AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i193_dna_polymerase_mgen_reg_100.orf -o193_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	RMG02591	234	Mycoplasma

Motif number 1

 TTAAATTGTTAATAACAAAAAAATCTCTA	1	10	1	TAATAACAAA	    0.981985	-225
AAAAAATCTCTATTAAAAAAACCAACTTTA	1	28	1	TATTAAAAAA	     0.98829	-207
TGGGCGCATATATTAATAAATTTTATTAAT	1	149	1	TATTAATAAA	    0.989294	-86
TTCTTGCTTATATTAATAAAATTTATTAAT	1	160	0	TATTAATAAA	    0.989294	-75
GTTTAAATTCTAATAAAGAATTAGATTGTT	1	188	0	TAATAAAGAA	    0.966904	-47
          **********

Masking position 5
Map Score:   8.61806

Number of sites scoring better than the average of aligned sites = 95
Number in coding regions = 75
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 2

          TTAAATTGTTAATAACAAAA	1	1	1	TTAAATTGTT	    0.974411	-234
TTTTTTTAATAGAGATTTTTTTGTTATTAA	1	19	0	AGAGATTTTT	    0.907306	-216
AAAGTTGGTTTGAAATTCTAAATGGCGCGC	1	57	1	TGAAATTCTA	    0.967679	-178
GCATATATTAATAAATTTTATTAATATAAG	1	154	1	ATAAATTTTA	    0.860747	-81
TAATAAAGAATTAGATTGTTCTTGCTTATA	1	178	0	TTAGATTGTT	    0.972124	-57
ATGAAATCGTTTAAATTCTAATAAAGAATT	1	196	0	TTAAATTCTA	    0.972292	-39
          **********

Masking position 5
Map Score:   5.81014

Number of sites scoring better than the average of aligned sites = 130
Number in coding regions = 112
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

CTATTAAAAAAACCAACTTTAAAGTTGGTT	1	37	1	AACCAACTTT	    0.996435	-198
TAGAATTTCAAACCAACTTTAAAGTTGGTT	1	47	0	AACCAACTTT	    0.996435	-188
          **********

Masking position 5
Map Score:   2.0876

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 4

TTCAAGTCCTATTGGGCGCGCCATTTAGAA	1	72	0	ATTGGGCGCG	    0.985083	-163
ACCAGAAGGTTATGGGTTCAAGTCCTATTG	1	88	0	TATGGGTTCA	    0.987573	-147
GGATAGAGTGTCTGGCTTCGGACCAGAAGG	1	109	0	TCTGGCTTCG	    0.974712	-126
CCGATTGAGCTATGGGCGCATATATTAATA	1	137	1	TATGGGCGCA	    0.994649	-98
          **********

Masking position 3
Map Score:   1.2885

Number of sites scoring better than the average of aligned sites = 5
Number in coding regions = 3
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 5

GCCATTTAGAATTTCAAACCAACTTTAAAG	1	53	0	ATTTCAAACC	     0.96665	-182
GAAGGTTATGGGTTCAAGTCCTATTGGGCG	1	84	0	GGTTCAAGTC	    0.984676	-151
TTGAACTATTAGATGAAATCGTTTAAATTC	1	208	0	AGATGAAATC	     0.96874	-27
TTCATCTAATAGTTCAAATCACAT      	1	221	1	AGTTCAAATC	    0.994438	-14
          **********

Masking position 6
Map Score:   2.08325

Number of sites scoring better than the average of aligned sites = 49
Number in coding regions = 33
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 6

          **********

No masking
Map Score:   -2.46258e-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:   -2.46258e-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 8

          **********

No masking
Map Score:   -2.46258e-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