AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i338_weak1_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	HI1556	59	2-hydroxyacid dehydrogenase
#2	HI1560	22	H. influenzae predicted coding region HI1560
#3	HI1561	106	peptide chain release factor 1 (prfA)

Motif number 1

     ATTTCATCAAAAGTGCGGTTAATTTTG	1	6	1	ATCAAAAGCG	    0.994174	-54
CCTTTTTTATATACAAAGTGCGGTCAAAATTA	1	30	0	ATACAAAGCG	    0.994786	-30
CACTTTGTATATAAAAAAGGAGCAATTA    	1	42	1	ATAAAAAGAG	    0.987688	-18
TGGGTAAATCACAAATAAAGCGTCTGAGATTC	3	11	1	ACAAATAGCG	    0.979272	-96
TCAATTTTCCCTAAAATCGGCTAGAATACGCC	3	61	1	CTAAAATGCT	    0.940274	-46
GTCACCGAAAATAAAATCGGCGTATTCTAGCC	3	79	0	ATAAAATGCG	    0.996421	-28
          *******  ***

Masking position 5
Map Score:   8.05067

Number of sites scoring better than the average of aligned sites = 515
Number in coding regions = 370
Number in noncoding regions = 145
Number of orfs with sites within 600 bp upstream = 115
Fraction of orfs with sites within 600 bp upstream = 0.0184709


Motif number 2

TTCATCAAAAGTGCGGTTAATTTTGACCGC	1	13	1	GTGCGGTTAA	    0.996838	-47
TATATACAAAGTGCGGTCAAAATTAACCGC	1	25	0	GTGCGGTCAA	    0.997995	-35
AATTTCCTTTTCGCTGTCAATTTTCCCTAA	3	45	1	TCGCTGTCAA	     0.98912	-62
          **********

Masking position 9
Map Score:   3.46262

Number of sites scoring better than the average of aligned sites = 418
Number in coding regions = 262
Number in noncoding regions = 156
Number of orfs with sites within 600 bp upstream = 127
Fraction of orfs with sites within 600 bp upstream = 0.0203983


Motif number 3

        TGATAGGGACATCTGATTTCAG	2	3	1	ATAGGGACAT	    0.960049	-20
GGGAAAATTGACAGCGAAAAGGAAATTAAG	3	42	0	ACAGCGAAAA	    0.993717	-65
CTAGCCGATTTTAGGGAAAATTGACAGCGA	3	55	0	TTAGGGAAAA	     0.99031	-52
   TTGTAAGTCACCGAAAATAAAATCGGC	3	90	0	TCACCGAAAA	    0.983344	-17
          **********

Masking position 7
Map Score:   2.16036

Number of sites scoring better than the average of aligned sites = 160
Number in coding regions = 133
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 4

ATTTCATCAAAAGTGCGGTTAATTTTGACC	1	11	1	AAGTGCGGTT	    0.947088	-49
TTTATATACAAAGTGCGGTCAAAATTAACC	1	27	0	AAGTGCGGTC	    0.991395	-33
          **********

Masking position 4
Map Score:   2.14656

Number of sites scoring better than the average of aligned sites = 439
Number in coding regions = 317
Number in noncoding regions = 122
Number of orfs with sites within 600 bp upstream = 111
Fraction of orfs with sites within 600 bp upstream = 0.0178285


Motif number 5

GACGCTTTATTTGTGATTTACCCA        	3	3	0	TTGTATTACC	    0.996293	-104
GCGTCTGAGATTCTTAATTTCCTTTTCGCTGT	3	30	1	TTCTATTTCC	    0.990123	-77
TTCCTTTTCGCTGTCAATTTTCCCTAAAATCG	3	48	1	CTGTATTTTC	    0.975415	-59
          TTGTAAGTCACCGAAAATAAAA	3	95	0	TTGTATCACC	    0.993696	-12
          **** * *****

Masking position 6
Map Score:   1.66716

Number of sites scoring better than the average of aligned sites = 43
Number in coding regions = 39
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 6

          **********

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 7

          **********

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 8

          **********

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