AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i342_weak3_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	HI1263	103	homoserine acetyltransferase (met2)

Motif number 1

  TGATGTGCGATAATTTAGCCGTTTAGACGGC	1	9	1	GAATTTAGCG	    0.999293	-95
AGCTTGTCAAGAAATTTTAGCCGTCTAAACGGC	1	28	0	GAATTTAGCG	    0.999293	-76
AAAATTTCTTGACAAGCTAATCGACTTACTGAT	1	43	1	GAAGCTAACG	    0.996828	-61
TCGACTTACTGATAGTTTAAACGCCATTCTGAT	1	63	1	GAATTTAACG	    0.998906	-41
          ** * ***** **

Masking position 8
Map Score:   8.67238

Number of sites scoring better than the average of aligned sites = 27
Number in coding regions = 21
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 2

ATTTTAGCCGTCTAAACGGCTAAATTATCG	1	18	0	TCTAAACGGC	    0.990366	-86
GTTTAAACTATCAGTAAGTCGATTAGCTTG	1	55	0	TCAGTAAGTC	    0.986978	-49
ATCGTAATAATCAGAATGGCGTTTAAACTA	1	75	0	TCAGAATGGC	    0.996809	-29
          **********

Masking position 6
Map Score:   1.33418

Number of sites scoring better than the average of aligned sites = 37
Number in coding regions = 35
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

TAAACGGCTAAATTATCGCACATCA     	1	6	0	AATTATCGCA	    0.986727	-98
ATGGCGTTTAAACTATCAGTAAGTCGATTA	1	60	0	AACTATCAGT	    0.982625	-44
AACCTATCGTAATAATCAGAATGGCGTTTA	1	80	0	AATAATCAGA	    0.989098	-24
          **********

Masking position 5
Map Score:   0.722567

Number of sites scoring better than the average of aligned sites = 64
Number in coding regions = 59
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

          **********

No masking
Map Score:   -5.44113e-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:   -5.44113e-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:   -5.44113e-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