AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i256_heat_shock1_hpyl_reg_300.orf -o256_hpyl_300.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

AACCACCTTTAATTGTTATGAATTGAGTTTGAT	1	12	1	AATTGTTGAT	    0.981574	-279
AATTGAGTTTGATTGATAGGGGTGATTATAGCA	1	32	1	GATTGTGGGT	    0.995243	-259
AACACTCCTTGATTTAGCGGATTTTACCGCATG	1	112	0	GATTTGGGAT	    0.927157	-179
ATGACAAATTGATTGTTTTGATTTTCTTCAAAA	1	180	0	GATTGTTGAT	    0.988303	-111
TACAACCTCTGATAGATAGGAATGACAAATTGA	1	201	0	GATAGTGGAT	    0.992661	-90
ATCATCCCATAATTGTTCGCATTATTCCTTTTT	1	241	0	AATTGTGCAT	    0.974704	-50
ATATTATAAAAATTGGTGGGAATGATAAG    	1	272	1	AATTGTGGAT	    0.995725	-19
CTTTATTTTGAATAAGTTGGGTTT         	2	2	0	AATAATGGGT	    0.862316	-59
          ***** * *** *

Masking position 2
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

TTGATTGATAGGGGTGATTATAGCATTTAT	1	40	1	GGGGTGATTA	    0.978214	-251
GCTAAATCAAGGAGTGTTATTATGGAAGCA	1	127	1	GGAGTGTTAT	    0.966698	-164
CTGATAGATAGGAATGACAAATTGATTGTT	1	196	0	GGAATGACAA	    0.982791	-95
GAACAATTATGGGATGATATTATAAAAATT	1	256	1	GGGATGATAT	    0.989638	-35
AAAATTGGTGGGAATGATAAG         	1	280	1	GGAATGATAA	    0.992173	-11
          **********

Masking position 5
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

TTTGCCCCATAAATGCTATAATCACCCCTATC	1	46	0	AAAGCTAAAT	     0.97811	-245
TATGGGGCAAAAAAAGTAGAATCTGTATCAAG	1	67	1	AAAAGTAAAT	    0.985881	-224
ATTAAGATGCATGCGGTAAAATCCGCTAAATC	1	103	1	ATGGGTAAAT	    0.955635	-188
TATAGTTGGAAAAAGGAATAATGCGAACAATT	1	232	1	AAAGGAAAAT	    0.979516	-59
TATTCAAAATAAAGAGTATAATTACAAATTAC	2	21	1	AAAAGTAAAT	    0.985881	-40
          *** **** ***

Masking position 8
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

TCAAACTCAATTCATAACAATTAAAGGTGG	1	14	0	TTCATAACAA	    0.977485	-277
TACCGCATGCATCTTAATAAAACTTGATAC	1	91	0	ATCTTAATAA	    0.943438	-200
TGCGTCTGCTTCCATAATAACACTCCTTGA	1	133	0	TCCATAATAA	    0.954226	-158
TCTTCAAAAAATCCTAATAGTGTGGTTGCG	1	159	0	ATCCTAATAG	    0.903928	-132
TTTGAAGAAAATCAAAACAATCAATTTGTC	1	181	1	ATCAAAACAA	    0.962093	-110
ACCCAACTTATTCAAAATAAAGAGTATAAT	2	13	1	TTCAAAATAA	    0.968283	-48
          **********

Masking position 6
Map Score:   4.2728

Number of sites scoring better than the average of aligned sites = 214
Number in coding regions = 181
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 5

AACTCAATTCATAACAATTAAAGGTGGTTA	1	11	0	ATAACAATTA	     0.79064	-280
ATAAAACTTGATACAGATTCTACTTTTTTT	1	75	0	ATACAGATTC	    0.912506	-216
ATGCATCTTAATAAAACTTGATACAGATTC	1	85	0	ATAAAACTTG	    0.956359	-206
TAGATAGGAATGACAAATTGATTGTTTTGA	1	192	0	TGACAAATTG	    0.904486	-99
TTTTCCAACTATACAACCTCTGATAGATAG	1	215	0	ATACAACCTC	    0.910894	-76
GGATGATATTATAAAAATTGGTGGGAATGA	1	267	1	ATAAAAATTG	    0.957187	-24
AAGAGTATAATTACAAATTACTTACAACTT	2	32	1	TTACAAATTA	    0.957759	-29
TACAAATTACTTACAACTTAAAGGGGAT  	2	43	1	TTACAACTTA	    0.956942	-18
          **********

Masking position 3
Map Score:   5.00604

Number of sites scoring better than the average of aligned sites = 149
Number in coding regions = 118
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


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


Motif number 8

          **********

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