AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i214_Ribosomal_Operon_1_hpyl_reg_300.orf -o214_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	RHP01041	300	AE000511

Motif number 1

ACTATTTGATCGTAAAAATACC        	1	3	0	CGTAAAAATA	    0.863826	-298
TTACCGCTTGATTAAAGATAAGCTCTTTAC	1	31	0	ATTAAAGATA	    0.843915	-270
CAAAAGACCGCTTAAAAAATTACCGCTTGA	1	50	0	CTTAAAAAAT	    0.964474	-251
TCCCTATCCCCTTAAGGAAATGAATTTTAC	1	133	1	CTTAAGGAAA	    0.982272	-168
ATGAATTTTACTTAAGAAATGAGTTTGACC	1	152	1	CTTAAGAAAT	    0.967118	-149
AATAAGGTTTTTTAAAAAATTTGTTTGACT	1	196	0	TTTAAAAAAT	    0.932457	-105
AAGTTTAAAGTTTAAAAATAAGGTTTTTTA	1	212	0	TTTAAAAATA	    0.932487	-89
TATTGCTGAATTTAAGGAAAGTTTAAAGTT	1	230	0	TTTAAGGAAA	    0.965563	-71
AGGAAATAAGCTTAAATATTGCTGAATTTA	1	246	0	CTTAAATATT	    0.820618	-55
AAGCACCCATTATAAGGAAATAAGCTTAAA	1	260	0	TATAAGGAAA	    0.816343	-41
          **********

Masking position 5
Map Score:   12.6345

Number of sites scoring better than the average of aligned sites = 1217
Number in coding regions = 958
Number in noncoding regions = 259
Number of orfs with sites within 600 bp upstream = 186
Fraction of orfs with sites within 600 bp upstream = 0.0298747


Motif number 2

CCCCTAACCCCAAAAGACCGCTTAAAAAATT	1	59	0	CAAAAGACCC	    0.991733	-242
AACCCCCAACTAAAAACCCCCTAACCCCAAA	1	76	0	TAAAAACCCC	    0.993798	-225
TAACCCTCCCCTACAACCCCCAACTAAAAAC	1	90	0	CTACAACCCC	    0.966249	-211
AGGTATTTTACAATAACCCTCCCCTACAACC	1	103	0	CAATAACCCC	      0.9814	-198
AGGGTTATTGTAAAATACCTCCCTATCCCCT	1	114	1	TAAAATACCC	    0.950092	-187
ACCATAAAATCAAAAGCAGTCAAACAAATTT	1	179	1	CAAAAGCAGC	     0.92075	-122
ACAAATTTTTTAAAAAACCTTATTTTTAAAC	1	202	1	TAAAAAACCT	    0.874908	-99
TTTGATAAAATTAAAGCACCCATTATAAGGA	1	272	0	TTAAAGCACC	    0.941867	-29
          ********* *

Masking position 5
Map Score:   8.46342

Number of sites scoring better than the average of aligned sites = 1312
Number in coding regions = 1163
Number in noncoding regions = 149
Number of orfs with sites within 600 bp upstream = 93
Fraction of orfs with sites within 600 bp upstream = 0.0149374


Motif number 3

TTCTTAAGTAAAATTCATTTCCTTAAGGGG	1	140	0	AAATTCATTT	    0.819864	-161
TTTTATGGTCAAACTCATTTCTTAAGTAAA	1	158	0	AAACTCATTT	    0.901872	-143
GTTTTTTAAAAAATTTGTTTGACTGCTTTT	1	190	0	AAATTTGTTT	    0.706659	-111
TTTTTTAAAAAACCTTATTTTTAAACTTTA	1	207	1	AACCTTATTT	    0.977065	-94
AGCAATATTTAAGCTTATTTCCTTATAATG	1	253	1	AAGCTTATTT	    0.977065	-48
          **********

Masking position 5
Map Score:   5.5184

Number of sites scoring better than the average of aligned sites = 125
Number in coding regions = 88
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 4

GCGGTCTTTTGGGGTTAGGGGGTTTTTAGT	1	69	1	GGGGTTAGGG	    0.998313	-232
TTTAGTTGGGGGTTGTAGGGGAGGGTTATT	1	93	1	GGTTGTAGGG	     0.99159	-208
ATTTCCTTAAGGGGATAGGGAGGTATTTTA	1	124	0	GGGGATAGGG	    0.998312	-177
          **********

Masking position 7
Map Score:   3.42735

Number of sites scoring better than the average of aligned sites = 61
Number in coding regions = 41
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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