AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -iaraC_pyro_opreg_300.orf -g0.419 -x5 
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 =  	0.419
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	PH1713	45	498aa long hypothetical sugar transport ATP-binding protein
#2	PH1714	300	405aa long hypothetical protein

Motif number 1

TTTATTCCTTTTTCCTTTTCTACCTTTAAG	1	15	1	TTTCCTTTTC	    0.962173	-31
AATATAAGTCTTTGATTCTCGTTAAGTGCC	2	16	0	TTTGATTCTC	    0.961248	-285
GTCCTCCTACTGAGATCCTCAAGAAAAACG	2	79	0	TGAGATCCTC	    0.963986	-222
TCGGTTTGCTTGTCCTCCTACTGAGATCCT	2	90	0	TGTCCTCCTA	    0.968886	-211
AGAATGACCTTTCCCTCTTCAGTTAACTTT	2	202	0	TTCCCTCTTC	    0.959667	-99
AAGAGGGAAAGGTCATTCTCATGCTCCTGG	2	213	1	GGTCATTCTC	    0.948059	-88
CCTCCTCAAATTTCATCCCCCTCCAGGAGC	2	235	0	TTTCATCCCC	    0.979436	-66
TATTTAACGATTACCTCCTCAAATTTCATC	2	248	0	TTACCTCCTC	    0.991985	-53
          **********

Masking position 6
Map Score:   7.66665

Number of sites scoring better than the average of aligned sites = 1761
Number in coding regions = 1631
Number in noncoding regions = 130
Number of orfs with sites within 600 bp upstream = 123
Fraction of orfs with sites within 600 bp upstream = 0.0197559


Motif number 2

GTCTTTGATTCTCGTTAAGTGCCCTAAA  	2	9	0	CTCGTTAAGT	    0.990993	-292
GAAATTACAGATCTTTAAACGTTTTTCTTG	2	60	1	ATCTTTAAAC	    0.918187	-241
TAAGTATTCTAGCGTTGAGTTTTAGTGTTG	2	123	0	AGCGTTGAGT	    0.949661	-178
TGAGTCCTAACTCTTTAAGTATTCTAGCGT	2	138	0	CTCTTTAAGT	    0.989139	-163
TGGTACCATAATCTATGAGTCCTAACTCTT	2	153	0	ATCTATGAGT	    0.913213	-148
TGAGGAGGTAATCGTTAAATATCCCACGAT	2	257	1	ATCGTTAAAT	    0.977733	-44
TCCCACGATTCTTTTTAAATTAGGTGGATA	2	278	1	CTTTTTAAAT	      0.8495	-23
          **********

Masking position 8
Map Score:   6.47379

Number of sites scoring better than the average of aligned sites = 378
Number in coding regions = 351
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 3

          AGTTTTTATTCCTTTTTCCT	1	1	1	AGTTTTTATT	    0.932525	-45
GTTTTTATTCCTTTTTCCTTTTCTACCTTT	1	12	1	CTTTTTCCTT	    0.948097	-34
CTGTAATTTCCGTTTATATTCCTCAATATA	2	40	0	CGTTTATATT	    0.956371	-261
GATCTTTAAACGTTTTTCTTGAGGATCTCA	2	69	1	CGTTTTTCTT	    0.993884	-232
GTGTTGAAATCGGTTTGCTTGTCCTCCTAC	2	99	0	CGGTTTGCTT	    0.977243	-202
          **********

Masking position 5
Map Score:   2.75228

Number of sites scoring better than the average of aligned sites = 91
Number in coding regions = 80
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 4

GGTAGAAAAGGAAAAAGGAATAAAAACT  	1	9	0	GAAAAAGGAA	    0.913954	-37
AATACTTAAAGAGTTAGGACTCATAGATTA	2	145	1	GAGTTAGGAC	    0.985053	-156
TATGGTACCAGAGATAGGCCAAAGCCTGTA	2	173	1	GAGATAGGCC	     0.99232	-128
TAACTGAAGAGGGAAAGGTCATTCTCATGC	2	207	1	GGGAAAGGTC	    0.982272	-94
          **********

Masking position 6
Map Score:   0.528068

Number of sites scoring better than the average of aligned sites = 125
Number in coding regions = 113
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 5

          **********

No masking
Map Score:   -2.60469e-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:   -2.60469e-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:   -2.60469e-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