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

Motif number 1

GAACCGGGGACTGACTTTTTTATTGTCAAGA	1	47	1	CTGCTTTTTT	    0.987712	-254
TACCATAATGATGTTTTTCTTGACAATAAAA	1	64	0	ATGTTTTCTT	    0.966135	-237
GCATATCGCACGGATTTTCTTCAATTTTTTC	1	108	0	CGGTTTTCTT	    0.991435	-193
ACAGCTCGTCCTTAGTTTTTTATAGAGGGTG	1	156	0	CTTGTTTTTT	    0.928951	-145
TCCTTGGATACGGCCTTTTTTATGTTTTTCT	1	188	1	CGGCTTTTTT	    0.992218	-113
GGCCTTTTTTATGTTTTTCTAGAGCACCTTC	1	199	1	ATGTTTTCTA	    0.912619	-102
TTCCGAAAAAAGGTGTTTTTTTGCGTGAATT	1	227	1	AGGGTTTTTT	    0.986412	-74
TGTCTCTCGCCGGCGTTTTTATTGCGGAGAA	1	269	1	CGGGTTTTTA	    0.985505	-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

ACTATAGAGCGATAATTGATCTAGGAACCGGGGA	1	23	1	GAAAGTCTAG	    0.987043	-278
TGCGATATGCGGGAGAGGTTCTAGCTACACCCTC	1	129	1	GGAGGTCTAG	    0.998536	-172
CTTAGTTTTTTATAGAGGGTGTAGCTAGAACCTC	1	143	0	TAAGGTGTAG	    0.989272	-158
ACCTTTTTTCGGAAGGTGCTCTAGAAAAACATAA	1	207	0	GGAGGTCTAG	    0.998536	-94
TTTTTTTGCGTGAATTAGCTGTAGCGATGTCTCT	1	242	1	TGATGTGTAG	    0.981237	-59
          ** **  * *****

Masking position 10
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	    0.969645	-211
CGTGCGATATGCGGGAGAGGTTCTAGCTAC	1	127	1	GCGGGAGAGG	    0.996521	-174
GCGTGAATTAGCTGTAGCGATGTCTCTCGC	1	249	1	GCTGTAGCGA	    0.963804	-52
CAATAAAAACGCCGGCGAGAGACATCGCTA	1	263	0	GCCGGCGAGA	    0.991799	-38
TTATTGCGGAGAAGGAGAGGAATC      	1	287	1	GAAGGAGAGG	    0.985153	-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	     0.88186	-248
CTAGCTACACCCTCTATAAAAAACTAAGGA	1	149	1	CCTCTATAAA	    0.889344	-152
CTCTAGAAAAACATAAAAAAGGCCGTATCC	1	193	0	ACATAAAAAA	    0.887618	-108
AGAGCACCTTCCGAAAAAAGGTGTTTTTTT	1	219	1	CCGAAAAAAG	    0.947482	-82
CAGCTAATTCACGCAAAAAAACACCTTTTT	1	233	0	ACGCAAAAAA	    0.986054	-68
CTCTCCTTCTCCGCAATAAAAACGCCGGCG	1	276	0	CCGCAATAAA	    0.983495	-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

TCCTAGATCAATTATCGCTCTATAGTGACG	1	19	0	ATTATCGCTC	    0.941524	-282
ACCTCTCCCGCATATCGCACGGATTTTCTT	1	118	0	CATATCGCAC	     0.95978	-183
CGTATCCAAGGATACAGCTCGTCCTTAGTT	1	170	0	GATACAGCTC	    0.976721	-131
TAGCTGTAGCGATGTCTCTCGCCGGCGTTT	1	257	1	GATGTCTCTC	    0.981606	-44
          GATTCCTCTCCTTCTCCGCA	1	291	0	GATTCCTCTC	    0.975446	-10
          **********

Masking position 3
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