AlignACE version 2.2  July 7, 1998
alignACE -z/skink1/amcguire/genomes/ecoli.fna -a/home/amcguire/alignace/lib/ORF_ecoli.txt -b/home/amcguire/alignace/lib/bimes_ecoli.txt -k0 -l300 -jhipB.reg -g0.5 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	181

Input sequences:
#1	hipB 188 bp hipB 88 1-267 CDS

Motif number 1

ATATCCGCGATCGCGGATAAAAAGGAGGAT	1	54	0	TCGCGGATAA	    0.997391	-135
TTATCCGCGATCGCGGATATCGCAGCGTTT	1	64	1	TCGCGGATAT	    0.992905	-125
TTATCCGCTCTACGGGATAAACGCTGCGAT	1	82	0	TACGGGATAA	    0.982783	-107
TTATCCCGTAGAGCGGATAAGATGTGTTTC	1	92	1	GAGCGGATAA	    0.997881	-97
TTATCCTTTAGTGAGGATAAGTCAATCTGG	1	121	0	GTGAGGATAA	    0.975162	-68
TTATCCTCACTAAAGGATAAAACTTATAAT	1	131	1	TAAAGGATAA	    0.961388	-58
TTATCCGCTTAAGGGGATATTATAAGTTTT	1	149	0	AAGGGGATAT	    0.983125	-40
ATATCCCCTTAAGCGGATAAACTTGCTGTG	1	159	1	AAGCGGATAA	    0.996726	-30
          **********

Masking position 7
Map Score:   19.7748

Number of sites scoring better than the average of aligned sites = 526
Number in coding regions = 458
Number in noncoding regions = 68
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 2

TCCTTTTTATCCGCGATCGCGGATATCGCAGC	1	58	1	CCCGATGCGG	    0.499996	-131
CAGCGTTTATCCCGTAGAGCGGATAAGATGTG	1	86	1	CCGTAGGCGG	    0.882908	-103
TAAGTTTTATCCTTTAGTGAGGATAAGTCAAT	1	125	0	CCTTAGGAGG	    0.940316	-64
CTTATAATATCCCCTTAAGCGGATAAACTTGC	1	153	1	CCCTTAGCGG	    0.515934	-36
          ** **** ****

Masking position 9
Map Score:   2.71694

Number of sites scoring better than the average of aligned sites = 280
Number in coding regions = 245
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

         TTAATATTGCCGACTTCAAAC	1	2	1	TAATATTGCC	    0.909266	-187
ATTGCCGACTTCAAACGGCGCATCAACGCC	1	16	1	TCAAACGGCG	    0.993652	-173
AGGAGGATTTAAATAAGGCGTTGATGCGCC	1	32	0	AAATAAGGCG	    0.976092	-157
CGATCGCGGATAAAAAGGAGGATTTAAATA	1	47	0	TAAAAAGGAG	    0.947268	-142
         GTCATACGTCCACAGCAAGTT	1	178	0	TCATACGTCC	    0.967221	-11
          **********

Masking position 5
Map Score:   0.655505

Number of sites scoring better than the average of aligned sites = 1446
Number in coding regions = 1299
Number in noncoding regions = 147
Number of orfs with sites within 600 bp upstream = 154
Fraction of orfs with sites within 600 bp upstream = 0.024735


Motif number 4

          **********

No masking
Map Score:   6.63809e-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:   6.63809e-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:   6.63809e-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