AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -iaraC_tpal_opreg_300.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

      AAGAATCCTCCCCCCTTTATCGAC	1	15	0	ATCCTCCCCC	    0.975838	-14
GCGGGTCGAGACACACGCCCCACT      	2	5	0	ACACACGCCC	    0.973113	-71
GCGTGTGTCTCGACCCGCCCGTGGTCAGTG	2	17	1	CGACCCGCCC	    0.991496	-59
TACTGGACGTCCCCATACCCACTGACCACG	2	36	0	CCCCATACCC	    0.954651	-40
          AGCCCCTCCCTCAAGTTCAT	2	66	0	AGCCCCTCCC	    0.997428	-10
AGGGTATTATCGCCTTTTCCCTGCTGCGGT	3	13	1	CGCCTTTTCC	    0.949885	-159
ACACACCTCTAGCCTCTCGCAAGACAGTTT	3	121	1	AGCCTCTCGC	    0.987251	-51
     TCTCTCCCCTCTCCCTGAGGC    	4	7	0	CCCCTCTCCC	    0.998233	-15
          **********

Masking position 4
Map Score:   13.2076

Number of sites scoring better than the average of aligned sites = 730
Number in coding regions = 595
Number in noncoding regions = 135
Number of orfs with sites within 600 bp upstream = 99
Fraction of orfs with sites within 600 bp upstream = 0.0159011


Motif number 2

  AAGAATCCTCCCCCCTTTATCGACAAAC	1	11	0	TCCCCCCTTT	    0.977889	-18
    AGCCCCTCCCTCAAGTTCATTACTGG	2	60	0	TCCCTCAAGT	     0.95938	-16
TATCGCCTTTTCCCTGCTGCGGTCAACATC	3	20	1	TCCCTGCTGC	    0.996706	-152
GCTCAGAGAGTCCCCGTTTCTTTTTCCCGT	3	59	0	TCCCCGTTTC	    0.981553	-113
CTCTCCCCTCTCCCTGAGGC          	4	1	0	TCCCTGAGGC	    0.991246	-21
          **********

Masking position 1
Map Score:   3.74342

Number of sites scoring better than the average of aligned sites = 205
Number in coding regions = 179
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 3

        GTTTGTCGATAAAGGGGGGAGGATTC	1	3	1	TTGTCGAAGG	    0.989733	-26
CCCATACCCACTGACCACGGGCGGGTCGAGACAC	2	21	0	CTGACCGGGG	    0.882495	-55
GGGTCAGATGTTGACCGCAGCAGGGAAAAGGCGA	3	22	0	TTGACCAGGG	    0.996499	-150
CGGTCAACATCTGACCCTAAACGGGAAAAAGAAA	3	39	1	CTGACCAAGG	    0.990659	-133
GTCAAGGATCTTGTCGCAAGGTTGCTCAGAGAGT	3	78	0	TTGTCGAGTG	    0.982041	-94
CACCTCTAGCCTCTCGCAAGACAGTTTCGCACCC	3	124	1	CTCTCGAGAG	    0.775325	-48
          ******  **  **

Masking position 2
Map Score:   3.86308

Number of sites scoring better than the average of aligned sites = 91
Number in coding regions = 81
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

GGGGACTCTCTGAGCAACCTTGCGACAAGA	3	74	1	TGAGCAACCT	    0.978483	-98
CTTGACAGAATTCGCACACACCTCTAGCCT	3	106	1	TTCGCACACA	    0.991214	-66
GCAAGACAGTTTCGCACCCTTAAAAAATAT	3	139	1	TTCGCACCCT	    0.994474	-33
AAAAATATAAGGAGCACACAC         	3	161	1	GGAGCACACA	    0.984727	-11
          **********

Masking position 6
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 5

AAGAATCCTCCCCCCTTTATCGACAAAC  	1	9	0	CCCCCTTTAT	    0.989849	-20
AGGGTATTATCGCCTTTTCCCTGCTGCGGT	3	13	1	CGCCTTTTCC	    0.972516	-159
CGTTTCTTTTTCCCGTTTAGGGTCAGATGT	3	45	0	TCCCGTTTAG	    0.973244	-127
CTCAGAGAGTCCCCGTTTCTTTTTCCCGTT	3	58	0	CCCCGTTTCT	    0.995469	-114
      TCTCTCCCCTCTCCCTGAGGC   	4	8	0	TCCCCTCTCC	    0.985496	-14
          **********

Masking position 6
Map Score:   3.73906

Number of sites scoring better than the average of aligned sites = 203
Number in coding regions = 177
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


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


Motif number 8

          **********

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