AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i157_Alkyl_Hydroperoxide_reductase_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 
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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	ahpC	300	alkyl hydroperoxide reductase (small subunit)

Motif number 1

         TATTCTGCTTTTGGCCATTGT	1	2	1	ATTCTGCTTT	    0.990897	-299
GCTTTTGGCCATTGTCCTTTGCCCTTGACC	1	17	1	ATTGTCCTTT	    0.965368	-284
ACGGCCTGGCATTCTGATTTACAAAAGTCC	1	76	1	ATTCTGATTT	    0.989028	-225
TGAGAGGCTGATTCTCAATTAGATAAGGTT	1	111	0	ATTCTCAATT	    0.964185	-190
TTATATATGAATTATTAATTAATATATATT	1	221	0	ATTATTAATT	     0.91714	-80
TATAATTAGAATTATTATTGAAAGCGATTA	1	246	1	ATTATTATTG	    0.886736	-55
ATTGAAAGCGATTATGCTTTCTAATACATT	1	262	1	ATTATGCTTT	    0.985761	-39
          **********

Masking position 1
Map Score:   8.38779

Number of sites scoring better than the average of aligned sites = 423
Number in coding regions = 355
Number in noncoding regions = 68
Number of orfs with sites within 600 bp upstream = 78
Fraction of orfs with sites within 600 bp upstream = 0.0125281


Motif number 2

ACATTTTATGACACCATGGTCAAGGGCAAAGGACAATGGCC	1	23	0	AATTAGCAAG	    0.973499	-278
CCATGGTGTCATAAAATGTTCAAATGCCAAAACGGCCTGGC	1	45	1	AATTAACCAA	    0.982011	-256
TAAGGTTTTCAGGGACTTTTGTAAATCAGAATGCCAGGCCG	1	77	0	AGTTAACAAA	    0.982011	-224
AAAGTCCCTGAAAACCTTATCTAATTGAGAATCAGCCTCTC	1	99	1	AATTAAGAAA	    0.986818	-202
CCTACCTGTCACACCTTTATTAAGATGAAAAAAAGTAGGTT	1	166	1	AATTAGGAAA	    0.980535	-135
TAATTAATATATATTTTTTGTCAAGCCATAACCTACTTTTT	1	195	0	AATGAACAAA	    0.981838	-106
ATTCCTCCTAAAAATGTATTAGAAAGCATAATCGCTTTCAA	1	263	0	AATTAACAAA	    0.994395	-38
          * *   *  *  **  ** **

Masking position 13
Map Score:   4.04155

Number of sites scoring better than the average of aligned sites = 187
Number in coding regions = 156
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 3

ACCATGGTGTCATAAAATGTTCAAATGCCA	1	44	1	CATAAAATGT	    0.982922	-257
TTATTAAGATGAAAAAAAGTAGGTTATGGC	1	182	1	GAAAAAAAGT	    0.955496	-119
TATGGCTTGACAAAAAATATATATTAATTA	1	206	1	CAAAAAATAT	    0.973405	-95
TATATTCCTCCTAAAAATGTATTAGAAAGC	1	277	0	CTAAAAATGT	    0.982921	-24
          **********

Masking position 5
Map Score:   2.10473

Number of sites scoring better than the average of aligned sites = 273
Number in coding regions = 201
Number in noncoding regions = 72
Number of orfs with sites within 600 bp upstream = 84
Fraction of orfs with sites within 600 bp upstream = 0.0134918


Motif number 4

    TATTCTGCTTTTGGCCATTGTCCTTT	1	7	1	GCTTTTGGCC	    0.991843	-294
AATGCCAGGCCGTTTTGGCATTTGAACATT	1	59	0	CGTTTTGGCA	    0.990048	-242
TGACAGGTAGGATTTAGGCATTTCTTTTAT	1	147	0	GATTTAGGCA	    0.974815	-154
AAAAAAAGTAGGTTATGGCTTGACAAAAAA	1	193	1	GGTTATGGCT	    0.983518	-108
          **********

Masking position 4
Map Score:   1.49856

Number of sites scoring better than the average of aligned sites = 297
Number in coding regions = 280
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 5

CCCTGAAAACCTTATCTAATTGAGAATCAG	1	104	1	CTTATCTAAT	    0.727753	-197
ATCAGCCTCTCATTTATTATAAAAGAAATG	1	129	1	CATTTATTAT	    0.948928	-172
AGGATTTAGGCATTTCTTTTATAATAAATG	1	139	0	CATTTCTTTT	     0.86931	-162
CTTGACAAAAAATATATATTAATTAATAAT	1	211	1	AATATATATT	    0.496994	-90
AATATATATTAATTAATAATTCATATATAA	1	221	1	AATTAATAAT	    0.770777	-80
ATTAATAATTCATATATAATTAGAATTATT	1	232	1	CATATATAAT	    0.713207	-69
TCCTCCTAAAAATGTATTAGAAAGCATAAT	1	272	0	AATGTATTAG	    0.769706	-29
          AATGTATATTCCTCCTAAAA	1	291	0	AATGTATATT	    0.713548	-10
          **********

Masking position 7
Map Score:   2.52836

Number of sites scoring better than the average of aligned sites = 882
Number in coding regions = 635
Number in noncoding regions = 247
Number of orfs with sites within 600 bp upstream = 267
Fraction of orfs with sites within 600 bp upstream = 0.0428847


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


Motif number 8

          **********

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