AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i025_1_2_1_2_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	yjgC	145	similar to formate dehydrogenase
#2	narQ	245	alternate gene name: narAA

Motif number 1

ACATGTGAGTGCGCTTTGTATGTTTTATTG	1	65	1	GCGCTTTGTA	    0.980293	-81
TTCCCCTTTCTTGCTTTATATACCGAATTA	1	121	0	TTGCTTTATA	    0.974618	-25
         AGTCCTTTATACAGAGGTGTC	2	2	1	GTCCTTTATA	    0.991418	-244
TAGCCGCCGTTCCTTTTATAACACGTGAGC	2	77	0	TCCTTTTATA	    0.962416	-169
TCCTGTAAAAGCCCTTTATATAGAGGGCTC	2	146	1	GCCCTTTATA	    0.996173	-100
GCAATGTTCCTGCCTTTATATTTTTTCACA	2	211	0	TGCCTTTATA	    0.984063	-35
          **********

Masking position 5
Map Score:   9.15263

Number of sites scoring better than the average of aligned sites = 227
Number in coding regions = 170
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 2

CCGTTTCCCCGTGTTTTTGCAACGAAACATGTGA	1	39	1	GGTTTCAACG	    0.996055	-107
ATGTTTTATTGAGTTGTTGTAAGGGAACTGAAAT	1	84	1	GGTGTTAAGG	    0.943749	-62
CCTTTATACAGAGGTGTCTCAGCGTGTCGACAAA	2	14	1	GGTGTCAGCG	    0.995149	-232
CAACGAACGCGGGGTTTGTCGACACGCTGAGACA	2	28	0	GGTTTCGACA	    0.974103	-218
GAGCACCAATGTGCATTGACAACGAACGCGGGGT	2	47	0	GGATTCAACG	    0.981279	-199
GATGACGGCGGTGTTTAGGCAGGACGCCTAAGCA	2	109	0	GGTTACAGGA	    0.958903	-137
TCTATATAAAGGGCTTTTACAGGATGTGATGACG	2	136	0	GGTTTCAGGA	    0.991181	-110
          * * ***  *****

Masking position 3
Map Score:   6.14281

Number of sites scoring better than the average of aligned sites = 286
Number in coding regions = 261
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 3

GATCTACCATTCCGTTTCCCCGTGTTTTTG	1	28	1	TCCGTTTCCC	    0.992566	-118
ATTACCTATTTCAGTTCCCTTACAACAACT	1	95	0	TCAGTTCCCT	    0.987316	-51
         CTCCATTCCCCTTTCTTGCTT	1	135	0	TCCATTCCCC	     0.99433	-11
GCATTTAGCCGCCGTTCCTTTTATAACACG	2	82	0	GCCGTTCCTT	    0.963893	-164
        TGTCTCTTCCCCTCCGCAATGT	2	234	0	TCTCTTCCCC	    0.984945	-12
          **********

Masking position 5
Map Score:   4.86975

Number of sites scoring better than the average of aligned sites = 288
Number in coding regions = 224
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 4

   GTTAATCCCTCCTAATTGATCTACCAT	1	8	1	CCTCCTAATT	     0.97224	-138
AGGCAGGACGCCTAAGCATTTAGCCGCCGT	2	97	0	CCTAAGCATT	    0.960699	-149
TCTTTTTGTGTCTCAGAATTCGACAAAATC	2	174	1	TCTCAGAATT	    0.957707	-72
TTTTCACACTCCTCGGATTTTGTCGAATTC	2	189	0	CCTCGGATTT	    0.967938	-57
TGTCTCTTCCCCTCCGCAATGTTCCTGCCT	2	226	0	CCTCCGCAAT	    0.983595	-20
          **********

Masking position 3
Map Score:   1.87514

Number of sites scoring better than the average of aligned sites = 402
Number in coding regions = 350
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 5

TCGTTGCAAAAACACGGGGAAACGGAATGG	1	34	0	AACACGGGGA	    0.981343	-112
TTTGCAACGAAACATGTGAGTGCGCTTTGT	1	54	1	AACATGTGAG	    0.986906	-92
TTCCTTTTATAACACGTGAGCACCAATGTG	2	68	0	AACACGTGAG	    0.973328	-178
          **********

Masking position 4
Map Score:   0.444713

Number of sites scoring better than the average of aligned sites = 19
Number in coding regions = 8
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 6

          **********

No masking
Map Score:   -6.86222e-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:   -6.86222e-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:   -6.86222e-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