AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i272_aful_mthe_100.orf -o272_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	RAG45611	139	Archaeoglobus_fulgidus

Motif number 1

CCCTTTATGGTTTCATCTCTGGCCTTTAAGG	1	11	0	TTTATCTCTG	    0.996741	-129
GAAACCTGCTTTTTATCTCCGCTATTATACC	1	41	1	TTTATCTCCG	     0.99698	-99
GATATCCGAAATAAATCACTGTGCTGGGTAT	1	67	0	ATAATCACTG	    0.951728	-73
AAATCGGTCGTGTGATATCCGAAATAAATCA	1	80	0	TGTATATCCG	    0.973979	-60
ATGAAAAATCTTAAATTTCTGACTACAAAGT	1	113	1	TTAATTTCTG	    0.981723	-27
          *** *******

Masking position 6
Map Score:   5.80669

Number of sites scoring better than the average of aligned sites = 123
Number in coding regions = 110
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 2

ATAGCGGAGATAAAAAGCAGGTTTCCCTTT	1	36	0	TAAAAAGCAG	     0.95127	-104
TGTGCTGGGTATAATAGCGGAGATAAAAAG	1	49	0	ATAATAGCGG	    0.979761	-91
AGCACAGTGATTTATTTCGGATATCACACG	1	73	1	TTTATTTCGG	    0.969022	-67
AGATTTTTCATTAAAATCGGTCGTGTGATA	1	94	0	TTAAAATCGG	    0.990365	-46
TGAAAAATCTTAAATTTCTGACTACAAAGT	1	114	1	TAAATTTCTG	    0.947491	-26
          **********

Masking position 4
Map Score:   3.4766

Number of sites scoring better than the average of aligned sites = 205
Number in coding regions = 178
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 3

TTCATCTCTGGCCTTTAAGG          	1	1	0	GCCTTTAAGG	    0.991499	-139
AAGCAGGTTTCCCTTTATGGTTTCATCTCT	1	22	0	CCCTTTATGG	    0.968875	-118
TCACACGACCGATTTTAATGAAAAATCTTA	1	96	1	GATTTTAATG	    0.951683	-44
          **********

Masking position 7
Map Score:   0.849832

Number of sites scoring better than the average of aligned sites = 174
Number in coding regions = 159
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

          **********

No masking
Map Score:   -1.82309e-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:   -1.82309e-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:   -1.82309e-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