AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i002_aful_mthe_300.orf -o002_aful_mthe_300.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	RAG23596	126	Archaeoglobus_fulgidus
#2	RTH01986	43	M.thermo
#3	RTH02089	56	M.thermo

Motif number 1

ACCTGAAAAGGTTTTAAAGCTGACGACAAT	1	19	0	GTTTTAAAGC	    0.905101	-108
GAATATTAACTTTTTCTCGCTATCGTGAAG	1	86	0	TTTTTCTCGC	    0.989292	-41
AATAAATCATTTTTTATAGC          	2	1	0	TTTTTATAGC	    0.994619	-43
AAAAATGATTTATTCATAGCACCCCATATA	2	17	1	TATTCATAGC	    0.984202	-27
TCCATTCGGTTTTTCATCGCTCGAGTTTTT	3	20	0	TTTTCATCGC	    0.995503	-37
          **********

Masking position 4
Map Score:   7.67063

Number of sites scoring better than the average of aligned sites = 75
Number in coding regions = 71
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

TGTCGTCAGCTTTAAAACCTTTTCAGGTGAG	1	21	1	TTAAAACCTT	    0.973209	-106
GTTGTTTATGTTTAAAAATTCTCACCTGAAA	1	41	0	TTAAAAATTC	    0.987332	-86
AACAACATTATCTATAACTTCTTCACGATAG	1	66	1	TCATAACTTC	    0.965042	-61
     TGAACTTCAAAAACTCTGAAAGAATA	1	111	0	TTAAAAACTC	    0.994338	-16
    CCAGGATCAAAAAACTCGAGCGATGAA	3	7	1	TCAAAAACTC	    0.994753	-50
          ** ********

Masking position 6
Map Score:   5.88319

Number of sites scoring better than the average of aligned sites = 203
Number in coding regions = 186
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 3

          **********

No masking
Map Score:   2.93755e-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:   2.93755e-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:   2.93755e-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