AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i282_hypothetical7_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	yrrK	300	similar to hypothetical proteins

Motif number 1

TCACCGTTTTGCACCTCTTTCCCAAATTCG	1	11	0	GCACCTCTTT	    0.995855	-290
TCAAACGAGCTCACCGTTTTGCACCTCTTT	1	21	0	TCACCGTTTT	    0.984205	-280
AAATTAAATTTCATCGTTTTATCAAACGAG	1	42	0	TCATCGTTTT	    0.954678	-259
ACTGTAATCAGCACCTCATTTACGTTAGTC	1	90	0	GCACCTCATT	     0.98341	-211
CTCGATTAATTCGTCTCTTTCAAGTTTGCG	1	232	0	TCGTCTCTTT	    0.984215	-69
 TCTTTATTTACGCCTCTTTATGCTGTTCT	1	282	0	ACGCCTCTTT	    0.986492	-19
          **********

Masking position 9
Map Score:   8.89017

Number of sites scoring better than the average of aligned sites = 548
Number in coding regions = 429
Number in noncoding regions = 119
Number of orfs with sites within 600 bp upstream = 121
Fraction of orfs with sites within 600 bp upstream = 0.0194346


Motif number 2

TCGTTTTATCAAACGAGCTCACCGTTTTGCACC	1	26	0	AACGGCTCAC	    0.985616	-275
ACGTTAGTCTCAGCAGAATCATCGGAGAAATTA	1	66	0	CACAAATCAC	    0.972907	-235
GCGCGTCATACACTGTAATCAGCACCTCATTTA	1	98	0	CATGAATCAC	    0.991679	-203
AAAAGGGCTACAATCCAATCAACCAGATTGTCG	1	137	1	CATCAATCAC	    0.971304	-164
CTAGGAATATAAGCGGGATCACCTGACAGCAAG	1	174	0	AACGGATCAC	    0.994692	-127
TTGCGAATTAAATTGCGAGCGTCACGATGCCTA	1	204	0	AATGGAGCGC	    0.940946	-97
          ** ** ***** *

Masking position 2
Map Score:   2.0726

Number of sites scoring better than the average of aligned sites = 573
Number in coding regions = 536
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 3

AGAGGTGCAAAACGGTGAGCTCGTTTGATAA	1	23	1	AACGGGAGCT	    0.972069	-278
CGTTTGATAAAACGATGAAATTTAATTTCTC	1	44	1	AACGAGAAAT	    0.988477	-257
CAGCAGAATCATCGGAGAAATTAAATTTCAT	1	58	0	ATCGGGAAAT	    0.989316	-243
CAAACTTGAAAGAGACGAATTAATCGAGGAA	1	234	1	AGAGAGAATT	    0.932575	-67
AGACGAATTAATCGAGGAATTGGTAAAGTCT	1	246	1	ATCGAGAATT	    0.988477	-55
          ***** *****

Masking position 8
Map Score:   2.07098

Number of sites scoring better than the average of aligned sites = 270
Number in coding regions = 240
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 4

          **********

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 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