AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i030_Glycerol_Uptake_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	glpF	178	glycerol uptake facilitator
#2	glpD	140	glycerol-3-phosphate dehydrogenase

Motif number 1

TCATGCACTGATACAATTGCACTAGGTTAAT	1	19	1	AACAATTGCA	    0.931119	-160
GAGAACTCGGAGACCACAGCAGCTCTTTACG	1	61	1	AACCACAGCA	    0.999047	-118
GAGAATAAAAAAACCACAACAAACCGCTTTA	1	111	0	AACCACAACA	    0.997185	-68
TGTAACCATTATACCATAGTATTACT     	2	6	0	AACCATAGTA	    0.982077	-135
AGATGAGGAGAGACCACAGCACCAAAGTGTA	2	57	1	AACCACAGCA	    0.999047	-84
ATAGAAAAAGAGACCACAACAGCCAAAGTGC	2	93	0	AACCACAACA	    0.997185	-48
          * *********

Masking position 6
Map Score:   15.4241

Number of sites scoring better than the average of aligned sites = 109
Number in coding regions = 91
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 2

TTGTATCAGTGCATGAAAGCGGTG       	1	4	0	GCATGAAAGG	    0.995363	-175
ATAAACATTTGCCGTAAAGAGCTGCTGTGGT	1	73	0	GCCGTAAAGG	    0.994367	-106
TGTTTATGCACCCGTAAAGCGGTTTGTTGTG	1	97	1	CCCGTAAAGG	    0.964756	-82
CGATTAAAAAGCATGATAGAGAAGAAGAGAA	1	137	0	GCATGATAGG	    0.981509	-42
CGTGACTTTAGGAGGAATGTGCT        	1	166	1	GGAGGAATGG	    0.964816	-13
AGAGACCACAGCACCAAAGTGTAAGCATGCA	2	65	1	GCACCAAAGG	    0.985393	-76
          ********* *

Masking position 6
Map Score:   5.51393

Number of sites scoring better than the average of aligned sites = 367
Number in coding regions = 324
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 3

GTTTTTTTATTCTCTTCTTCTCTATCATGCT	1	128	1	TCTCTCTTCT	    0.994826	-51
TCAGGACCGTTCTTATTAACTTGTAACCATT	2	27	0	TCTTTTAACT	    0.925268	-114
TGCTGTGGTCTCTCCTCATCTCAGGACCGTT	2	47	0	TCTCTCATCT	    0.994826	-94
GCTGTTGTGGTCTCTTTTTCTATTTACCGTG	2	101	1	TCTCTTTTCT	     0.99202	-40
          **** ******

Masking position 6
Map Score:   3.17169

Number of sites scoring better than the average of aligned sites = 171
Number in coding regions = 128
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 4

 CACCGCTTTCATGCACTGATACAATTGCA	1	10	1	CATGCACTGA	     0.98285	-169
GCACTAGGTTAATACATTGTGATGGAGAAC	1	37	1	AATACATTGT	    0.876802	-142
TCTTCTCTATCATGCTTTTTAATCGTGACT	1	143	1	CATGCTTTTT	    0.959278	-36
AAAGTGCATGCTTACACTTTGGTGCTGTGG	2	70	0	CTTACACTTT	    0.959287	-71
AAAGTGTAAGCATGCACTTTGGCTGTTGTG	2	80	1	CATGCACTTT	    0.994286	-61
          **********

Masking position 3
Map Score:   2.76197

Number of sites scoring better than the average of aligned sites = 391
Number in coding regions = 347
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 5

TCATGCTTTTTAATCGTGACTTTAGGAGGA	1	152	1	TAATCGTGAC	    0.994786	-27
TACTATGGTATAATGGTTACAAGTTAATAA	2	16	1	TAATGGTTAC	    0.974469	-125
CTTTTTCTATTTACCGTGACAACAAGGAGG	2	114	1	TTACCGTGAC	    0.988916	-27
          **********

Masking position 3
Map Score:   0.27705

Number of sites scoring better than the average of aligned sites = 52
Number in coding regions = 46
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 6

          **********

No masking
Map Score:   -1.17788e-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:   -1.17788e-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 8

          **********

No masking
Map Score:   -1.17788e-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