AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -irpoE_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	PH1410	117	332aa long hypothetical dipeptide transport system permease protein dppB
#2	PH1414	26	129aa long hypothetical protein
#3	PH1415	93	343aa long hypothetical 5' nuclease

Motif number 1

GGGCAATAAAGAAAAGAGAGAAGAAAGATTA    	1	7	0	GAAAGAAAGA	    0.979684	-111
AAATTTTGGTGTTTAAATAAGGGCAATAAAGAAAA	1	27	0	GTTATAGGGA	    0.949255	-91
GAACAAGAATGTACAAGGAGGGGCAAAT       	1	100	1	GTAAGAGGGA	    0.997964	-18
  CAAAAATTGAAAAAAGAAGAGGATAT       	2	4	0	GAAAGAGAGA	    0.996802	-23
CCCCTCACCTGAAAGGTGATGAGCACACCGGTAGG	3	55	1	GAAGGAGAGA	    0.996145	-39
GAGCACACCGGTAGGCTGAGGGTGATAAT      	3	75	1	GTAGGAGGTA	    0.984341	-19
          *** *  ** *** *

Masking position 9
Map Score:   5.94451

Number of sites scoring better than the average of aligned sites = 273
Number in coding regions = 254
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 2

TTTCTTCTCTCTTTTCTTTATTGCCCTTAT	1	16	1	CTTTTCTTTA	     0.94387	-102
AATAAAAATTTTGGTGTTTAAATAAGGGCA	1	37	0	TTGGTGTTTA	    0.953677	-81
AACACCAAAATTTTTATTTATGCGATAATA	1	49	1	TTTTTATTTA	    0.960049	-69
TTGTACATTCTTGTTCTATAACATCGTTTG	1	86	0	TTGTTCTATA	    0.983239	-32
         ATTGTTATAAACTTTCAGAGA	3	2	1	TTGTTATAAA	    0.917577	-92
          **********

Masking position 5
Map Score:   1.40199

Number of sites scoring better than the average of aligned sites = 110
Number in coding regions = 94
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

AAAAGAGAGAAGAAAGATTA          	1	1	0	AGAAAGATTA	    0.956347	-117
TTATAGAACAAGAATGTACAAGGAGGGGCA	1	95	1	AGAATGTACA	    0.910661	-23
TTGATATCTCTGAAAGTTTATAACAAT   	3	8	0	TGAAAGTTTA	    0.971929	-86
TCAGGTGAGGGGAAGGTTCATCATCAGACT	3	37	0	GGAAGGTTCA	    0.960684	-57
TCCCCTCACCTGAAAGGTGATGAGCACACC	3	54	1	TGAAAGGTGA	    0.964077	-40
          **********

Masking position 4
Map Score:   0.873881

Number of sites scoring better than the average of aligned sites = 328
Number in coding regions = 292
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 4

          **********

No masking
Map Score:   1.87173e-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 5

          **********

No masking
Map Score:   1.87173e-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:   1.87173e-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