AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i257_hsp60_hsp10_mgen_reg_100.orf -o257_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	RMG04338	167	Mycoplasma

Motif number 1

TGAGATATTGTTAATTTTTAAATACAAA  	1	9	0	TTAATTTTTA	     0.97561	-159
TAAACATTAATTAATATTTAGTGAGATATT	1	30	0	TTAATATTTA	    0.808586	-138
TAAATATTAATTAATGTTTAGCGCTAATAT	1	40	1	TTAATGTTTA	    0.890318	-128
TAAATTTAAGATAACTTTTACTTTCTTTTA	1	74	1	ATAACTTTTA	    0.965055	-94
TTCTTTTAAATTAGTTTTTAATTATTAAAA	1	96	1	TTAGTTTTTA	    0.988473	-72
          **********

Masking position 7
Map Score:   9.33259

Number of sites scoring better than the average of aligned sites = 68
Number in coding regions = 47
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

TATTTAGTGAGATATTGTTAATTTTTAAATACA	1	13	0	GATTTTAATT	    0.990829	-155
GAAAGTAAAAGTTATCTTAAATTTATCTGATAT	1	66	0	GTTTCTAATT	    0.988996	-102
TAACTTTTACTTTCTTTTAAATTAGTTTTTAAT	1	85	1	TTTTTTAATT	    0.985563	-83
ATAATAAAAATATTTTAATAATTAAAAACTAAT	1	105	0	TATTTAAATT	    0.936007	-63
GAATTGGCGTTATGTTCATAATAAAAATATTTT	1	122	0	TATTTAAATA	    0.882231	-46
AAACCAAGACGTTGTCATGAATTGGCGTTATGT	1	140	0	GTTTCTAATT	    0.989001	-28
          *** ** * ****

Masking position 5
Map Score:   6.46606

Number of sites scoring better than the average of aligned sites = 167
Number in coding regions = 144
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 3

         TTTGTATTTAAAAATTAACAA	1	2	1	TTGTATTTAA	    0.911577	-166
TCTCACTAAATATTAATTAATGTTTAGCGC	1	34	1	TATTAATTAA	    0.922162	-134
AAAAGTTATCTTAAATTTATCTGATATTAG	1	63	0	TTAAATTTAT	    0.735228	-105
TTTACTTTCTTTTAAATTAGTTTTTAATTA	1	90	1	TTTAAATTAG	    0.953505	-78
TTAAATTAGTTTTTAATTATTAAAATATTT	1	101	1	TTTTAATTAT	    0.985577	-67
TATTAAAATATTTTTATTATGAACATAACG	1	118	1	TTTTTATTAT	    0.944237	-50
          **********

Masking position 7
Map Score:   4.29634

Number of sites scoring better than the average of aligned sites = 351
Number in coding regions = 275
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 4

          **********

No masking
Map Score:   -1.11255e-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:   -1.11255e-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:   -1.11255e-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