AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i185_4_6_1_10_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	ykvJ	300	similar to hypothetical proteins

Motif number 1

GAACCGGGGACTGACTTTTTTATTGTCAAGA	1	47	1	CTGCTTTTTT	    0.986136	-254
TACCATAATGATGTTTTTCTTGACAATAAAA	1	64	0	ATGTTTTCTT	    0.961897	-237
GCATATCGCACGGATTTTCTTCAATTTTTTC	1	108	0	CGGTTTTCTT	    0.990332	-193
ACAGCTCGTCCTTAGTTTTTTATAGAGGGTG	1	156	0	CTTGTTTTTT	    0.920444	-145
TCCTTGGATACGGCCTTTTTTATGTTTTTCT	1	188	1	CGGCTTTTTT	    0.991214	-113
GGCCTTTTTTATGTTTTTCTAGAGCACCTTC	1	199	1	ATGTTTTCTA	    0.902361	-102
TTCCGAAAAAAGGTGTTTTTTTGCGTGAATT	1	227	1	AGGGTTTTTT	    0.984671	-74
TGTCTCTCGCCGGCGTTTTTATTGCGGAGAA	1	269	1	CGGGTTTTTA	     0.98365	-32
          *** *******

Masking position 6
Map Score:   12.3705

Number of sites scoring better than the average of aligned sites = 1084
Number in coding regions = 827
Number in noncoding regions = 257
Number of orfs with sites within 600 bp upstream = 225
Fraction of orfs with sites within 600 bp upstream = 0.0361388


Motif number 2

TCCCCGGTTCCTAGATCAATTATCGCTCTATAGT	1	23	0	CTAGACTTTC	    0.986269	-278
GAGGGTGTAGCTAGAACCTCTCCCGCATATCGCA	1	129	0	CTAGACCTCC	    0.998447	-172
GAGGTTCTAGCTACACCCTCTATAAAAAACTAAG	1	143	1	CTACACCTTA	    0.988631	-158
TTATGTTTTTCTAGAGCACCTTCCGAAAAAAGGT	1	207	1	CTAGACCTCC	    0.998447	-94
AGAGACATCGCTACAGCTAATTCACGCAAAAAAA	1	242	0	CTACACATCA	    0.980124	-59
          ***** *  ** **

Masking position 5
Map Score:   4.4345

Number of sites scoring better than the average of aligned sites = 22
Number in coding regions = 19
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 3

TGGTAAGATAGCAGAAGTGAAAAAATTGAA	1	90	1	GCAGAAGTGA	    0.968299	-211
CGTGCGATATGCGGGAGAGGTTCTAGCTAC	1	127	1	GCGGGAGAGG	    0.996367	-174
GCGTGAATTAGCTGTAGCGATGTCTCTCGC	1	249	1	GCTGTAGCGA	    0.962234	-52
CAATAAAAACGCCGGCGAGAGACATCGCTA	1	263	0	GCCGGCGAGA	     0.99143	-38
TTATTGCGGAGAAGGAGAGGAATC      	1	287	1	GAAGGAGAGG	    0.984483	-14
          **********

Masking position 4
Map Score:   2.69312

Number of sites scoring better than the average of aligned sites = 514
Number in coding regions = 458
Number in noncoding regions = 56
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 4

GTTTTTCTTGACAATAAAAAAGTCAGTCCC	1	53	0	ACAATAAAAA	    0.881498	-248
CTAGCTACACCCTCTATAAAAAACTAAGGA	1	149	1	CCTCTATAAA	    0.889002	-152
CTCTAGAAAAACATAAAAAAGGCCGTATCC	1	193	0	ACATAAAAAA	    0.887271	-108
AGAGCACCTTCCGAAAAAAGGTGTTTTTTT	1	219	1	CCGAAAAAAG	    0.947309	-82
CAGCTAATTCACGCAAAAAAACACCTTTTT	1	233	0	ACGCAAAAAA	    0.986006	-68
CTCTCCTTCTCCGCAATAAAAACGCCGGCG	1	276	0	CCGCAATAAA	    0.983438	-25
          **********

Masking position 6
Map Score:   2.69605

Number of sites scoring better than the average of aligned sites = 1342
Number in coding regions = 1104
Number in noncoding regions = 238
Number of orfs with sites within 600 bp upstream = 231
Fraction of orfs with sites within 600 bp upstream = 0.0371025


Motif number 5

CGTCACTATAGAGCGATAATTGATCTAGGA	1	19	1	GAGCGATAAT	    0.944052	-282
AAGAAAATCCGTGCGATATGCGGGAGAGGT	1	118	1	GTGCGATATG	     0.96155	-183
AACTAAGGACGAGCTGTATCCTTGGATACG	1	170	1	GAGCTGTATC	    0.977686	-131
AAACGCCGGCGAGAGACATCGCTACAGCTA	1	257	0	GAGAGACATC	     0.98239	-44
TGCGGAGAAGGAGAGGAATC          	1	291	1	GAGAGGAATC	    0.976534	-10
          **********

Masking position 8
Map Score:   0.853103

Number of sites scoring better than the average of aligned sites = 567
Number in coding regions = 515
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


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