AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i249_min_operon_hpyl_reg_300.orf -o249_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	RHP01276	248	AE000511
#2	RHP01277	24	AE000511

Motif number 1

ATTATAATAGAAAAAACGCATCGTTTAAGT	1	18	1	AAAAAACGCA	    0.973089	-231
TGATTATAGCAAGAAAAGCTAATTTTTCAC	1	46	0	AAGAAAAGCT	     0.97205	-203
AGCACTTTTAAAGAAGTGAAACGATGATTA	1	70	0	AAGAAGTGAA	    0.804466	-179
TTCACTTCTTTAAAAGTGCTCGTAGCTCAG	1	80	1	TAAAAGTGCT	    0.910919	-169
GCAGAATATTAAGAAATGGTGTGCTCGGAG	1	158	0	AAGAAATGGT	    0.965852	-91
ATAATGTTTAAAAACATGCAGAATATTAAG	1	175	0	AAAACATGCA	    0.963323	-74
ATTATGGTAAAATAAATACTTGCTTAAACA	1	212	1	AATAAATACT	    0.776705	-37
AATACTTGCTTAAACACGCTAGGAGATTTG	1	226	1	TAAACACGCT	    0.873115	-23
 ATCATTTAAAATAAAAGGAATCAT     	2	10	1	AATAAAAGGA	    0.815928	-15
          **********

Masking position 4
Map Score:   5.04175

Number of sites scoring better than the average of aligned sites = 3175
Number in coding regions = 2858
Number in noncoding regions = 317
Number of orfs with sites within 600 bp upstream = 216
Fraction of orfs with sites within 600 bp upstream = 0.0346932


Motif number 2

TATTCAGCTGAGCTACGAGCACTTTTAAAG	1	87	0	AGCTACGAGC	    0.991709	-162
AGGGATTCAAACCCCCGACCTACAGGACCG	1	130	0	ACCCCCGACC	    0.994792	-119
GGGTTTGAATCCCTCCGAGCACACCATTTC	1	146	1	CCCTCCGAGC	    0.998054	-103
    AATCAAATCTCCTAGCGTGTTTAAGC	1	233	0	ATCTCCTAGC	    0.987762	-16
          **********

Masking position 8
Map Score:   3.35974

Number of sites scoring better than the average of aligned sites = 6
Number in coding regions = 3
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

TTTTTCTATTATAATTTAAGGC        	1	3	0	ATAATTTAAG	    0.964696	-246
GAAAAAACGCATCGTTTAAGTGAAAAATTA	1	27	1	ATCGTTTAAG	    0.994082	-222
TGCTATAATCATCGTTTCACTTCTTTAAAA	1	65	1	ATCGTTTCAC	    0.981669	-184
          ATCATTTAAAATAAAAGGAA	2	1	1	ATCATTTAAA	    0.975486	-24
          **********

Masking position 5
Map Score:   2.41601

Number of sites scoring better than the average of aligned sites = 87
Number in coding regions = 76
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 4

CGATGCGTTTTTTCTATTATAATTTAAGGC	1	11	0	TTTCTATTAT	    0.953031	-238
TTAGCTTTTCTTGCTATAATCATCGTTTCA	1	54	1	TTGCTATAAT	    0.987583	-195
CCGCAACCTGTTGCTCTATTCAGCTGAGCT	1	103	0	TTGCTCTATT	    0.934224	-146
AGTATTTATTTTACCATAATGGGAGCGATA	1	202	0	TTACCATAAT	    0.929351	-47
      ATGATTCCTTTTATTTTAAATGAT	2	11	0	TTCCTTTTAT	    0.922816	-14
          **********

Masking position 7
Map Score:   1.05275

Number of sites scoring better than the average of aligned sites = 192
Number in coding regions = 150
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 5

          **********

No masking
Map Score:   -2.81785e-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:   -2.81785e-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:   -2.81785e-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