AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i339_weak10_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	ykrW	196	similar to ribulose-bisphosphate carboxylase

Motif number 1

TCTTATCAAGAGCAGGCAGAGGGACGAGCCCG	1	50	1	AGCAGGAGAG	    0.995969	-147
CAGAGGGACGAGCCCGATGAAGCCCGGCAACC	1	66	1	AGCCCGTGAG	    0.997367	-131
GTGCTTTATAAGTCGGTTGCCGGGCTTCATCG	1	80	0	AGTCGGTGCG	    0.994352	-117
CGACTTATAAAGCACGGTGCTAATTCTTGCAG	1	97	1	AGCACGTGCA	    0.983225	-100
CTTATCTCTCAGCCGCTAGCTGCAAGAATTAG	1	116	0	AGCCGCAGCG	    0.994269	-81
TAGACGCGATTGCAGTTTGAAGAGGTTTTTTG	1	173	1	TGCAGTTGAG	    0.956126	-24
          ****** *** *

Masking position 9
Map Score:   6.79381

Number of sites scoring better than the average of aligned sites = 1188
Number in coding regions = 1120
Number in noncoding regions = 68
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 2

         CGATGGGATAATTCAAAATAA	1	2	1	GATGGGATAA	    0.977756	-195
GCCTGCTCTTGATAAGAAAATATAGATTTT	1	37	0	GATAAGAAAA	    0.958688	-160
GCGGCTGAGAGATAAGATTCGGACGAGAAA	1	132	1	GATAAGATTC	    0.972519	-65
ATAAGATTCGGACGAGAAACGAAACCTCTT	1	143	1	GACGAGAAAC	    0.988646	-54
AACCTCTTTAGACGCGATTGCAGTTTGAAG	1	165	1	GACGCGATTG	    0.965268	-32
          **********

Masking position 7
Map Score:   1.64215

Number of sites scoring better than the average of aligned sites = 521
Number in coding regions = 469
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 3

GACGAGAAACGAAACCTCTTTAGACGCGAT	1	153	1	GAAACCTCTT	    0.994396	-44
     ATCAAAAAACCTCTTCAAACTGCAA	1	182	0	AAAACCTCTT	    0.976155	-15
          **********

Masking position 4
Map Score:   1.032

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 12
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

CTCTGCCTGCTCTTGATAAGAAAATATAGA	1	41	0	TCTTGATAAG	    0.989879	-156
TTAGCACCGTGCTTTATAAGTCGGTTGCCG	1	90	0	GCTTTATAAG	    0.989795	-107
AAACGAAACCTCTTTAGACGCGATTGCAGT	1	159	1	TCTTTAGACG	      0.9879	-38
          **********

Masking position 6
Map Score:   0.960805

Number of sites scoring better than the average of aligned sites = 110
Number in coding regions = 94
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 5

          **********

No masking
Map Score:   3.50598e-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:   3.50598e-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:   3.50598e-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