AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00730_aful_reg_100.orf -o00730_aful_100.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/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	AF0734	50	conserved hypothetical protein
#2	AF2075	61	hydroxyethylthiazole kinase (thiM)
#3	AF2079	33	A. fulgidus predicted coding region AF2079
#4	AF2081	111	A. fulgidus predicted coding region AF2081
#5	AF2207	300	formylmethanofuran:tetrahydromethanopterin formyltransferase (ftr-2)

Motif number 1

ATGGAGCAAAAAAGTTTAAGTTCTTTTCTC	1	24	0	AAAGTTTAAG	    0.969441	-27
ATTGTGCAAAAAAATTGAAAA         	2	2	0	AAAATTGAAA	    0.952382	-60
AAGTTGCGTCAAGGATTAAGAACTTTTGCT	2	37	0	AAGGATTAAG	    0.969104	-25
TTTCCTCATAAAAAATTAAATTTGAGAGC 	3	10	0	AAAAATTAAA	    0.927111	-24
AAATCAGGGTAAAAATTAAGGAGGA     	4	6	0	AAAAATTAAG	    0.952775	-106
AAGCATGAGCAAGGTTGAAAGGCTTGCGGT	5	99	0	AAGGTTGAAA	    0.968843	-202
AAAATTTTTAAAGATTGAAGTGATTTAACT	5	221	0	AAGATTGAAG	    0.980514	-80
CAAAAATAAAAAGATTTAAATCGCTTCTAC	5	259	1	AAGATTTAAA	    0.970029	-42
          **********

Masking position 8
Map Score:   12.0307

Number of sites scoring better than the average of aligned sites = 243
Number in coding regions = 191
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 2

   AGAGGAAATGGAGCAAAAAAGTTTAAGTT	1	32	0	AGAGCAAAAA	    0.980894	-19
TTGCTCACTGATTGTGCAAAAAAATTGAAAA 	2	10	0	ATTGCAAAAA	    0.964924	-52
TTGCACAATCAGTGAGCAAAAGTTCTTAATCC	2	23	1	ATAGCAAAAG	    0.980635	-39
CACGTTACTCAACAAACAAAAGCCTCAAATTC	5	52	0	ACAACAAAAG	    0.974736	-249
AAAATTTTCCAGCTTGCAAAAATAAAAAGATT	5	243	1	ACTGCAAAAA	    0.986358	-58
AATCGCTTCTACCAAACAAAAAGCAGGTGATA	5	277	1	ACAACAAAAA	    0.978964	-24
          * * ********

Masking position 8
Map Score:   5.18159

Number of sites scoring better than the average of aligned sites = 60
Number in coding regions = 45
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 3

    AAAAAGAGTTTCGGAGAAAAGAACTT	1	7	1	AGTTTCGGAG	    0.948644	-44
GCTCGGAGTGAGGCTTGAGGATGAGCTTTC	5	14	0	AGGCTTGAGG	    0.990727	-287
ATTCTATCTAAGGCTCGGAGTGAGGCTTGA	5	26	0	AGGCTCGGAG	    0.996581	-275
CAAGGTTGAAAGGCTTGCGGTGAGATACAA	5	90	0	AGGCTTGCGG	    0.993709	-211
          **********

Masking position 5
Map Score:   1.69348

Number of sites scoring better than the average of aligned sites = 201
Number in coding regions = 185
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

TAAAAAATTAAATTTGAGAGC         	3	2	0	AATTTGAGAG	    0.940966	-32
TTCTGATTTTATTTTCAAATATTATATATA	4	40	1	ATTTTCAAAT	     0.84589	-72
AGCATGAGCAAGGTTGAAAGGCTTGCGGTG	5	98	0	AGGTTGAAAG	      0.9429	-203
ACTTCAAAGGATTTTGAAAGCATGAGCAAG	5	116	0	ATTTTGAAAG	    0.982887	-185
TCAGAGAGATAACTTCAAAGGATTTTGAAA	5	127	0	AACTTCAAAG	    0.930957	-174
AAGCTGGAAAATTTTTAAAGATTGAAGTGA	5	228	0	ATTTTTAAAG	    0.938924	-73
          **********

Masking position 5
Map Score:   1.65916

Number of sites scoring better than the average of aligned sites = 256
Number in coding regions = 214
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 5

ATTAAGAACTTTTGCTCACTGATTGTGCAAAAA	2	20	0	TTTGACTGAT	    0.925617	-42
          TTACTTTCCTCATAAAAAATTAA	3	21	0	TTACCCTCAT	    0.953772	-13
TCCTCCTTAATTTTTACCCTGATTTTGGCTTCT	4	11	1	TTTTCCTGAT	    0.987395	-101
TTACCCTGATTTTGGCTTCTGATTTTATTTTCA	4	24	1	TTTGTCTGAT	    0.956414	-88
          TTTTTCACCTCTTACTCGGCATT	4	99	0	TTTTCCTCTT	    0.962885	-13
TCCTTTGAAGTTATCTCTCTGATGGACTCAATG	5	135	1	TTATTCTGAT	    0.953111	-166
AAATGTTCCTTTATCAGCCTCTTAACGAAATTC	5	175	1	TTATCCTCTT	    0.952208	-126
          ****   ******

Masking position 10
Map Score:   2.32307

Number of sites scoring better than the average of aligned sites = 185
Number in coding regions = 174
Number in noncoding regions = 11
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:   4.00336e-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:   4.00336e-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:   4.00336e-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