AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -iflhCD_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	TP0708	65	T. pallidum predicted coding region TP0708
#2	TP0709	55	RNA polymerase sigma-28 factor
#3	TP0721	21	flagellar motor switch protein (fliM)
#4	TP0726	57	flagellar protein (flbD)
#5	TP0727	70	flagellar hook protein (flgE)
#6	TP0728	75	flagellar hook assembly scaffolding protein (flgD)

Motif number 1

ATCAGCTATAACAGTAGAGGGCACGGGA        	2	38	1	AAGTGAGGGG	    0.995246	-18
       CGGAAAGATCACGGGGATGCT        	3	4	1	AAGACACGGG	    0.954941	-18
CGGCAGGTGGCGTGATGGGGATGAGGG         	4	41	1	CTGAGGGGAG	    0.992785	-17
ACAGAGAAAGAGAGATTAGGAAAATGAGTCACATGA	5	29	1	AAGATAGGAG	    0.973006	-42
AAATGAGTCACATGAGGAGGACACAGAGCAT     	5	50	1	CTGAGAGGAG	    0.995394	-21
TTTTGCCTACCCTGTAGGGGGGTCAGCGTACACAAC	6	24	1	CTGTGGGGGG	    0.992404	-52
ACCGGTGAAAAAAGAGGAGGGCCGGGGC        	6	58	1	AAGAGAGGGG	    0.997926	-18
          * *** *****    *

Masking position 10
Map Score:   8.04812

Number of sites scoring better than the average of aligned sites = 182
Number in coding regions = 161
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 2

CTGTTTCCAAGCGTGTAGTGTGAGCT     	1	6	0	GCTGTAGTGT	    0.990819	-60
CTAGTCTGCAGCTGGTTTTTTGTTTCGTCAA	1	41	0	GCGGTTTTTT	    0.989938	-25
   CGAGCCGGCTTGTATTTTCATTCTGAAA	2	8	1	GCTGTATTTT	    0.958677	-48
ATCTTAAGCGGCAGGTGGCGTGATGGGGATG	4	33	1	GCGGTGGCGT	    0.989909	-25
  ATAGGCGCGCCGGTTTTGCCTACCCTGTA	6	9	1	GCGGTTTTGC	     0.99069	-67
CTCTTTTTTCACCGGTTGTGTACGCTGACCC	6	43	0	ACGGTTGTGT	    0.986076	-33
          ** ********

Masking position 6
Map Score:   6.24873

Number of sites scoring better than the average of aligned sites = 253
Number in coding regions = 230
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 3

      AGCTCACACTACACGCTTGGAAACA	1	5	1	CACCTACACG	     0.97584	-61
TACATTTTCACACAGTCGACACA        	4	3	0	CACGTCGACA	    0.992195	-55
ATCTCTCTTTCTCTGTTCACAAACCATACAA	5	14	0	CTCGTTCACA	    0.974343	-57
GACCCCCCTACAGGGTAGGCAAAACCGGCGC	6	17	0	CAGGTAGGCA	    0.985298	-59
GTAGGGGGGTCAGCGTACACAACCGGTGAAA	6	37	1	CAGGTACACA	    0.995407	-39
          *** *******

Masking position 6
Map Score:   1.56117

Number of sites scoring better than the average of aligned sites = 121
Number in coding regions = 111
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

          **********

No masking
Map Score:   -8.21797e-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:   -8.21797e-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:   -8.21797e-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