AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i138_Transmembrane_Transport_11_pyro_reg_300.orf -o138_pyro_300.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	RPH00338	102	Pyrococcus_OT3
#2	RPH00337	40	Pyrococcus_OT3
#3	RPH00336	19	Pyrococcus_OT3
#4	RPH01519	185	Pyrococcus_OT3

Motif number 1

CTTATTTCCATATATTTAAGACAAAAATCC	1	23	1	TATATTTAAG	      0.9654	-80
AGGATCAAGGTATATATAGGATTTTTGTCT	1	41	0	TATATATAGG	    0.843135	-62
GCAACCTAGACAAATTTGAGGATCAAGGTA	1	59	0	CAAATTTGAG	    0.982326	-44
AATAAAAGAGCAAATTTATGCCTTAAAAAC	2	11	0	CAAATTTATG	    0.875257	-30
       TGGCATATTTATCCAAATC    	3	4	1	CATATTTATC	    0.840777	-16
TTAAGTTAAGCAAATATTAGCATGGTGATT	4	15	0	CAAATATTAG	    0.808041	-171
GCACAAGGTTTAAATTTAAGTTAAGCAAAT	4	30	0	TAAATTTAAG	    0.965553	-156
AAACCTTGTGCATTTTTGGGCAATCCTTTT	4	49	1	CATTTTTGGG	    0.938781	-137
AGTTACATAACCTTTTTAAGGAAGTATTAA	4	142	1	CCTTTTTAAG	    0.851688	-44
TTAAGGCAACCAAATTTTGGCGAGGGAT  	4	168	1	CAAATTTTGG	    0.947313	-18
          **********

Masking position 5
Map Score:   11.0554

Number of sites scoring better than the average of aligned sites = 448
Number in coding regions = 371
Number in noncoding regions = 77
Number of orfs with sites within 600 bp upstream = 89
Fraction of orfs with sites within 600 bp upstream = 0.0142949


Motif number 2

        CTCTTCCACCTCCTTATTTCCA	1	3	1	CTTCCACCTC	    0.955685	-100
CTATATATACCTTGATCCTCAAATTTGTCT	1	52	1	CTTGATCCTC	    0.964913	-51
GCAAAAATGATTGCAACCTAGACAAATTTG	1	71	0	TTGCAACCTA	    0.878882	-32
          TTTAAACCCCAATAAAAGAG	2	31	0	TTTAAACCCC	    0.963688	-10
TTAACTTAAATTTAAACCTTGTGCATTTTT	4	36	1	TTTAAACCTT	    0.964611	-150
TTTAGACGTTTTGAAAACTCACAGAGGATA	4	76	1	TTGAAAACTC	    0.928271	-110
AATTGTGGAGTTTTATCCTCTGTGAGTTTT	4	89	0	TTTTATCCTC	    0.949826	-97
ATTTGGTTGCCTTAATACTTCCTTAAAAAG	4	153	0	CTTAATACTT	    0.792065	-33
          **********

Masking position 2
Map Score:   4.26378

Number of sites scoring better than the average of aligned sites = 1184
Number in coding regions = 1057
Number in noncoding regions = 127
Number of orfs with sites within 600 bp upstream = 130
Fraction of orfs with sites within 600 bp upstream = 0.0208802


Motif number 3

ATGATTGCAACCTAGACAAATTTGAGGATC	1	65	0	CCTAGACAAA	    0.967719	-38
 CCCACCACCCCTGCAAAAATGATTGCAAC	1	84	0	CCTGCAAAAA	    0.926759	-19
GTCTAAAAGGATTGCCCAAAAATGCACAAG	4	53	0	ATTGCCCAAA	    0.883289	-133
AGAGGATAAAACTCCACAATTTCTTGAATT	4	98	1	ACTCCACAAT	    0.975897	-88
GTAACTGAACATTCGACAATAATTCAAGAA	4	118	0	ATTCGACAAT	    0.916744	-68
       ATCCCTCGCCAAAATTTGGTTGC	4	173	0	CCTCGCCAAA	    0.989803	-13
          **********

Masking position 3
Map Score:   2.71421

Number of sites scoring better than the average of aligned sites = 343
Number in coding regions = 292
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 4

          **********

No masking
Map Score:   3.07965e-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:   3.07965e-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:   3.07965e-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