AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i283_hypothetical8_pyro_reg_100.orf -o283_pyro_100.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 =  	0.42
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RPH00500	97	Pyrococcus_OT3
#2	RPH00499	300	Pyrococcus_OT3

Motif number 1

AAAATTCCTGGTGCCCCGGCCGGGATTTGA	2	128	1	GTGCCCCGGC	    0.999513	-173
TTTCGAGCCCGCGCCCCGGGTTCAAATCCC	2	149	0	GCGCCCCGGG	    0.998449	-152
CCCCGGTGGTGTAGCCCGGCCAAACATGCG	2	183	0	GTAGCCCGGC	    0.994784	-118
GCTAATGGGTCTGCCCCGGTGGTGTAGCCC	2	196	0	CTGCCCCGGT	    0.996491	-105
          **********

Masking position 5
Map Score:   6.64624

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 4
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

AAGAAAGGTTAATAAAAGTTTCG        	1	3	0	AAAAAAGTTT	    0.935183	-95
AGATTTTAGTAAAGAAAGGTTAATAAAAGTT	1	14	0	AAGAAAGGTT	    0.949842	-84
TGTTGATCCTCACAAGATTTTAGTAAAGAAA	1	28	0	CAAAGATTTT	    0.865441	-70
TCTTGTGAGGATCAACAGGTTTAAATTCCAA	1	42	1	ATAACAGGTT	    0.858545	-56
GGGAGAGTAAAATAAATTGTTTGGAGGTGAT	1	73	1	AAAAATTGTT	      0.7734	-25
CATGTTCTGCAAGAACAGGCTTAGGGCATAA	2	20	0	AAAACAGGCT	     0.96849	-281
CCTGTTCTTGCAGAACATGTTAGGGAATATC	2	32	1	CAAACATGTT	     0.96696	-269
ACCCCTTTCTCAAAAGAGACTGTGAAGATTG	2	90	0	CAAAGAGACT	    0.747827	-211
ATCGAAAATTAAGGAAATGCTAATGGGTCTG	2	213	0	AAGAAATGCT	    0.894244	-88
AGCTTCACCTCAGAAAATTTTCATTCATTGA	2	278	0	CAAAAATTTT	    0.907463	-23
          ** ********

Masking position 5
Map Score:   5.76795

Number of sites scoring better than the average of aligned sites = 447
Number in coding regions = 383
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 63
Fraction of orfs with sites within 600 bp upstream = 0.0101189


Motif number 3

 CGAAACTTTTATTAACCTTTCTTTACTAA	1	10	1	TATTAACCTT	    0.929937	-88
         GCATAAAACTTATGCCCTAAG	2	2	1	CATAAAACTT	    0.934606	-299
AAGGGGTAAGCATGAAAATTCCTGGTGCCC	2	114	1	CATGAAAATT	    0.977927	-187
GGGGCAGACCCATTAGCATTTCCTTAATTT	2	209	1	CATTAGCATT	    0.928058	-92
ATTCATTGAATATTAAAATTGCGTCAGTTC	2	257	0	TATTAAAATT	    0.949357	-44
ATATTCAATGAATGAAAATTTTCTGAGGTG	2	274	1	AATGAAAATT	    0.899293	-27
          **********

Masking position 5
Map Score:   2.77015

Number of sites scoring better than the average of aligned sites = 122
Number in coding regions = 101
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 4

TCCCTTGGAATTTAAACCTGTTGATCCTCA	1	47	0	TTTAAACCTG	    0.971115	-51
CCGGCCGGGATTTGAACCCGGGGCGCGGGC	2	143	1	TTTGAACCCG	    0.996017	-158
ATGCGGGCCTTTCGAGCCCGCGCCCCGGGT	2	158	0	TTCGAGCCCG	    0.994372	-143
          **********

Masking position 5
Map Score:   0.387506

Number of sites scoring better than the average of aligned sites = 37
Number in coding regions = 13
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 5

TCTGCAAGAACAGGCTTAGGGCATAAGTTT	2	16	0	CAGGCTTAGG	    0.985067	-285
TCTTGCAGAACATGTTAGGGAATATCTAGA	2	37	1	CATGTTAGGG	    0.978027	-264
CAGGAATTTTCATGCTTACCCCTTTCTCAA	2	108	0	CATGCTTACC	     0.97672	-193
GAAAGGCCCGCATGTTTGGCCGGGCTACAC	2	175	1	CATGTTTGGC	    0.991187	-126
          **********

Masking position 6
Map Score:   0.259057

Number of sites scoring better than the average of aligned sites = 58
Number in coding regions = 52
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 6

          **********

No masking
Map Score:   -8.92852e-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:   -8.92852e-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:   -8.92852e-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