCT	2	46	0	CTTTTTCATT	    0.738244	-255
ATGAAAAAGATAAACTCTTTTTAGCAAGAA	2	57	1	TAAACTCTTT	    0.853304	-244
TAAAATACCTCTTTTTCTTGCTAAAAAGAG	2	71	0	CTTTTTCTTG	    0.806954	-230
TTGGCTTCTCCATATGCTTTTAAAATACCT	2	91	0	CATATGCTTT	    0.931611	-210
TAACCCTTTATAAATTCTTTTTTCAGCAAT	2	122	0	TAAATTCTTT	    0.938104	-179
AAAGAAACTGCTAACCCTTTATAAATTCTT	2	133	0	CTAACCCTTT	     0.81467	-168
AAAGGGTTAGCAGTTTCTTTTAATAATACT	2	143	1	CAGTTTCTTT	    0.974734	-158
TTTAATAATACTGATTCTTTTAATGGTAGT	2	161	1	CTGATTCTTT	    0.987302	-140
GGTTATTTTGCTGATGGTTTAATTAAAGAA	2	272	1	CTGATGGTTT	    0.888482	-29
     TGAGATAGTTTCTTTAATTAAACCA	2	286	0	TAGTTTCTTT	    0.934098	-15
          **********

Masking position 9
Map Score:   9.5642

Number of sites scoring better than the average of aligned sites = 710
Number in coding regions = 670
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 2

AATGGTTTTGTTTTGGTTATCACCACT   	2	8	0	TTTTGGTTAT	    0.869279	-293
GAGAAGCCAATATTGCTGAAAAAAGAATTT	2	111	1	TATTGCTGAA	     0.93646	-190
TTTCTTTTAATAATACTGATTCTTTTAATG	2	156	1	TAATACTGAT	    0.903599	-145
ATACTGATTCTTTTAATGGTAGTGATATTA	2	168	1	TTTTAATGGT	    0.793537	-133
ATGGTAGTGATATTAGTGATTCCATTACAA	2	183	1	TATTAGTGAT	     0.98124	-118
ATTATGTGTCTATTTGTAATGGAATCACTA	2	196	0	TATTTGTAAT	    0.825625	-105
CTCAAAACCTTATTTATGATGCTAGTGGTA	2	234	1	TATTTATGAT	    0.941863	-67
TTCTAGGTTATTTTGCTGATGGTTTAATTA	2	267	1	TTTTGCTGAT	    0.980865	-34
          **********

Masking position 4
Map Score:   5.54572

Number of sites scoring better than the average of aligned sites = 447
Number in coding regions = 427
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 3

         TTATAATCACCTGATTAATTG	1	2	1	TATAATCACC	    0.931038	-24
TTGTTTTGGTTATCACCACT          	2	1	0	TATCACCACT	    0.942212	-300
ACCAAAACAAAACCATTCCCCGCAAAGGCG	2	21	1	AACCATTCCC	    0.926502	-280
TCTTTTTCATTAACATCGCCTTTGCGGGGA	2	37	0	TAACATCGCC	    0.937746	-264
GAATCACTAATATCACTACCATTAAAAGAA	2	175	0	TATCACTACC	    0.983835	-126
CCTAGAAGGTTACCACTAGCATCATAAATA	2	244	0	TACCACTAGC	    0.975835	-57
TCTTTAATTAAACCATCAGCAAAATAACCT	2	271	0	AACCATCAGC	    0.967789	-30
          **********

Masking position 5
Map Score:   4.27363

Number of sites scoring better than the average of aligned sites = 297
Number in coding regions = 281
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 4

          **********

No masking
Map Score:   6.91659e-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:   6.91659e-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:   6.91659e-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