AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i170_Urease_hpyl_reg_100.orf -o170_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	RHP01027	28	AE000511
#2	RHP01028	22	AE000511
#3	RHP01030	192	AE000511
#4	RHP01032	300	AE000511

Motif number 1

   AAAAGAAATAGAAAAATAACAA     	2	8	1	ATAGAAAAAT	    0.840786	-15
TTTTTTGATAAACAAAAAATCAGAGAGCTA	3	49	0	AACAAAAAAT	    0.990477	-144
TTTTTTGTTTATCAAAAAATTGGGGGCTTT	3	60	1	ATCAAAAAAT	    0.986119	-133
AAAAAATAAAAACAAAAAAAGCCCCCAATT	3	77	0	AACAAAAAAA	    0.936043	-116
ATAGTAAATTGACAAAAAATAAAAACAAAA	3	90	0	GACAAAAAAT	    0.955931	-103
AGCTAATCATAAAGAAAAATAGTAAATTGA	3	108	0	AAAGAAAAAT	    0.885471	-85
TAGCTCAAGCAACAAAAGTTATTCGTAAGG	3	133	1	AACAAAAGTT	     0.88478	-60
TTTCCTTCCAAACAAAAATTTTTACAACAA	3	168	0	AACAAAAATT	    0.970474	-25
ATTTATAAAGATCAAAAACTCGCAAAAAAA	4	86	0	ATCAAAAACT	    0.949673	-215
ATCTTAGTAAATCAAAACATTGCTACAATT	4	220	1	ATCAAAACAT	    0.943179	-81
          **********

Masking position 5
Map Score:   14.3601

Number of sites scoring better than the average of aligned sites = 446
Number in coding regions = 365
Number in noncoding regions = 81
Number of orfs with sites within 600 bp upstream = 65
Fraction of orfs with sites within 600 bp upstream = 0.0104401


Motif number 2

TAATCTCAAATTGAAAGGAATTTT        	1	15	1	TTGAAAGATT	    0.875176	-14
AACTAAGGATTTAAGGAGCGTTGCTCCTAAAA	3	15	0	TTAAGGGCTT	    0.989097	-178
AAAGTTATTCGTAAGGTGCGTTTGTTGTAAAA	3	147	1	GTAAGGGCTT	    0.960152	-46
TTATAAATTCTAAAGGGGTATTAAACGCACTT	4	108	1	TAAAGGGTTT	     0.91818	-193
AAATCGTTATTAGAAGTGCGTTTAATACCCCT	4	121	0	TAGAAGGCTT	    0.970769	-180
TGTTATATCTTTGAAGCGCTATAAAATCGTTA	4	144	0	TTGAAGGCAT	    0.942053	-157
TAATTATTATTTAAAATGAATTAGTGTTATAT	4	168	0	TTAAAAGATT	    0.877347	-133
TCTCCTATTCTTAAAGTGTTTTTCCTTGAAGA	4	274	0	TTAAAGGTTT	    0.969014	-27
          ****** ** **

Masking position 4
Map Score:   5.17205

Number of sites scoring better than the average of aligned sites = 1117
Number in coding regions = 1002
Number in noncoding regions = 115
Number of orfs with sites within 600 bp upstream = 97
Fraction of orfs with sites within 600 bp upstream = 0.0155798


Motif number 3

AAGAAATAGAAAAATAACAA          	2	13	1	AAAATAACAA	    0.905845	-10
AGAGAGCTAAAAACTAAGGATTTAAGGAGC	3	28	0	AAACTAAGGA	    0.834096	-165
TGATAAACAAAAAATCAGAGAGCTAAAAAC	3	44	0	AAAATCAGAG	     0.95198	-149
TGTTTATCAAAAAATTGGGGGCTTTTTTTG	3	65	1	AAAATTGGGG	    0.897836	-128
AAATTGACAAAAAATAAAAACAAAAAAAGC	3	85	0	AAAATAAAAA	    0.779113	-108
ATCATAAAGAAAAATAGTAAATTGACAAAA	3	103	0	AAAATAGTAA	    0.849053	-90
AATGAGAATTAAAATTGGAGTGATAATGGT	4	58	0	AAAATTGGAG	    0.953355	-243
AACTCGCAAAAAAATGAGAATTAAAATTGG	4	70	0	AAAATGAGAA	    0.908617	-231
TAAAGATCAAAAACTCGCAAAAAAATGAGA	4	81	0	AAACTCGCAA	    0.816148	-220
AAACACTTTAAGAATAGGAGAATAAG    	4	285	1	AGAATAGGAG	     0.90739	-16
          **********

Masking position 5
Map Score:   4.6244

Number of sites scoring better than the average of aligned sites = 721
Number in coding regions = 600
Number in noncoding regions = 121
Number of orfs with sites within 600 bp upstream = 106
Fraction of orfs with sites within 600 bp upstream = 0.0170254


Motif number 4

ACCTTGACATGGTAGTGGCCGCTGGTTCAAGT	4	14	1	GGTATGGCGC	    0.998022	-287
AAATTGGAGTGATAATGGTGGCCACGACTGGA	4	45	0	GATATGGGGC	    0.985706	-256
ATTCTAAAGGGGTATTAAACGCACTTCTAATA	4	114	1	GGTATAACGC	    0.987871	-187
ATAATAATTAGTTAATGAACGCTTCTGTTAAT	4	190	1	GTTATGACGC	    0.991709	-111
          **** *** ***

Masking position 6
Map Score:   0.525569

Number of sites scoring better than the average of aligned sites = 38
Number in coding regions = 34
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 5

          **********

No masking
Map Score:   1.74326e-12

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:   1.74326e-12

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:   1.74326e-12

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