AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i338_weak1_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	bioB	86	biotin synthesis, sulfur insertion?
#2	HI1556	59	2-hydroxyacid dehydrogenase
#3	HI1560	22	H. influenzae predicted coding region HI1560
#4	HI1561	106	peptide chain release factor 1 (prfA)

Motif number 1

AATCTTTTCAATTTGGTTTACAAGTCGATT	1	11	0	ATTTGGTTTA	    0.926408	-76
ATTGAAAAGATTTAGGTTTACAAGTCTACA	1	29	1	TTTAGGTTTA	    0.912673	-58
TTTGTTGTTAATTCGGTGTAGACTTGTAAA	1	45	0	ATTCGGTGTA	    0.979836	-42
AAAAAACACGTTTTGGAGAAGCCCC     	1	72	1	TTTTGGAGAA	    0.904777	-15
TTAACCGCACTTTTGATGAAAT        	2	3	0	TTTTGATGAA	    0.930073	-57
TTCATCAAAAGTGCGGTTAATTTTGACCGC	2	13	1	GTGCGGTTAA	    0.964579	-47
TATATACAAAGTGCGGTCAAAATTAACCGC	2	25	0	GTGCGGTCAA	    0.924509	-35
GACGCTTTATTTGTGATTTACCCA      	4	5	0	TTGTGATTTA	    0.828209	-102
TTAATTTCCTTTTCGCTGTCAATTTTCCCT	4	43	1	TTTCGCTGTC	    0.904268	-64
CCGATTTTATTTTCGGTGACTTACAA    	4	91	1	TTTCGGTGAC	    0.982779	-16
          **********

Masking position 2
Map Score:   9.47251

Number of sites scoring better than the average of aligned sites = 2308
Number in coding regions = 2083
Number in noncoding regions = 225
Number of orfs with sites within 600 bp upstream = 261
Fraction of orfs with sites within 600 bp upstream = 0.041921


Motif number 2

CACTTTGTATATAAAAAAGGAGCAATTA  	2	42	1	ATAAAAAAGG	    0.940207	-18
          CTGAAATCAGATGTCCCTAT	3	13	0	CTGAAATCAG	    0.886114	-10
TCAATTTTCCCTAAAATCGGCTAGAATACG	4	61	1	CTAAAATCGG	    0.995856	-46
CTAAAATCGGCTAGAATACGCCGATTTTAT	4	71	1	CTAGAATACG	    0.951425	-36
GTCACCGAAAATAAAATCGGCGTATTCTAG	4	81	0	ATAAAATCGG	    0.991481	-26
          **********

Masking position 5
Map Score:   4.32478

Number of sites scoring better than the average of aligned sites = 222
Number in coding regions = 202
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 3

   AATCGACTTGTAAACCAAATTGAAAAG	1	8	1	TTGTAAACCA	    0.819397	-79
CGGTGTAGACTTGTAAACCTAAATCTTTTC	1	32	0	TTGTAAACCT	    0.963331	-55
TGACCGCACTTTGTATATAAAAAAGGAGCA	2	36	1	TTGTATATAA	     0.71468	-24
         TGGGTAAATCACAAATAAAGC	4	2	1	GGGTAAATCA	    0.967313	-105
          TTGTAAGTCACCGAAAATAA	4	97	0	TTGTAAGTCA	    0.986112	-10
          **********

Masking position 5
Map Score:   4.17446

Number of sites scoring better than the average of aligned sites = 117
Number in coding regions = 92
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 4

          **********

No masking
Map Score:   2.79544e-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:   2.79544e-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:   2.79544e-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