AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i116_ecoli_bsub_100.orf -o116_ecoli_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -x5 -e 
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 =  	0.47
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	sapA	248	homolog of Salmonella peptide transport periplasmic protein

Motif number 1

GTACGAATGTTGAACAGATGGCGACGTCAC	1	116	1	TGAACAGATG	    0.988401	-133
GGTTGGTCGTTGAACAGGTGACGTCGCCAT	1	133	0	TGAACAGGTG	    0.989246	-116
GTTCAGGGGTCGTAATGAGGGCCGTGTGGT	1	160	0	CGTAATGAGG	    0.943472	-89
TTACCGTTTGTGTTCAGGGGTCGTAATGAG	1	171	0	TGTTCAGGGG	    0.989043	-78
AGGGATTTTATGTAAAGAGGCTATCTTACT	1	222	0	TGTAAAGAGG	    0.991876	-27
          **********

Masking position 7
Map Score:   5.21437

Number of sites scoring better than the average of aligned sites = 235
Number in coding regions = 206
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 2

  TAACAATGACACGCACTGCAGCGTGCTT	1	9	1	ACACGCACTG	    0.981812	-240
AGAAACCCATTAAAGCACGCTGCAGTGCGT	1	21	0	TAAAGCACGC	    0.925648	-228
CTCACGATCGTACCGCTCTGCTCCTCGCTA	1	49	1	TACCGCTCTG	    0.918081	-200
TCTATAACTATAACTCACAGAACAACTTAG	1	76	0	TAACTCACAG	    0.952814	-173
TAGTTATAGAGAAATCACGGGTACGAATGT	1	96	1	GAAATCACGG	    0.944013	-153
TTCAACGACCAACCACACGGCCCTCATTAC	1	149	1	AACCACACGG	    0.986093	-100
CGACCCCTGAACACAAACGGTAATGGCAAA	1	178	1	ACACAAACGG	    0.901937	-71
          **********

Masking position 8
Map Score:   1.8139

Number of sites scoring better than the average of aligned sites = 2782
Number in coding regions = 2622
Number in noncoding regions = 160
Number of orfs with sites within 600 bp upstream = 192
Fraction of orfs with sites within 600 bp upstream = 0.0308384


Motif number 3

GGAGCAGAGCGGTACGATCGTGAGAAACCC	1	43	0	GGTACGATCG	    0.995998	-206
AGAAATCACGGGTACGAATGTTGAACAGAT	1	105	1	GGTACGAATG	     0.99103	-144
ATTAAATATTAGTAAGATAGCCTCTTTACA	1	212	1	AGTAAGATAG	    0.965057	-37
          **********

Masking position 4
Map Score:   0.369612

Number of sites scoring better than the average of aligned sites = 61
Number in coding regions = 57
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 4

          **********

No masking
Map Score:   -4.23894e-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:   -4.23894e-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:   -4.23894e-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