AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i119_Spermidine_putrescine_Transport_aful_reg_100.orf -o119_aful_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	RAG47245	31	Archaeoglobus_fulgidus
#2	RAG47166	300	Archaeoglobus_fulgidus

Motif number 1

AAGTCGCTTTTAAGGACATTTTCCACTCTTTT	2	75	0	TAAGCATTTT	    0.993239	-226
TTTAGTTTTAAAAGGACAGTTTTTAGATTTTC	2	115	0	AAAGCAGTTT	     0.95941	-186
CTTTTAAAACTAAAATCATTATCCAAGGTCTG	2	133	1	TAAACATTAT	    0.936797	-168
TATGCCAATTAAAGCTCTTTTTTCTGCGTAAA	2	195	1	AAAGCTTTTT	    0.963153	-106
ATAAACATTCTAAATGCTTTTTACGCAGAAAA	2	214	0	TAAACTTTTT	    0.620617	-87
AACTTTCGTGTCAGCCCAATTTTTTATCTAAT	2	250	0	TCAGCAATTT	    0.961286	-51
 AGAACACAATCAATCCATTTTGTATAAAAAA	2	280	0	TCAACATTTT	    0.978199	-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

GTCCAAAAGAGTGGAAAATGTCCTTAAAAG	2	71	1	GTGGAAAATG	     0.97825	-230
GACTTTGGTTTTTGAAAATCTAAAAACTGT	2	102	1	TTTGAAAATC	    0.989705	-199
TTATCAGACCTTGGATAATGATTTTAGTTT	2	139	0	TTGGATAATG	    0.957138	-162
CTGATAAATTTTTGAAATTCTGATTTTCAA	2	162	1	TTTGAAATTC	     0.95955	-139
TTGGCATAAAATTGAAAATCAGAATTTCAA	2	173	0	ATTGAAAATC	    0.974393	-128
TTTATCTAATGTTGATAAACATTCTAAATG	2	230	0	GTTGATAAAC	     0.91359	-71
          **********

Masking position 5
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	    0.972223	-300
GTTTTAAAAGGACAGTTTTTAGATTTTCAA	2	113	0	GACAGTTTTT	    0.975797	-188
TCCAAGGTCTGATAAATTTTTGAAATTCTG	2	154	1	GATAAATTTT	    0.921433	-147
GCCAATTAAAGCTCTTTTTTCTGCGTAAAA	2	198	1	GCTCTTTTTT	    0.896919	-103
TTTCGTGTCAGCCCAATTTTTTATCTAATG	2	249	0	GCCCAATTTT	    0.971886	-52
GGGCTGACACGAAAGTTTTTTATACAAAAT	2	265	1	GAAAGTTTTT	    0.904118	-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