AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i243_regulatory_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HI0979	148	nitrogen fixation protein (nifR3)

Motif number 1

TACACTTTTTTTGATTGACAAAAAGAAA   	1	8	0	TTGATGACAA	    0.863251	-141
AAAGTGAAATTTGTTTAAAAAATACACTTTT	1	30	0	TTGTTAAAAA	    0.614397	-119
GCATTTTGCCTTGCTTTGCAAAGTGAAATTT	1	49	0	TTGCTTGCAA	    0.527002	-100
TTATATCGAACTGCTCGACAACCGACAAGGC	1	94	0	CTGCTGACAA	    0.900392	-55
AGATTTAGGCTTGCTAGGAAAGGAACGTAAA	1	128	1	TTGCTGGAAA	    0.811307	-21
          ***** *****

Masking position 5
Map Score:   5.62598

Number of sites scoring better than the average of aligned sites = 222
Number in coding regions = 197
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 2

GCCTTGCTTTGCAAAGTGAAATTTGTTTAAAA	1	41	0	GCAATGAAAT	    0.994018	-108
ACTTTGCAAAGCAAGGCAAAATGCCGTATTAA	1	56	1	GCAACAAAAT	    0.995885	-93
CGGTTGTCGAGCAGTTCGATATAAATTAGATT	1	101	1	GCAGCGATAT	    0.993517	-48
TCCTTTCCTAGCAAGCCTAAATCTAATTTATA	1	120	0	GCAACTAAAT	    0.995886	-29
          ****  ******

Masking position 9
Map Score:   3.93717

Number of sites scoring better than the average of aligned sites = 51
Number in coding regions = 45
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

          **********

No masking
Map Score:   2.43208e-15

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 4

          **********

No masking
Map Score:   2.43208e-15

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:   2.43208e-15

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