AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i005_Pyrimidine_Biosynthesis_aful_reg_300.orf -o005_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	RAG50088	101	Archaeoglobus_fulgidus
#2	RAG50299	300	Archaeoglobus_fulgidus
#3	RAG01787	33	Archaeoglobus_fulgidus
#4	RAG50155	30	Archaeoglobus_fulgidus
#5	RAG46689	78	Archaeoglobus_fulgidus

Motif number 1

TAACCAAGCAAAAGCTTAAATAATTATGAA	1	24	0	AAAGCTTAAA	    0.969075	-78
CATACGGGAGAAAGTTTAAAACCGTAAAAG	1	69	1	AAAGTTTAAA	    0.990276	-33
TCTTCTCCGTAAGGTAAAAA          	2	1	0	AAGGTAAAAA	    0.928415	-300
TTTGCAGCGCAAAGTATAAATCTCCTTGAC	2	227	1	AAAGTATAAA	    0.977927	-74
AGTTATTTTAAAAATTTAAAAATA      	4	5	0	AAAATTTAAA	    0.965256	-26
AGATTAAACAAAAGTTAAAAAACTTCCTGG	5	24	0	AAAGTTAAAA	    0.977927	-55
TTAATCTCAAAAGATTTAAACCTCTCCGCA	5	47	1	AAGATTTAAA	    0.949225	-32
          **********

Masking position 8
Map Score:   10.9802

Number of sites scoring better than the average of aligned sites = 92
Number in coding regions = 41
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 76
Fraction of orfs with sites within 600 bp upstream = 0.0122069


Motif number 2

AAAACCGTAAAAGGAGAGGAGGTGTG    	1	86	1	AAGGAGAGGA	    0.904011	-16
TTTTTACCTTACGGAGAAGATTGACGTGCC	2	11	1	ACGGAGAAGA	    0.983046	-290
ACGTGCCCGAGCAGATAACCACAAAAGACT	2	34	1	GCAGATAACC	    0.903069	-267
TTCAGACCGTACAGAGCACCATAAACTAGC	2	68	0	ACAGAGCACC	    0.964182	-233
GTCTGAATAAACAAAGAACCTTAGTTAGGA	2	91	1	ACAAAGAACC	    0.957785	-210
TCTCACAGGGACAGAGAAGAATGGTGCAGC	2	181	1	ACAGAGAAGA	    0.978279	-120
AATATAGGCGACGGAGAGCTGCACCATTCT	2	198	0	ACGGAGAGCT	    0.976384	-103
         AGAAAAGAACCCTTTAACAGG	2	290	0	GAAAAGAACC	    0.786556	-11
ATCCCGTCATGCGGAGAGGTTTAAATCTTT	5	56	0	GCGGAGAGGT	    0.964946	-23
          **********

Masking position 5
Map Score:   7.48774

Number of sites scoring better than the average of aligned sites = 1499
Number in coding regions = 1401
Number in noncoding regions = 98
Number of orfs with sites within 600 bp upstream = 70
Fraction of orfs with sites within 600 bp upstream = 0.0112432


Motif number 3

GAAAGTTTAAAACCGTAAAAGGAGAGGAGGT	1	78	1	AACCTAAAAG	    0.985451	-24
CCGAGCAGATAACCACAAAAGACTATGTGCT	2	40	1	AACCCAAAAG	    0.994616	-261
AATGCTGCCCAATCCAAAAAGCTCAAGGGCT	2	128	0	AATCAAAAAG	    0.981484	-173
AACCTCTGAAAACCCAGGAAGTTTTTTAACT	5	11	1	AACCAGGAAG	    0.960376	-68
ACTTTTGTTTAATCTCAAAAGATTTAAACCT	5	39	1	AATCCAAAAG	    0.987951	-40
          **** ******

Masking position 9
Map Score:   4.4805

Number of sites scoring better than the average of aligned sites = 48
Number in coding regions = 37
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 4

AGCTTTTTGGATTGGGCAGCATTACAGATT	2	136	1	ATTGGGCAGC	    0.992267	-165
ACAGAGAAGAATGGTGCAGCTCTCCGTCGC	2	191	1	ATGGTGCAGC	      0.9972	-110
CGTCGCCTATATTTTGCAGCGCAAAGTATA	2	215	1	ATTTTGCAGC	    0.983219	-86
TGGTTGCGCAACGGTGCAACTTATAACGG 	3	10	0	ACGGTGCAAC	    0.981333	-24
          **********

Masking position 8
Map Score:   3.58724

Number of sites scoring better than the average of aligned sites = 37
Number in coding regions = 32
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 5

ATTATTTAAGCTTTTGCTTGGTTATATCAAG	1	30	1	CTTTTGTTGG	    0.953482	-72
AAACAAAGAACCTTAGTTAGGATGATGGAAG	2	99	1	CCTTAGTAGG	    0.864793	-202
AGCTCTCTCACCTCTCACAGGGACAGAGAAG	2	169	1	CCTCTCCAGG	    0.627955	-132
CCTTGACGATCCTCTGGTTGGGATAGACAGT	2	250	1	CCTCTGTTGG	    0.989346	-51
AGAAAAGAACCCTTTAACAGGAAATTTTCTA	2	280	0	CCTTTACAGG	    0.909199	-21
          ****** ****

Masking position 3
Map Score:   1.34901

Number of sites scoring better than the average of aligned sites = 179
Number in coding regions = 164
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 6

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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 8

          **********

No masking
Map Score:   1.3033e-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