AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i111_Amino_Acid_Transport_2_aful_reg_100.orf -o111_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	RAG47603	30	Archaeoglobus_fulgidus
#2	RAG47602	57	Archaeoglobus_fulgidus
#3	RAG47874	261	Archaeoglobus_fulgidus

Motif number 1

     ATTTGAATTTTTGTCGTTCAACTAT	2	43	0	AATTTTTGTC	     0.98198	-15
        AGCATTTTGGTTCAAACAATTC	3	3	1	CATTTTGGTT	    0.949212	-259
TGGTTCAAACAATTCTGGTCTGTGCGGTTA	3	18	1	AATTCTGGTC	     0.99574	-244
GCAACTTGGAAATTCTCGTCAGAGAAGCTC	3	57	0	AATTCTCGTC	    0.988661	-205
AAAGATGTGCATTTTTGGTCCATTTTTCCA	3	172	0	ATTTTTGGTC	    0.985032	-90
          **********

Masking position 6
Map Score:   6.33431

Number of sites scoring better than the average of aligned sites = 156
Number in coding regions = 57
Number in noncoding regions = 99
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

     CCATATATACTGCGATGGCTTCTTG	1	6	1	TATACTGCGA	    0.955918	-25
ATAAAGGATTTTATCTGCAAAGGGCGAAGG	3	116	0	TTATCTGCAA	    0.969857	-146
ATAATGAACTTAATCTGGAAAAATGGACCA	3	157	1	TAATCTGGAA	    0.985332	-105
GGGGAGTATATAACCTGGGAGAAAGAAAGA	3	197	0	TAACCTGGGA	    0.988675	-65
CTCTCATGCCTTAACTGGCAGCGGGGAGTA	3	219	0	TTAACTGGCA	    0.975252	-43
          **********

Masking position 6
Map Score:   2.7596

Number of sites scoring better than the average of aligned sites = 72
Number in coding regions = 64
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

          GATAACAAGAAGCCATCGCA	1	21	0	GATAACAAGA	    0.976558	-10
TCGGAAGTCTGAGAAAAGGAGCAACTTGGA	3	77	0	GAGAAAAGGA	    0.972237	-185
CATTATAGATGAAAACAATAAAGGATTTTA	3	133	0	GAAAACAATA	      0.9023	-129
ACTTAATCTGGAAAAATGGACCAAAAATGC	3	164	1	GAAAAATGGA	    0.969695	-98
TAACCTGGGAGAAAGAAAGATGTGCATTTT	3	187	0	GAAAGAAAGA	    0.969208	-75
GAGGAATTTGGATTGCTGGACTCGTA    	3	246	1	GATTGCTGGA	    0.877729	-16
          **********

Masking position 2
Map Score:   2.56515

Number of sites scoring better than the average of aligned sites = 625
Number in coding regions = 567
Number in noncoding regions = 58
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


Motif number 4

          **********

No masking
Map Score:   -8.99385e-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:   -8.99385e-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 6

          **********

No masking
Map Score:   -8.99385e-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