AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i131_Transmembrane_Transport_5_aful_reg_300.orf -o131_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	RAG50353	300	Archaeoglobus_fulgidus

Motif number 1

GATTATGTGGATAAAAATTTTG        	1	3	0	ATAAAAATTT	    0.890498	-298
ATTTTTATCCACATAATCTCCCGAGTTTGT	1	15	1	ACATAATCTC	    0.932577	-286
TTTCATTTTAACACAAACTCGGGAGATTAT	1	27	0	ACACAAACTC	     0.94521	-274
ACCCAGATTTATAAAATTTCATTTTAACAC	1	43	0	ATAAAATTTC	    0.948404	-258
CAAAACTTATACAAAATAACATGAAACCCA	1	68	0	ACAAAATAAC	    0.773098	-233
GCTTTTTAATATCAAAACTTATACAAAATA	1	80	0	ATCAAAACTT	    0.809312	-221
TGACTATTACACTACATCTCATGCAGCGTA	1	111	0	ACTACATCTC	      0.9447	-190
TCAGTGAAAAACTAAAACTCACAAAATATT	1	138	1	ACTAAAACTC	    0.973997	-163
ACTAAAACTCACAAAATATTCTTACAGAAC	1	148	1	ACAAAATATT	    0.933762	-153
GACCCCAGTGACAACAATTTATTAAATTAA	1	263	1	ACAACAATTT	    0.894691	-38
AATTTATTAAATTAAATTTTCCATTAAATC	1	278	1	ATTAAATTTT	    0.813962	-23
          **********

Masking position 6
Map Score:   9.58127

Number of sites scoring better than the average of aligned sites = 828
Number in coding regions = 694
Number in noncoding regions = 134
Number of orfs with sites within 600 bp upstream = 150
Fraction of orfs with sites within 600 bp upstream = 0.0240925


Motif number 2

TAACTCTCAAAATAAATTACCAAATCCAAT	1	224	1	AATAAATTAC	    0.967826	-77
TACCAAATCCAATCAATTAACCGACCCCAG	1	241	1	AATCAATTAA	    0.967827	-60
ACAACAATTTATTAAATTAAATTTTCCATT	1	273	1	ATTAAATTAA	    0.980862	-28
TAAATTTTCCATTAAATCAAT         	1	290	1	ATTAAATCAA	    0.967815	-11
          **********

Masking position 5
Map Score:   2.24629

Number of sites scoring better than the average of aligned sites = 12
Number in coding regions = 5
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

GAGTTTGTGTTAAAATGAAATTTTATAAAT	1	37	1	TAAAATGAAA	     0.97911	-264
TTATACAAAATAACATGAAACCCAGATTTA	1	62	0	TAACATGAAA	     0.95492	-239
GTAAGCTTTTTAATATCAAAACTTATACAA	1	84	0	TAATATCAAA	    0.884124	-217
TATTCTTACAGAACATGGAAAAGGCTACTT	1	164	1	GAACATGGAA	    0.956587	-137
CAACAATTTATTAAATTAAATTTTCCATTA	1	274	1	TTAAATTAAA	    0.789076	-27
     ATTGATTTAATGGAAAATTTAATTT	1	286	0	TTTAATGGAA	    0.681623	-15
          **********

Masking position 5
Map Score:   2.5435

Number of sites scoring better than the average of aligned sites = 111
Number in coding regions = 95
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 4

AAAATGAAATTTTATAAATCTGGGTTTCAT	1	48	1	TTTATAAATC	    0.950468	-253
AGAAGGAACCTTGCCAACTCGGTCTGGTGA	1	195	0	TTGCCAACTC	    0.976931	-106
GGCAAGGTTCCTTCTAACTCTCAAAATAAA	1	210	1	CTTCTAACTC	    0.954598	-91
TCAAAATAAATTACCAAATCCAATCAATTA	1	230	1	TTACCAAATC	    0.979024	-71
AAAATTTAATTTAATAAATTGTTGTCACTG	1	268	0	TTAATAAATT	    0.786196	-33
          **********

Masking position 6
Map Score:   0.435794

Number of sites scoring better than the average of aligned sites = 169
Number in coding regions = 139
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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 7

          **********

No masking
Map Score:   7.91135e-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