AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i238_sensory_cassete4_aful_reg_300.orf -o238_aful_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	RAG47833	220	Archaeoglobus_fulgidus

Motif number 1

GCTTATAATATATAAAAGCCTTTTTCCGCT	1	24	1	TATAAAAGCC	     0.99577	-197
TTTTCAAACTTATAAAAGCGGAAAAAGGCT	1	40	0	TATAAAAGCG	    0.985262	-181
CTTTTATAAGTTTGAAAACCGGAAATCGCT	1	52	1	TTTGAAAACC	    0.954364	-169
GGAAATCGCTTAAGAAAACTACTTAAGCAA	1	72	1	TAAGAAAACT	    0.893586	-149
TTTTTAAAAGTATAAACTCCACAGTAGTTT	1	103	0	TATAAACTCC	     0.97553	-118
TATTTCTCGCTAAAAACGCCTTTTTTTAAA	1	125	0	TAAAAACGCC	    0.985695	-96
TAAAAAGCTTTATAAAAACAAACAGTCGAA	1	179	1	TATAAAAACA	    0.966313	-42
          **********

Masking position 5
Map Score:   9.11489

Number of sites scoring better than the average of aligned sites = 141
Number in coding regions = 111
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 2

         GATTTCCACTTTGGCTTATAA	1	2	1	ATTTCCACTT	    0.980302	-219
ATAAAAGCCTTTTTCCGCTTTTATAAGTTT	1	35	1	TTTTCCGCTT	     0.99732	-186
TTCTTAAGCGATTTCCGGTTTTCAAACTTA	1	58	0	ATTTCCGGTT	    0.986624	-163
TCCACAGTAGTTTTTTGCTTAAGTAGTTTT	1	86	0	TTTTTTGCTT	    0.969373	-135
TTGGGGATTATTTCTCGCTAAAAACGCCTT	1	133	0	TTTCTCGCTA	    0.957654	-88
          **********

Masking position 3
Map Score:   5.10899

Number of sites scoring better than the average of aligned sites = 342
Number in coding regions = 304
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 3

TTTATATATTATAAGCCAAAGTGGAAATC 	1	10	0	ATAAGCCAAA	    0.983796	-211
AGAAAACTACTTAAGCAAAAAACTACTGTG	1	84	1	TTAAGCAAAA	    0.868604	-137
TTTTAAAAGTATAAACTCCACAGTAGTTTT	1	102	0	ATAAACTCCA	    0.960518	-119
TTAGCGAGAAATAATCCCCAAACGACATAA	1	142	1	ATAATCCCCA	     0.98976	-79
CCCAAACGACATAATCCCAAATAAAAAGCT	1	158	1	ATAATCCCAA	    0.991487	-63
AAAAAGCTTTATAAAAACAAACAGTCGAAC	1	180	1	ATAAAAACAA	    0.888955	-41
          **********

Masking position 4
Map Score:   5.62196

Number of sites scoring better than the average of aligned sites = 305
Number in coding regions = 259
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 4

          **********

No masking
Map Score:   2.72438e-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:   2.72438e-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:   2.72438e-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