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

        TCCCGTGCCCTCTACTGTTATA	2	44	0	CCGTGCCCTC	    0.997036	-12
   AGCATCCCCGTGATCTTTCCG      	3	5	0	CCGTGATCTT	    0.951579	-17
          CCCTCATCCCCATCACGCCA	4	48	0	CCCTCATCCC	    0.969435	-10
ATCTCTCTTTCTCTGTTCACAAACCATACA	5	15	0	CTCTGTTCAC	    0.934485	-56
     ATGCTCTGTGTCCTCCTCATGTGAC	5	56	0	CTGTGTCCTC	    0.986628	-15
CGGTTGTGTACGCTGACCCCCCTACAGGGT	6	32	0	CGCTGACCCC	    0.989772	-44
        GCCCCGGCCCTCCTCTTTTTTC	6	64	0	CCCGGCCCTC	    0.992721	-12
          **********

Masking position 8
Map Score:   7.46485

Number of sites scoring better than the average of aligned sites = 378
Number in coding regions = 330
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 52
Fraction of orfs with sites within 600 bp upstream = 0.00835207


Motif number 2

    AGCTCACACTACACGCTTGGAAACAG	1	7	1	CACTACACGC	    0.985042	-59
TGGAAACAGGTCCTTGACGAAACAAAAAAC	1	28	1	TCCTTGACGA	    0.651254	-38
AGAATGAAAATACAAGCCGGCTCG      	2	5	0	TACAAGCCGG	    0.920456	-51
TCAGCTATAACAGTAGAGGGCACGGGA   	2	39	1	CAGTAGAGGG	    0.878275	-17
CCCATCACGCCACCTGCCGCTTAAGATACA	4	30	0	CACCTGCCGC	    0.956444	-28
  CCCTCATCCCCATCACGCCACCTGCCGC	4	40	0	CCCATCACGC	    0.975278	-18
GAAAATGAGTCACATGAGGAGGACACAGAG	5	48	1	CACATGAGGA	    0.949307	-23
ACAGGGTAGGCAAAACCGGCGCGCCTAT  	6	9	0	CAAAACCGGC	    0.896044	-67
ACGCTGACCCCCCTACAGGGTAGGCAAAAC	6	23	0	CCCTACAGGG	    0.917485	-53
GGTCAGCGTACACAACCGGTGAAAAAAGAG	6	44	1	CACAACCGGT	    0.943972	-32
          **********

Masking position 9
Map Score:   7.33379

Number of sites scoring better than the average of aligned sites = 1552
Number in coding regions = 1437
Number in noncoding regions = 115
Number of orfs with sites within 600 bp upstream = 98
Fraction of orfs with sites within 600 bp upstream = 0.0157404


Motif number 3

GTTTGTGAACAGAGAAAGAGAGATTAGGAA	5	21	1	AGAGAAAGAG	    0.980653	-50
AGAGAGATTAGGAAAATGAGTCACATGAGG	5	37	1	GGAAAATGAG	    0.989565	-34
CACATGAGGAGGACACAGAGCAT       	5	58	1	GGACACAGAG	    0.991606	-13
CACAACCGGTGAAAAAAGAGGAGGGCCGGG	6	54	1	GAAAAAAGAG	    0.983689	-22
          **********

Masking position 5
Map Score:   2.68932

Number of sites scoring better than the average of aligned sites = 50
Number in coding regions = 43
Number in noncoding regions = 7
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:   -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