AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00920_ctra_reg_300.orf -o00920_ctra_300.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -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 =  	0.41
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	fusA	41	Elongation Factor G
#2	rs7	49	S7 Ribosomal Protein
#3	rs12	259	S12 Ribosomal Protein

Motif number 1

CCTAAACCTAAAGAAAAGAAATACGAAGAGGT	2	19	1	AAGAAAAAAT	    0.957669	-31
CAAAAACTTGAAAACAAGACTTGTATC     	3	6	0	AAAACAAATT	    0.977279	-254
ACAGTATTCGAAGAAAACATTTTATCAGCAAG	3	43	1	AAGAAAAATT	    0.992085	-217
AATAATTAATAAAAAAAGAGTTAAATCCTTGC	3	70	0	AAAAAAAATT	    0.987546	-190
AGATTTTCTTAAAACAAGCCTTCCCTAAAAAT	3	99	0	AAAACAACTT	     0.97685	-161
GGCTTGTTTTAAGAAAATCTTTTGGAGGAAAT	3	111	1	AAGAAAACTT	    0.990837	-149
ACAATTTTATTAAAAAACATTTCCTCCAAAAG	3	129	0	TAAAAAAATT	    0.934483	-131
AATATAGAATAAGAATATCTTTGTTTGCAAGG	3	201	0	AAGAATACTT	    0.928904	-59
          ******* * **

Masking position 7
Map Score:   13.1674

Number of sites scoring better than the average of aligned sites = 160
Number in coding regions = 160
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 2

GTTTAACATTCGTGTGTGAGAGGCAAAAAAGTT	1	17	1	CGTGTGGAGG	    0.981065	-25
AAGAAAACATTTTATCAGCAAGGATTTAACTCT	3	53	1	TTTATGAAGG	    0.988924	-207
TTATTAATTATTTTTAGGGAAGGCTTGTTTTAA	3	90	1	TTTTTGAAGG	    0.988977	-170
AAGAAAATCTTTTGGAGGAAATGTTTTTTAATA	3	121	1	TTTGGGAATG	    0.963622	-139
TAAGAATATCTTTGTTTGCAAGGGGTTATTTCT	3	191	0	TTTGTGAAGG	    0.997868	-69
TATTTCCCTGTTTGTAAGAGAGGTTGAATCGAG	3	229	1	TTTGTGGAGG	     0.99743	-31
          *****  * ****

Masking position 3
Map Score:   7.50798

Number of sites scoring better than the average of aligned sites = 38
Number in coding regions = 38
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 3

    ATAAACTCAACCTCTTCGTATTTCTT	2	34	0	TCAACCTCTT	    0.991197	-16
AAAAAAAGAGTTAAATCCTTGCTGATAAAA	3	62	0	TTAAATCCTT	    0.905451	-198
ATAGAGATCGATAAACTCTTACTAGACCTA	3	162	1	ATAAACTCTT	    0.969969	-98
AGACCTAGAAATAACCCCTTGCAAACAAAG	3	185	1	ATAACCCCTT	    0.987435	-75
TCTTCTCGATTCAACCTCTCTTACAAACAG	3	236	0	TCAACCTCTC	    0.980667	-24
          **********

Masking position 4
Map Score:   3.66705

Number of sites scoring better than the average of aligned sites = 86
Number in coding regions = 86
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 4

TAACATTCGTGTGTGAGAGGCAAAAAAGTT	1	20	1	GTGTGAGAGG	    0.986165	-22
TACAAGTCTTGTTTTCAAGTTTTTGAACTA	3	13	1	GTTTTCAAGT	    0.886866	-247
TGAACTAACAGTATTCGAAGAAAACATTTT	3	36	1	GTATTCGAAG	    0.929156	-224
TAATAAAATTGTTATAGAGATCGATAAACT	3	149	1	GTTATAGAGA	    0.888116	-111
GAATATCTTTGTTTGCAAGGGGTTATTTCT	3	191	0	GTTTGCAAGG	    0.984078	-69
TTCCCTGTTTGTAAGAGAGGTTGAATCGAG	3	232	1	GTAAGAGAGG	    0.978475	-28
          **********

Masking position 8
Map Score:   2.08497

Number of sites scoring better than the average of aligned sites = 201
Number in coding regions = 200
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

          **********

No masking
Map Score:   -3.59945e-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:   -3.59945e-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 7

          **********

No masking
Map Score:   -3.59945e-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