AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i119_Spermidine_putrescine_Transport_aful_reg_300.orf -o119_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	RAG47245	31	Archaeoglobus_fulgidus
#2	RAG47166	300	Archaeoglobus_fulgidus

Motif number 1

AAGTCGCTTTTAAGGACATTTTCCACTCTTTT	2	75	0	TAAGCATTTT	    0.992978	-226
TTTAGTTTTAAAAGGACAGTTTTTAGATTTTC	2	115	0	AAAGCAGTTT	    0.957861	-186
CTTTTAAAACTAAAATCATTATCCAAGGTCTG	2	133	1	TAAACATTAT	    0.934479	-168
TATGCCAATTAAAGCTCTTTTTTCTGCGTAAA	2	195	1	AAAGCTTTTT	    0.961934	-106
ATAAACATTCTAAATGCTTTTTACGCAGAAAA	2	214	0	TAAACTTTTT	    0.623745	-87
AACTTTCGTGTCAGCCCAATTTTTTATCTAAT	2	250	0	TCAGCAATTT	    0.959787	-51
 AGAACACAATCAATCCATTTTGTATAAAAAA	2	280	0	TCAACATTTT	    0.977471	-21
          ****  ******

Masking position 3
Map Score:   6.31898

Number of sites scoring better than the average of aligned sites = 149
Number in coding regions = 123
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 2

CTTTTAAGGACATTTTCCACTCTTTTGGAC	2	71	0	CATTTTCCAC	    0.978661	-230
ACAGTTTTTAGATTTTCAAAAACCAAAGTC	2	102	0	GATTTTCAAA	    0.989902	-199
AAACTAAAATCATTATCCAAGGTCTGATAA	2	139	1	CATTATCCAA	    0.957931	-162
TTGAAAATCAGAATTTCAAAAATTTATCAG	2	162	0	GAATTTCAAA	      0.9603	-139
TTGAAATTCTGATTTTCAATTTTATGCCAA	2	173	1	GATTTTCAAT	    0.974875	-128
CATTTAGAATGTTTATCAACATTAGATAAA	2	230	1	GTTTATCAAC	    0.914439	-71
          **********

Masking position 6
Map Score:   6.13822

Number of sites scoring better than the average of aligned sites = 146
Number in coding regions = 130
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 3

TGGGAGTCTAGCCAACTTTT          	2	1	0	GCCAACTTTT	    0.972397	-300
GTTTTAAAAGGACAGTTTTTAGATTTTCAA	2	113	0	GACAGTTTTT	    0.975944	-188
TCCAAGGTCTGATAAATTTTTGAAATTCTG	2	154	1	GATAAATTTT	    0.921896	-147
GCCAATTAAAGCTCTTTTTTCTGCGTAAAA	2	198	1	GCTCTTTTTT	    0.897514	-103
TTTCGTGTCAGCCCAATTTTTTATCTAATG	2	249	0	GCCCAATTTT	    0.972062	-52
GGGCTGACACGAAAGTTTTTTATACAAAAT	2	265	1	GAAAGTTTTT	    0.904584	-36
          **********

Masking position 7
Map Score:   2.67571

Number of sites scoring better than the average of aligned sites = 186
Number in coding regions = 168
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 4

          **********

No masking
Map Score:   -2.46258e-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:   -2.46258e-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:   -2.46258e-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