AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i116_ecoli_mtub_100.orf -o116_ecoli_mtub_100.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 =  	0.58
 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	    0.989235	-133
GGTTGGTCGTTGAACAGGTGACGTCGCCAT	1	133	0	TGAACAGGTG	     0.99002	-116
GTTCAGGGGTCGTAATGAGGGCCGTGTGGT	1	160	0	CGTAATGAGG	     0.94735	-89
TTACCGTTTGTGTTCAGGGGTCGTAATGAG	1	171	0	TGTTCAGGGG	    0.989831	-78
AGGGATTTTATGTAAAGAGGCTATCTTACT	1	222	0	TGTAAAGAGG	    0.992462	-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

AAGCACGCTGCAGTGCGTGTCATTGTTA  	1	9	0	CAGTGCGTGT	    0.980833	-240
ACGCACTGCAGCGTGCTTTAATGGGTTTCT	1	21	1	GCGTGCTTTA	     0.92189	-228
TAGCGAGGAGCAGAGCGGTACGATCGTGAG	1	49	0	CAGAGCGGTA	    0.913974	-200
CTAAGTTGTTCTGTGAGTTATAGTTATAGA	1	76	1	CTGTGAGTTA	    0.950354	-173
ACATTCGTACCCGTGATTTCTCTATAACTA	1	96	0	CCGTGATTTC	    0.941124	-153
GTAATGAGGGCCGTGTGGTTGGTCGTTGAA	1	149	0	CCGTGTGGTT	    0.985342	-100
TTTGCCATTACCGTTTGTGTTCAGGGGTCG	1	178	0	CCGTTTGTGT	    0.897112	-71
          **********

Masking position 3
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

GGGTTTCTCACGATCGTACCGCTCTGCTCC	1	43	1	CGATCGTACC	    0.996195	-206
ATCTGTTCAACATTCGTACCCGTGATTTCT	1	105	0	CATTCGTACC	    0.991664	-144
TGTAAAGAGGCTATCTTACTAATATTTAAT	1	212	0	CTATCTTACT	    0.967761	-37
          **********

Masking position 8
Map Score:   0.369612

Number of sites scoring better than the average of aligned sites = 77
Number in coding regions = 73
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