AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i179_aful_mthe_100.orf -o179_aful_mthe_100.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RAG46815	38	Archaeoglobus_fulgidus
#2	RAG26652	64	Archaeoglobus_fulgidus
#3	RTH01987	83	M.thermo

Motif number 1

AAACTTGAAATATAACTTTTTGC        	1	3	0	TAAACTTTTT	    0.975777	-36
AGATAACTCTTAAAACCTTTGCCTTCTTACG	2	17	0	TAAACCTTTG	    0.992913	-48
ACCTCAGGCGTAGAACTTCTGAGATAACTCT	2	38	0	TAAACTTCTG	    0.981382	-27
        GATATCACCTCAGGCGTAGAACT	2	52	0	TACACCTCAG	    0.962284	-13
GTTTGAATACTCTAACCTTGTAGGAGAAATA	3	43	0	TCAACCTTGT	    0.971961	-41
GTTAGAGTATTCAAACATCTTTATAAAGATT	3	58	1	TCAACATCTT	    0.968094	-26
          ** ********

Masking position 5
Map Score:   5.4034

Number of sites scoring better than the average of aligned sites = 265
Number in coding regions = 229
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 2

       GTGTCCACCTCACAGAAACTTGA	1	26	0	TCCACCTCAC	    0.989961	-13
TTTGCCTTCTTACGCCACAC          	2	1	0	TACGCCACAC	    0.992167	-64
TCAGAAGTTCTACGCCTGAGGTGATATC  	2	47	1	TACGCCTGAG	    0.981679	-18
     CGGTATTCACCATATGAGAACTTGC	3	6	1	TTCACCATAT	    0.971608	-78
GAGAACTTGCTTCCCCTTATTTCTCCTACA	3	26	1	TTCCCCTTAT	    0.976312	-58
          **********

Masking position 9
Map Score:   2.81152

Number of sites scoring better than the average of aligned sites = 314
Number in coding regions = 292
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

          **********

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 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