AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i016_aful_mthe_100.orf -o016_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	RAG21749	39	Archaeoglobus_fulgidus
#2	RAG45764	139	Archaeoglobus_fulgidus

Motif number 1

TTTAATCTTTTTTCTGCCAAGACCAGAC    	1	22	1	TTTCTGCAGA	    0.966677	-18
   TTTCATTTTTCTGTCAGAATGAGCTTCAG	2	8	1	TTTCTGCAAA	     0.98827	-132
TCAGACGCAATTTCAGGTGGAATTCTGAAGCT	2	32	0	TTTCAGTGAA	    0.844651	-108
CTGGATAGAATTTCAAAGGAAATCAGACGCAA	2	54	0	TTTCAAGGAA	    0.787381	-86
CCTTATTGAGTTTGAGAGGTAAACACCGAAGA	2	90	0	TTTGAGGGAA	    0.987974	-50
   AGCAGATTTGCTGAGGGAATGCATAAAGC	2	121	0	TTGCTGGGAA	    0.988441	-19
          ****** ** **

Masking position 2
Map Score:   5.99491

Number of sites scoring better than the average of aligned sites = 512
Number in coding regions = 481
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 2

TCTGAAGCTCATTCTGACAGAAAAATGAAA	2	11	0	ATTCTGACAG	     0.92147	-129
GAGCTTCAGAATTCCACCTGAAATTGCGTC	2	31	1	ATTCCACCTG	    0.977075	-109
TCCACCTGAAATTGCGTCTGATTTCCTTTG	2	43	1	ATTGCGTCTG	    0.996139	-97
ATTGCGTCTGATTTCCTTTGAAATTCTATC	2	53	1	ATTTCCTTTG	    0.956423	-87
ATAAAGCCTTATTGAGTTTGAGAGGTAAAC	2	98	0	ATTGAGTTTG	    0.943534	-42
GGCTTTATGCATTCCCTCAGCAAATCTGCT	2	120	1	ATTCCCTCAG	    0.992822	-20
          **********

Masking position 3
Map Score:   5.24654

Number of sites scoring better than the average of aligned sites = 384
Number in coding regions = 356
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 3

          **********

No masking
Map Score:   3.08538e-14

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:   3.08538e-14

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:   3.08538e-14

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