AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -iaraC_tpal_opreg_100.orf -g0.528 -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 =  	0.528
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	TP0319	28	membrane lipoprotein (tmpC)
#2	TP0321	75	ribose/galactose ABC transporter, ATP-binding protein (rbsA-2)
#3	TP1018	171	conserved hypothetical protein
#4	TP1019	21	glu-tRNA amidotransferase, subunit C (gatC)

Motif number 1

TTTGTCGATAAAGGGGGGAGGATTCTT   	1	12	1	AAGGGGGGAG	    0.979249	-17
         AGTGGGGCGTGTGTCTCGACC	2	2	1	GTGGGGCGTG	    0.989951	-74
CTGACCACGGGCGGGTCGAGACACACGCCC	2	15	0	GCGGGTCGAG	    0.992245	-61
CCCGTGGTCAGTGGGTATGGGGACGTCCAG	2	34	1	GTGGGTATGG	    0.972083	-42
TAATGAACTTGAGGGAGGGGCT        	2	64	1	GAGGGAGGGG	    0.988787	-12
         GGAGGGTATTATCGCCTTTTC	3	2	1	GAGGGTATTA	    0.852474	-170
TGTCTTGCGAGAGGCTAGAGGTGTGTGCGA	3	117	0	GAGGCTAGAG	    0.985888	-55
GCCTCAGGGAGAGGGGAGAGA         	4	11	1	GAGGGGAGAG	    0.998042	-11
          **********

Masking position 4
Map Score:   12.7757

Number of sites scoring better than the average of aligned sites = 563
Number in coding regions = 458
Number in noncoding regions = 105
Number of orfs with sites within 600 bp upstream = 73
Fraction of orfs with sites within 600 bp upstream = 0.011725


Motif number 2

TCTTGTCGCAAGGTTGCTCAGAGAGTCCCC	3	74	0	AGGTTGCTCA	    0.976469	-98
AGGCTAGAGGTGTGTGCGAATTCTGTCAAG	3	106	0	TGTGTGCGAA	    0.990434	-66
ATATTTTTTAAGGGTGCGAAACTGTCTTGC	3	139	0	AGGGTGCGAA	    0.993952	-33
         GTGTGTGCTCCTTATATTTTT	3	161	0	TGTGTGCTCC	    0.983448	-11
          **********

Masking position 5
Map Score:   2.14624

Number of sites scoring better than the average of aligned sites = 173
Number in coding regions = 158
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 3

        GTTTGTCGATAAAGGGGGGAGG	1	3	1	TTGTCGATAA	    0.722591	-26
CCCATACCCACTGACCACGGGCGGGTCGAG	2	25	0	CTGACCACGG	    0.953125	-51
GGGTCAGATGTTGACCGCAGCAGGGAAAAG	3	26	0	TTGACCGCAG	    0.928432	-146
CGGTCAACATCTGACCCTAAACGGGAAAAA	3	39	1	CTGACCCTAA	     0.97806	-133
GTCAAGGATCTTGTCGCAAGGTTGCTCAGA	3	82	0	TTGTCGCAAG	    0.930706	-90
CACCTCTAGCCTCTCGCAAGACAGTTTCGC	3	124	1	CTCTCGCAAG	    0.957096	-48
  TCTCTCCCCTCTCCCTGAGGC       	4	4	0	CTCTCCCTGA	    0.943166	-18
          **********

Masking position 2
Map Score:   1.76174

Number of sites scoring better than the average of aligned sites = 515
Number in coding regions = 470
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 4

  AAGAATCCTCCCCCCTTTATCGACAAAC	1	11	0	TCCCCCCTTT	    0.968115	-18
TATCGCCTTTTCCCTGCTGCGGTCAACATC	3	20	1	TCCCTGCTGC	    0.995094	-152
CCGTTTCTTTTTCCCGTTTAGGGTCAGATG	3	46	0	TTCCCGTTTA	    0.929774	-126
GCTCAGAGAGTCCCCGTTTCTTTTTCCCGT	3	59	0	TCCCCGTTTC	    0.996356	-113
CTCTCCCCTCTCCCTGAGGC          	4	1	0	TCCCTGAGGC	    0.970683	-21
          **********

Masking position 1
Map Score:   2.56298

Number of sites scoring better than the average of aligned sites = 281
Number in coding regions = 260
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 5

          **********

No masking
Map Score:   -2.39152e-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:   -2.39152e-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:   -2.39152e-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