AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -ifadR_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	PH0677	225	350aa long hypothetical acyl carrier protein synthetase
#2	PH0803	56	110aa long hypothetical protein

Motif number 1

TGTAGTTTTCGGTGGAGGTACTAAGACATT	1	75	1	GGTGGAGGTA	    0.984075	-151
AATATATGTAGGTAATGATAGCATTTGACA	1	113	0	GGTAATGATA	    0.990054	-113
AAAGACTTTCGGTAATAGTACAATCTAAAA	1	156	0	GGTAATAGTA	    0.943268	-70
AAGGCTAATAGGTGAAGAAAAGAAAAGGTG	1	199	1	GGTGAAGAAA	    0.988222	-27
GAAAAGAAAAGGTGATGAAGA         	1	215	1	GGTGATGAAG	    0.968433	-11
AAAACGTTAGGGTAAAGTTAAGTTTGATAA	2	35	1	GGTAAAGTTA	    0.975249	-22
          **********

Masking position 3
Map Score:   6.36938

Number of sites scoring better than the average of aligned sites = 310
Number in coding regions = 272
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 2

AGATTAATTGAAAGCTTAAGGGGGCAAAAAA	1	12	0	AAAGCTAAGG	    0.967914	-214
ATCTAACTTAAAAACTCTAGATTGAACTCAG	1	41	0	AAAACCTAGA	    0.950046	-185
TGGAGGTACTAAGACATTACGACAATTGTCA	1	87	1	AAGACTTACG	    0.985411	-139
CCCTTTATAAAAGACTTTCGGTAATAGTACA	1	164	0	AAGACTTCGG	    0.990751	-62
TAAAGCATATAAAACGTTAGGGTAAAGTTAA	2	25	1	AAAACTTAGG	    0.995482	-32
          ***** *****

Masking position 2
Map Score:   2.75994

Number of sites scoring better than the average of aligned sites = 196
Number in coding regions = 173
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 3

TAATCTGAGTTCAATCTAGAGTTTTTAAGT	1	37	1	TCAATCTAGA	    0.890765	-189
ACTACATAAATCTAACTTAAAAACTCTAGA	1	51	0	TCTAACTTAA	     0.95658	-175
CGGTAATAGTACAATCTAAAATCGTTGATC	1	147	0	ACAATCTAAA	    0.968081	-79
     GGTTATCAAACTTAACTTTACCCTA	2	42	0	TCAAACTTAA	    0.975181	-15
          **********

Masking position 4
Map Score:   2.29305

Number of sites scoring better than the average of aligned sites = 28
Number in coding regions = 25
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 4

          **********

No masking
Map Score:   -7.57276e-14

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:   -7.57276e-14

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:   -7.57276e-14

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