AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i157_Alkyl_Hydroperoxide_reductase_bsub_reg_300.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

ACAATGGCCAAAAGCAGAATA         	1	2	0	AAAGCAGAAT	    0.989111	-299
GGTCAAGGGCAAAGGACAATGGCCAAAAGC	1	17	0	AAAGGACAAT	    0.958783	-284
GGACTTTTGTAAATCAGAATGCCAGGCCGT	1	76	0	AAATCAGAAT	     0.98688	-225
AACCTTATCTAATTGAGAATCAGCCTCTCA	1	111	1	AATTGAGAAT	    0.957383	-190
AATATATATTAATTAATAATTCATATATAA	1	221	1	AATTAATAAT	    0.902308	-80
TAATCGCTTTCAATAATAATTCTAATTATA	1	246	0	CAATAATAAT	    0.867249	-55
AATGTATTAGAAAGCATAATCGCTTTCAAT	1	262	0	AAAGCATAAT	    0.982984	-39
          **********

Masking position 6
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

GCAAAGGACAATGGCCAAAAGCAGAATA  	1	9	0	ATGGCCAAAA	    0.989894	-292
AAAATGTTCAAATGCCAAAACGGCCTGGCA	1	57	1	AATGCCAAAA	    0.993452	-244
TGGCATTCTGATTTACAAAAGTCCCTGAAA	1	82	1	ATTTACAAAA	    0.948343	-219
TTATAAAAGAAATGCCTAAATCCTACCTGT	1	145	1	AATGCCTAAA	    0.978781	-156
TAGGTTATGGCTTGACAAAAAATATATATT	1	201	1	CTTGACAAAA	    0.977491	-100
          **********

Masking position 8
Map Score:   5.25473

Number of sites scoring better than the average of aligned sites = 480
Number in coding regions = 423
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 67
Fraction of orfs with sites within 600 bp upstream = 0.0107613


Motif number 3

CCCTGAAAACCTTATCTAATTGAGAATCAG	1	104	1	CTTATCTAAT	    0.748888	-197
ATCAGCCTCTCATTTATTATAAAAGAAATG	1	129	1	CATTTATTAT	    0.934992	-172
AGGATTTAGGCATTTCTTTTATAATAAATG	1	139	0	CATTTCTTTT	    0.890866	-162
CTTGACAAAAAATATATATTAATTAATAAT	1	211	1	AATATATATT	    0.498749	-90
AATATATATTAATTAATAATTCATATATAA	1	221	1	AATTAATAAT	    0.747129	-80
ATTAATAATTCATATATAATTAGAATTATT	1	232	1	CATATATAAT	    0.870195	-69
TATGCTTTCTAATACATTTTTAGGAGGAAT	1	274	1	AATACATTTT	    0.759312	-27
          AATGTATATTCCTCCTAAAA	1	291	0	AATGTATATT	    0.641587	-10
          **********

Masking position 7
Map Score:   2.94492

Number of sites scoring better than the average of aligned sites = 817
Number in coding regions = 580
Number in noncoding regions = 237
Number of orfs with sites within 600 bp upstream = 250
Fraction of orfs with sites within 600 bp upstream = 0.0401542


Motif number 4

TTGAACATTTTATGACACCATGGTCAAGGGC	1	37	0	TATGACACCT	    0.957411	-264
TAAATCAGAATGCCAGGCCGTTTTGGCATTT	1	66	0	TGCCAGGCCT	      0.9916	-235
AAATCCTACCTGTCACACCTTTATTAAGATG	1	162	1	TGTCACACCT	    0.995841	-139
ATATATTTTTTGTCAAGCCATAACCTACTTT	1	197	0	TGTCAAGCCT	    0.992689	-104
          ********* *

Masking position 5
Map Score:   0.697587

Number of sites scoring better than the average of aligned sites = 142
Number in coding regions = 127
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


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