AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i334_1_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	ywlC	156	alternate gene name: ipc-29d; similar to hypothetical proteins
#2	prfA	125	peptide chain release factor 1

Motif number 1

    GTGCAGTTTATACACATACTTATCCA	1	7	1	TTTATACACA	    0.946296	-150
TATACACATACTTATCCACTTCTTTATTAG	1	19	1	CTTATCCACT	     0.98814	-138
CTTTATTAGCGTTGTCCACAATTTGTGGAT	1	40	1	GTTGTCCACA	    0.991189	-117
TAAAACAAGCGTTATCCACAAATTGTGGAC	1	53	0	GTTATCCACA	    0.997278	-104
GACCAAACTCCTTATTCACAACAATAAAAC	1	133	0	CTTATTCACA	    0.988371	-24
TTTGACTGGGGTTAATCACTATACTATAAT	2	70	1	GTTAATCACT	    0.945813	-56
TAATGAGAATGTTACGCACAGGAAAACAGA	2	96	1	GTTACGCACA	    0.980381	-30
          **********

Masking position 8
Map Score:   12.2045

Number of sites scoring better than the average of aligned sites = 112
Number in coding regions = 80
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 2

GGACAACGCTAATAAAGAAGTGGATAAGTA	1	27	0	AATAAAGAAG	    0.919244	-130
GATGTCCTGTAATAAAACAAGCGTTATCCA	1	65	0	AATAAAACAA	     0.96408	-92
TCCTTTTGAAAGTATAAAAGATGTCCTGTA	1	84	0	AGTATAAAAG	    0.948769	-73
GGATTACACGCGTAAAACAATCGTTTTATT	1	111	1	CGTAAAACAA	    0.948017	-46
TATTCACAACAATAAAACGATTGTTTTACG	1	121	0	AATAAAACGA	    0.938265	-36
CTCGAATTCCAGTATAGCAGAGGGAGCTTT	2	19	1	AGTATAGCAG	    0.985194	-107
TTCTCATTATAGTATAGTGATTAACCCCAG	2	75	0	AGTATAGTGA	    0.786104	-51
TGTTACGCACAGGAAAACAGAGGTGAAGAC	2	105	1	AGGAAAACAG	    0.966585	-21
          **********

Masking position 6
Map Score:   6.43421

Number of sites scoring better than the average of aligned sites = 1507
Number in coding regions = 1317
Number in noncoding regions = 190
Number of orfs with sites within 600 bp upstream = 190
Fraction of orfs with sites within 600 bp upstream = 0.0305172


Motif number 3

GTTTATACACATACTTATCCACTTCTTTAT	1	16	1	ATACTTATCC	     0.95344	-141
CTTCTTTATTAGCGTTGTCCACAATTTGTG	1	37	1	AGCGTTGTCC	    0.991744	-120
TAATAAAACAAGCGTTATCCACAAATTGTG	1	56	0	AGCGTTATCC	    0.996268	-101
TTGTTTTACGCGTGTAATCCTTTTGAAAGT	1	101	0	CGTGTAATCC	    0.956606	-56
TCTGACCAAACTCCTTATTCACAACAATAA	1	136	0	CTCCTTATTC	     0.94392	-21
          **********

Masking position 5
Map Score:   2.29594

Number of sites scoring better than the average of aligned sites = 502
Number in coding regions = 461
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 4

TTACGCGTGTAATCCTTTTGAAAGTATAAAAGA	1	93	0	AATCCTGAAA	    0.974678	-64
         CATCCCTCCTCGAATTCCAGTATA	2	2	1	ATCCCTCGAA	    0.995618	-124
AAGCATTTCAATCCCAGCTGGAAAAGCTCCCTC	2	38	0	ATCCCTGGAA	    0.991848	-88
TATAGTGATTAACCCCAGTCAAAAGCATTTCAA	2	60	0	AACCCTCAAA	    0.993512	-66
          *****   *****

Masking position 9
Map Score:   1.09354

Number of sites scoring better than the average of aligned sites = 82
Number in coding regions = 66
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 5

          **********

No masking
Map Score:   -7.57276e-14

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:   -7.57276e-14

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:   -7.57276e-14

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