AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -intrC_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	PH0359	300	443aa long hypothetical glutamine synthetase
#2	PH1815	24	284aa long hypothetical cobalt transport ATP-binding protein

Motif number 1

TGGAACCCTGTTAATGATAATTTCTCTAAT	1	27	1	TTAATGATAA	    0.898569	-274
GATAATTTCTCTAATAGTCAGGGAGCACTT	1	42	1	CTAATAGTCA	    0.909276	-259
ATTTCTTCGTCTAATGTTCAATGTTCATGA	1	216	1	CTAATGTTCA	    0.981164	-85
TAAGTCTTTACTCATGAACATTGAACATTA	1	227	0	CTCATGAACA	    0.980374	-74
TCATCCGCTTTTAGTGAACAATATACCAAA	1	259	0	TTAGTGAACA	    0.967533	-42
GAATAGTTATCTAATGATCATCCGCTTTTA	1	276	0	CTAATGATCA	     0.99529	-25
          CTAGTGAATAGTTATCTAAT	1	291	0	CTAGTGAATA	    0.944134	-10
          **********

Masking position 10
Map Score:   7.47599

Number of sites scoring better than the average of aligned sites = 115
Number in coding regions = 98
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 2

AGTGCTCCCTGACTATTAGAGAAATTATCA	1	41	0	GACTATTAGA	     0.97422	-260
ATTTTTGACAGTATATTAGTGGGTAGAAGA	1	187	1	GTATATTAGT	    0.956328	-114
CATGAACATTGAACATTAGACGAAGAAATC	1	215	0	GAACATTAGA	    0.990223	-86
AATGTTCAATGTTCATGAGTAAAGACTTAT	1	228	1	GTTCATGAGT	    0.956433	-73
AAAAGCGGATGATCATTAGATAACTATTCA	1	277	1	GATCATTAGA	    0.990194	-24
          **********

Masking position 5
Map Score:   4.22712

Number of sites scoring better than the average of aligned sites = 58
Number in coding regions = 53
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

        TATTCGCCTTCCTTTATGGAAC	1	3	1	TTCGCCTTCC	    0.988652	-298
TTTATATAGCCTTGACTCTCGGAAGTGCTC	1	64	0	CTTGACTCTC	    0.982554	-237
ACTAAGTTTACTTGCCTTCCTAACCCTCTT	1	93	1	CTTGCCTTCC	    0.995551	-208
        TACTCCCCTCTCCTTGGGAGCA	2	13	0	CTCCCCTCTC	    0.992315	-12
          **********

Masking position 7
Map Score:   2.40269

Number of sites scoring better than the average of aligned sites = 138
Number in coding regions = 132
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 4

AAATTATCATTAACAGGGTTCCATAAAGGA	1	20	0	TAACAGGGTT	    0.983814	-281
CCCCAGCAAGTAAGAGGGTTAGGAAGGCAA	1	104	0	TAAGAGGGTT	    0.993915	-197
TCAGTTAAAATTTGGGGGTTATTGTGCTTT	1	158	0	TTTGGGGGTT	    0.981933	-143
TGACAGTATATTAGTGGGTAGAAGATTTCT	1	192	1	TTAGTGGGTA	    0.973452	-109
          **********

Masking position 9
Map Score:   2.33936

Number of sites scoring better than the average of aligned sites = 116
Number in coding regions = 107
Number in noncoding regions = 9
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:   3.36387e-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:   3.36387e-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:   3.36387e-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