AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i334_1_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	HI0658	160	ABC transporter, ATP-binding protein
#2	HI1560	22	H. influenzae predicted coding region HI1560
#3	HI1561	106	peptide chain release factor 1 (prfA)

Motif number 1

AAACTATTTATAATATAACAAGTCAATATA	1	22	0	TAATATAACA	    0.653077	-139
AAAAGCCACGTATAATAAGACGCAATAAAA	1	50	0	TATAATAAGA	    0.828603	-111
ATTTTCTAGTCAAAAAAGCCACGTATAATA	1	63	0	CAAAAAAGCC	    0.877678	-98
AGAAAATCGATAAAATCGGAATAGACTGTT	1	86	1	TAAAATCGGA	     0.97949	-75
AAAAATATTGCAAAATAGCCTCAAATTAAG	1	127	1	CAAAATAGCC	    0.966575	-34
AAAATAGCCTCAAATTAAGACCTATGTAGA	1	138	1	CAAATTAAGA	    0.942598	-23
         CTGAAATCAGATGTCCCTATC	2	12	0	TGAAATCAGA	    0.870154	-11
GGGTAAATCACAAATAAAGCGTCTGAGATT	3	12	1	CAAATAAAGC	    0.845386	-95
CAGCGAAAAGGAAATTAAGAATCTCAGACG	3	31	0	GAAATTAAGA	    0.823437	-76
CAATTTTCCCTAAAATCGGCTAGAATACGC	3	62	1	TAAAATCGGC	    0.984636	-45
TCACCGAAAATAAAATCGGCGTATTCTAGC	3	80	0	TAAAATCGGC	    0.984636	-27
          **********

Masking position 4
Map Score:   11.539

Number of sites scoring better than the average of aligned sites = 1521
Number in coding regions = 1254
Number in noncoding regions = 267
Number of orfs with sites within 600 bp upstream = 226
Fraction of orfs with sites within 600 bp upstream = 0.0362994


Motif number 2

TGACTAGAAAATCGATAAAATCGGAATAGA	1	81	1	ATCGATAAAA	    0.854484	-80
AATAGACTGTTCCGAGAAAAGAAAAAATAT	1	105	1	TCCGAGAAAA	    0.989984	-56
GGGAAAATTGACAGCGAAAAGGAAATTAAG	3	42	0	ACAGCGAAAA	    0.989991	-65
CTAGCCGATTTTAGGGAAAATTGACAGCGA	3	55	0	TTAGGGAAAA	    0.971543	-52
   TTGTAAGTCACCGAAAATAAAATCGGC	3	90	0	TCACCGAAAA	    0.975714	-17
          **********

Masking position 7
Map Score:   2.27964

Number of sites scoring better than the average of aligned sites = 261
Number in coding regions = 220
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 3

          **********

No masking
Map Score:   3.08538e-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 4

          **********

No masking
Map Score:   3.08538e-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:   3.08538e-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