AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00561_pyro_reg_300.orf -o00561_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	PH1884	27	231aa long hypothetical triosephosphate isomerase
#2	PH1886	206	272aa long hypothetical L-isoaspartyl protein carboxyl methyltransferase

Motif number 1

CTTTATAAATCTAATCCAGGAGCACACGATAGAG	2	48	1	CATCCAGGCA	     0.98525	-159
CCAGGCTACACCACCCCGGCCACTCTATCGTGTG	2	70	0	CACCCGGCCT	    0.998019	-137
GTCCCCTGTGCTAACCAGGCTACACCACCCCGGC	2	84	0	CACCAGGCCA	    0.998009	-123
TGTGGATCCCCTGGCCCGGGTTCAAATCCCGGCC	2	118	1	CGCCCGGGCA	    0.869324	-89
GTTCAAATCCCGGCCCCGGCCCCAGAAACAGACT	2	137	1	CGCCCGGCCA	    0.839621	-70
          * * ******  **

Masking position 6
Map Score:   9.39774

Number of sites scoring better than the average of aligned sites = 25
Number in coding regions = 12
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 2

AGGAGCACACGATAGAGTGGCCGGGGTGGTGT	2	65	1	GTGAGTGGCC	    0.996354	-142
GAGTGGCCGGGGTGGTGTAGCCTGGTTAGCAC	2	79	1	GTGTGTAGCC	    0.997696	-128
TAGCACAGGGGACTGTGGATCCCCTGGCCCGG	2	105	1	GCGTGGATCC	    0.989895	-102
AGAAAAGTCTGTTTCTGGGGCCGGGGCCGGGA	2	144	0	GTCTGGGGCC	    0.995774	-63
          * * ********

Masking position 7
Map Score:   2.04339

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 40
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

AGTTTTCGCCAAAATCGAGAGAAGAAGGAG	2	20	0	AAAATCGAGA	    0.908376	-187
TAATCCAGGAGCACACGATAGAGTGGCCGG	2	59	1	GCACACGATA	    0.980441	-148
AGCCTGGTTAGCACAGGGGACTGTGGATCC	2	97	1	GCACAGGGGA	    0.986632	-110
GCCGGGATTTGAACCCGGGCCAGGGGATCC	2	121	0	GAACCCGGGC	     0.97486	-86
GCTTCTTCAAGCAATCGAGAC         	2	196	1	GCAATCGAGA	    0.991488	-11
          **********

Masking position 3
Map Score:   1.4835

Number of sites scoring better than the average of aligned sites = 186
Number in coding regions = 163
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 4

GATTTTGGCGAAAACTTTATAAATCTAATC	2	34	1	AAAACTTTAT	    0.963465	-173
ATTTTCAGAAAAGTCTGTTTCTGGGGCCGG	2	152	0	AAGTCTGTTT	    0.951677	-55
AAGCTTTGTTAAATCTTTATTTTCAGAAAA	2	170	0	AAATCTTTAT	    0.982601	-37
AAGATTTAACAAAGCTTCTTCAAGCAATCG	2	183	1	AAAGCTTCTT	    0.961022	-24
          **********

Masking position 6
Map Score:   0.405541

Number of sites scoring better than the average of aligned sites = 102
Number in coding regions = 55
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 67
Fraction of orfs with sites within 600 bp upstream = 0.0107613


Motif number 5

          **********

No masking
Map Score:   7.34864e-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:   7.34864e-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 7

          **********

No masking
Map Score:   7.34864e-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