AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00150_hpyl_reg_100.orf -o00150_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	HP1067	290	chemotaxis protein (cheY)

Motif number 1

          TTACTTGTAAAATCCTTGTCT	1	1	1	TTCTTGTAAA	    0.985499	-290
CCTTGTCTTTCTTTTTTCAAACCATCCAATG	1	24	1	CTTTTTCAAA	    0.947804	-267
AGTTATTTTATTACTTTTAAACGATTATCAT	1	75	1	TTCTTTTAAA	    0.990191	-216
ATGAGCGTTCTTATTTGTAAAAAAATTCAGT	1	115	0	TTTTTGTAAA	    0.970506	-176
TTAAATTAGGCTCTTTTTAAACAGCCAAAGC	1	245	0	CTTTTTTAAA	    0.983347	-46
CCTTTTAAGATTGCATTTAAATTAGGCTCTT	1	261	0	TTCATTTAAA	      0.9544	-30
   AGTGCTTCTCCTTTTAAGATTGCATTTA	1	273	0	CTCTTTTAAG	    0.974044	-18
          ** ********

Masking position 9
Map Score:   10.4052

Number of sites scoring better than the average of aligned sites = 564
Number in coding regions = 436
Number in noncoding regions = 128
Number of orfs with sites within 600 bp upstream = 97
Fraction of orfs with sites within 600 bp upstream = 0.0155798


Motif number 2

GAGTGCGATAAAGGGTCATTGGATGGTTTG	1	41	0	AAGGGTCATT	    0.814601	-250
TGTTTGCTATGATAATCGTTTAAAAGTAAT	1	84	0	GATAATCGTT	    0.927936	-207
TGGAGCGTTCAATGAGCGTTCTTATTTGTA	1	127	0	AATGAGCGTT	     0.91864	-164
CATTGGCTAAATGGAGCGTTCAATGAGCGT	1	138	0	ATGGAGCGTT	    0.980577	-153
CTTGACCGACAATAATCATTGGCTAAATGG	1	154	0	AATAATCATT	    0.728088	-137
CCTTATAATAATAAATCGTTCCAAATAATA	1	205	0	ATAAATCGTT	    0.957964	-86
ATTTATTATTATAAGGCGTTAGAGACGCTT	1	219	1	ATAAGGCGTT	    0.948995	-72
          **********

Masking position 9
Map Score:   5.54707

Number of sites scoring better than the average of aligned sites = 1110
Number in coding regions = 972
Number in noncoding regions = 138
Number of orfs with sites within 600 bp upstream = 119
Fraction of orfs with sites within 600 bp upstream = 0.0191134


Motif number 3

GATGGTTTGAAAAAAGAAAGACAAGGATTT	1	20	0	AAAAAGAAAG	    0.952071	-271
TTTTTTTACAAATAAGAACGCTCATTGAAC	1	121	1	AATAAGAACG	    0.969238	-170
ATCATTGGCTAAATGGAGCGTTCAATGAGC	1	140	0	AAATGGAGCG	    0.972665	-151
AATCGTTCCAAATAATAGCATGTTTTGATT	1	192	0	AATAATAGCA	    0.864906	-99
TTGGCTGTTTAAAAAGAGCCTAATTTAAAT	1	248	1	AAAAAGAGCC	    0.984825	-43
ATGCAATCTTAAAAGGAGAAGCACT     	1	276	1	AAAAGGAGAA	    0.955812	-15
          **********

Masking position 7
Map Score:   3.63153

Number of sites scoring better than the average of aligned sites = 1455
Number in coding regions = 1325
Number in noncoding regions = 130
Number of orfs with sites within 600 bp upstream = 102
Fraction of orfs with sites within 600 bp upstream = 0.0163829


Motif number 4

          **********

No masking
Map Score:   -3.38628e-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:   -3.38628e-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:   -3.38628e-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