AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i267_hypothetical12_hpyl_reg_300.orf -o267_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	RHP00088	297	AE000511
#2	RHP00089	82	AE000511

Motif number 1

AGAGTATGAAAATTTTTAAAAATTTACAAA	1	79	1	AATTTTTAAA	     0.96489	-219
TGTTCTTTCTCATTTTTGTAAATTTTTAAA	1	93	0	CATTTTTGTA	    0.920495	-205
TAAAAGGGGATATTTTTATATAATATGTAA	1	215	1	TATTTTTATA	    0.936384	-83
ATGTAAAAAGCATTCTTAAATCTAAAAATG	1	239	1	CATTCTTAAA	    0.978748	-59
AACATTGTAGCATTTTTAGATTTAAGAATG	1	249	0	CATTTTTAGA	    0.985386	-49
CTACAATGTTTATCTTTAAAACGAAAGGGC	1	269	1	TATCTTTAAA	    0.879507	-29
         TAATTTTTAGCGTTTTTAAGA	2	2	1	AATTTTTAGC	    0.858185	-81
TATAACTAATCATTCTTAAAAACGCTAAAA	2	15	0	CATTCTTAAA	    0.978748	-68
          **********

Masking position 2
Map Score:   9.30923

Number of sites scoring better than the average of aligned sites = 521
Number in coding regions = 412
Number in noncoding regions = 109
Number of orfs with sites within 600 bp upstream = 98
Fraction of orfs with sites within 600 bp upstream = 0.0157404


Motif number 2

AGTATGAAAATTTTTAAAAATTTACAAAAA	1	81	1	TTTTTAAAAA	    0.499552	-217
TTCTTTCTCATTTTTGTAAATTTTTAAAAA	1	91	0	TTTTTGTAAA	    0.785958	-207
TACCTAATTCTCATTAAATAGATTTTTATG	1	156	0	TCATTAAATA	    0.834157	-142
CAACCCCTTTTTTTTACCTAATTCTCATTA	1	170	0	TTTTTACCTA	    0.818305	-128
AAAGGGGATATTTTTATATAATATGTAAAA	1	217	1	TTTTTATATA	      0.9206	-81
TTAAGAATGCTTTTTACATATTATATAAAA	1	228	0	TTTTTACATA	    0.923805	-70
GTAAAAAGCATTCTTAAATCTAAAAATGCT	1	241	1	TTCTTAAATC	    0.927792	-57
ACAATGTTTATCTTTAAAACGAAAGGGCAA	1	271	1	TCTTTAAAAC	    0.862279	-27
TAACTAATCATTCTTAAAAACGCTAAAAAT	2	13	0	TTCTTAAAAA	    0.630216	-70
GTTAGTAGCGTTATTATAACTAATCATTCT	2	29	0	TTATTATAAC	     0.83959	-54
          **********

Masking position 5
Map Score:   9.21708

Number of sites scoring better than the average of aligned sites = 1678
Number in coding regions = 1251
Number in noncoding regions = 427
Number of orfs with sites within 600 bp upstream = 223
Fraction of orfs with sites within 600 bp upstream = 0.0358175


Motif number 3

TAAACCAACACAAAGGAGATACT       	1	4	0	CAAAGGAGAT	    0.950113	-294
ATGATAATGAAAAAGTAAATGAGAGTATGA	1	58	1	AAAAGTAAAT	    0.813351	-240
TTAGGTAAAAAAAAGGGGTTGGCATCAATA	1	179	1	AAAAGGGGTT	    0.983784	-119
GTTGGCATCAATAGGGGGTTAAAAGGGGAT	1	196	1	ATAGGGGGTT	    0.926342	-102
ATAGGGGGTTAAAAGGGGATATTTTTATAT	1	206	1	AAAAGGGGAT	     0.98983	-92
TATAATATGTAAAAAGCATTCTTAAATCTA	1	233	1	AAAAAGCATT	     0.74569	-65
CTTTAAAACGAAAGGGCAATTTAACC    	1	282	1	AAAGGGCAAT	    0.959756	-16
CTAAAATCTATTAAGGAAATCAGT      	2	69	1	TTAAGGAAAT	    0.747845	-14
          **********

Masking position 3
Map Score:   4.76512

Number of sites scoring better than the average of aligned sites = 1733
Number in coding regions = 1461
Number in noncoding regions = 272
Number of orfs with sites within 600 bp upstream = 191
Fraction of orfs with sites within 600 bp upstream = 0.0306778


Motif number 4

ATTATCATTTATGCTATAATTATGGGACAA	1	36	0	ATGCTATAAT	    0.926464	-262
ATAGATTTTTATGATAAAATCTAAGCTTTA	1	139	0	ATGATAAAAT	    0.933291	-159
CTTTTTACATATTATATAAAAATATCCCCT	1	219	0	ATTATATAAA	    0.728696	-79
AGCATTCTTAAATCTAAAAATGCTACAATG	1	247	1	AATCTAAAAA	    0.951215	-51
TTTCGTTTTAAAGATAAACATTGTAGCATT	1	265	0	AAGATAAACA	    0.838282	-33
ATTCTTAAAAACGCTAAAAATTA       	2	4	0	ACGCTAAAAA	    0.966981	-79
ATAACTAATCATTCTTAAAAACGCTAAAAA	2	14	0	ATTCTTAAAA	    0.819919	-69
AACAACACTCAAGCTAAAATCTATTAAGGA	2	56	1	AAGCTAAAAT	    0.968826	-27
          **********

Masking position 8
Map Score:   6.52443

Number of sites scoring better than the average of aligned sites = 1380
Number in coding regions = 1157
Number in noncoding regions = 223
Number of orfs with sites within 600 bp upstream = 182
Fraction of orfs with sites within 600 bp upstream = 0.0292323


Motif number 5

          **********

No masking
Map Score:   2.36911e-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:   2.36911e-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:   2.36911e-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