AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -iaraC_pyro_opreg_100.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

CTTAAAGGTAGAAAAGGAAAAAGGAATAAA	1	15	0	GAAAAGGAAA	    0.955688	-31
GGCACTTAACGAGAATCAAAGACTTATATT	2	16	1	GAGAATCAAA	    0.954612	-285
CGTTTTTCTTGAGGATCTCAGTAGGAGGAC	2	79	1	GAGGATCTCA	    0.957919	-222
AGGATCTCAGTAGGAGGACAAGCAAACCGA	2	90	1	TAGGAGGACA	    0.963509	-211
AAAGTTAACTGAAGAGGGAAAGGTCATTCT	2	202	1	GAAGAGGGAA	    0.952774	-99
CCAGGAGCATGAGAATGACCTTTCCCTCTT	2	213	0	GAGAATGACC	    0.939308	-88
GCTCCTGGAGGGGGATGAAATTTGAGGAGG	2	235	1	GGGGATGAAA	    0.975838	-66
GATGAAATTTGAGGAGGTAATCGTTAAATA	2	248	1	GAGGAGGTAA	    0.990561	-53
          **********

Masking position 5
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

  TTTAGGGCACTTAACGAGAATCAAAGAC	2	9	1	ACTTAACGAG	    0.991505	-292
CAAGAAAAACGTTTAAAGATCTGTAATTTC	2	60	0	GTTTAAAGAT	    0.922502	-241
CAACACTAAAACTCAACGCTAGAATACTTA	2	123	1	ACTCAACGCT	     0.95241	-178
ACGCTAGAATACTTAAAGAGTTAGGACTCA	2	138	1	ACTTAAAGAG	    0.989755	-163
AAGAGTTAGGACTCATAGATTATGGTACCA	2	153	1	ACTCATAGAT	    0.917765	-148
ATCGTGGGATATTTAACGATTACCTCCTCA	2	257	0	ATTTAACGAT	    0.978971	-44
TATCCACCTAATTTAAAAAGAATCGTGGGA	2	278	0	ATTTAAAAAG	    0.856703	-23
          **********

Masking position 5
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

AGGAAAAAGGAATAAAAACT          	1	1	0	AATAAAAACT	    0.933689	-45
AAAGGTAGAAAAGGAAAAAGGAATAAAAAC	1	12	0	AAGGAAAAAG	    0.949006	-34
TATATTGAGGAATATAAACGGAAATTACAG	2	40	1	AATATAAACG	    0.957142	-261
TGAGATCCTCAAGAAAAACGTTTAAAGATC	2	69	0	AAGAAAAACG	    0.993996	-232
GTAGGAGGACAAGCAAACCGATTTCAACAC	2	99	1	AAGCAAACCG	    0.977654	-202
          **********

Masking position 6
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

  AGTTTTTATTCCTTTTTCCTTTTCTACC	1	9	1	TTCCTTTTTC	    0.918203	-37
TAATCTATGAGTCCTAACTCTTTAAGTATT	2	145	0	GTCCTAACTC	    0.985835	-156
TACAGGCTTTGGCCTATCTCTGGTACCATA	2	173	0	GGCCTATCTC	     0.99266	-128
GCATGAGAATGACCTTTCCCTCTTCAGTTA	2	207	0	GACCTTTCCC	    0.983197	-94
          **********

Masking position 5
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