AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i116_Peptide_Transport_ecoli_reg_100.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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 = 	0

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

Motif number 1

GTGACGTCGCCATCTGTTCAACATTCGTAC	1	116	0	CATCTGTTCA	    0.989618	-133
ATGGCGACGTCACCTGTTCAACGACCAACC	1	133	1	CACCTGTTCA	    0.990375	-116
ACCACACGGCCCTCATTACGACCCCTGAAC	1	160	1	CCTCATTACG	    0.949141	-89
CTCATTACGACCCCTGAACACAAACGGTAA	1	171	1	CCCCTGAACA	    0.990194	-78
AGTAAGATAGCCTCTTTACATAAAATCCCT	1	222	1	CCTCTTTACA	    0.992731	-27
          **********

Masking position 4
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	    0.980754	-240
AGAAACCCATTAAAGCACGCTGCAGTGCGT	1	21	0	TAAAGCACGC	    0.921585	-228
CTCACGATCGTACCGCTCTGCTCCTCGCTA	1	49	1	TACCGCTCTG	    0.913641	-200
TCTATAACTATAACTCACAGAACAACTTAG	1	76	0	TAACTCACAG	    0.950154	-173
TAGTTATAGAGAAATCACGGGTACGAATGT	1	96	1	GAAATCACGG	    0.940889	-153
TTCAACGACCAACCACACGGCCCTCATTAC	1	149	1	AACCACACGG	    0.985281	-100
CGACCCCTGAACACAAACGGTAATGGCAAA	1	178	1	ACACAAACGG	    0.896721	-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	    0.996092	-206
AGAAATCACGGGTACGAATGTTGAACAGAT	1	105	1	GGTACGAATG	     0.99133	-144
ATTAAATATTAGTAAGATAGCCTCTTTACA	1	212	1	AGTAAGATAG	    0.966331	-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