AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i256_heat_shock1_hpyl_reg_100.orf -o256_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 =  	0.39
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RHP01432	290	AE000511
#2	RHP01433	60	AE000511

Motif number 1

ATCAAACTCAATTCATAACAATTAAAGGTGGTT	1	12	0	ATCAACAATT	    0.981462	-279
TGCTATAATCACCCCTATCAATCAAACTCAATT	1	32	0	ACCCACAATC	    0.995214	-259
CATGCGGTAAAATCCGCTAAATCAAGGAGTGTT	1	112	1	ATCCCAAATC	     0.92674	-179
TTTTGAAGAAAATCAAAACAATCAATTTGTCAT	1	180	1	ATCAACAATC	    0.988231	-111
TCAATTTGTCATTCCTATCTATCAGAGGTTGTA	1	201	1	ATCCACTATC	    0.992616	-90
AAAAAGGAATAATGCGAACAATTATGGGATGAT	1	241	1	ATGCACAATT	    0.974552	-50
    CTTATCATTCCCACCAATTTTTATAATAT	1	272	0	ATCCACAATT	    0.995698	-19
         AAACCCAACTTATTCAAAATAAAG	2	2	1	ACCCATTATT	    0.861582	-59
          * *** * *****

Masking position 11
Map Score:   10.9698

Number of sites scoring better than the average of aligned sites = 255
Number in coding regions = 234
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 2

ATAAATGCTATAATCACCCCTATCAATCAA	1	40	0	TAATCACCCC	    0.978214	-251
TGCTTCCATAATAACACTCCTTGATTTAGC	1	127	0	ATAACACTCC	    0.966698	-164
AACAATCAATTTGTCATTCCTATCTATCAG	1	196	1	TTGTCATTCC	    0.982791	-95
AATTTTTATAATATCATCCCATAATTGTTC	1	256	0	ATATCATCCC	    0.989638	-35
         CTTATCATTCCCACCAATTTT	1	280	0	TTATCATTCC	    0.992173	-11
          **********

Masking position 6
Map Score:   5.81217

Number of sites scoring better than the average of aligned sites = 33
Number in coding regions = 27
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

GATAGGGGTGATTATAGCATTTATGGGGCAAA	1	46	1	ATTTAGCTTT	    0.977977	-245
CTTGATACAGATTCTACTTTTTTTGCCCCATA	1	67	0	ATTTACTTTT	    0.985795	-224
GATTTAGCGGATTTTACCGCATGCATCTTAAT	1	103	0	ATTTACCCAT	    0.955374	-188
AATTGTTCGCATTATTCCTTTTTCCAACTATA	1	232	0	ATTTTCCTTT	    0.979392	-59
GTAATTTGTAATTATACTCTTTATTTTGAATA	2	21	0	ATTTACTTTT	    0.985795	-40
          *** **** ***

Masking position 5
Map Score:   2.6479

Number of sites scoring better than the average of aligned sites = 58
Number in coding regions = 39
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 4

ACTCAATTCATAACAATTAAAGGTGGTTA 	1	10	0	TAACAATTAA	    0.838353	-281
CCCCTATCAATCAAACTCAATTCATAACAA	1	24	0	TCAAACTCAA	     0.87874	-267
TGCATCTTAATAAAACTTGATACAGATTCT	1	84	0	TAAAACTTGA	    0.957205	-207
AGATAGGAATGACAAATTGATTGTTTTGAT	1	191	0	GACAAATTGA	     0.86737	-100
TATTCCTTTTTCCAACTATACAACCTCTGA	1	222	0	TCCAACTATA	    0.732616	-69
GATGATATTATAAAAATTGGTGGGAATGAT	1	268	1	TAAAAATTGG	    0.852219	-23
CCCAACTTATTCAAAATAAAGAGTATAATT	2	14	1	TCAAAATAAA	    0.870084	-47
AGAGTATAATTACAAATTACTTACAACTTA	2	33	1	TACAAATTAC	    0.883598	-28
ACAAATTACTTACAACTTAAAGGGGAT   	2	44	1	TACAACTTAA	    0.973518	-17
          **********

Masking position 5
Map Score:   2.41001

Number of sites scoring better than the average of aligned sites = 426
Number in coding regions = 312
Number in noncoding regions = 114
Number of orfs with sites within 600 bp upstream = 110
Fraction of orfs with sites within 600 bp upstream = 0.0176678


Motif number 5

          **********

No masking
Map Score:   3.7902e-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:   3.7902e-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:   3.7902e-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