AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -ifruR_mgen_opreg_100.orf -g0.317 -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 =  	0.317
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	MG040	158	lipoprotein, putative
#2	MG062	300	PTS system, fructose-specific IIABC component (fruA)

Motif number 1

CTTTTTTGCAAAATAACTAACTAAATACTAGAAG	1	19	0	AAATAACTAA	     0.98535	-140
AGTAAATCACAACTATAAAACTAATCCTTTTTTG	1	45	0	AACTAACTAA	    0.926826	-114
ACTACTTTTTATAGAGATACCAAAAAGTAAATCA	1	70	0	ATAGAACAAA	    0.875242	-89
ATCTCTATAAAAAGTAGTATCAAACATTTTTTTA	1	86	1	AAAGTACAAA	    0.963314	-73
TATTTTTAGTAAAAAGAAATCAAAAGATAAAAAA	1	113	0	AAAAAACAAA	    0.966952	-46
TTTTTACTAAAAATAATTAGCTAAAATACCGTCA	1	132	1	AAATAACTAA	     0.98535	-27
ACTAATTTTAAAAGCTGTAGCTAATTGTTTTTTA	2	31	1	AAAGCACTAA	    0.947648	-270
TTTTTTAGAACAAACTGAATCAAAGAATTTGAAA	2	58	1	CAAACACAAA	    0.798982	-243
TTGTTAACAGCATTTAACAACAAAATTGAATAAA	2	102	1	CATTTACAAA	    0.747965	-199
AATTGAATAAAAATAAAAAACAGACCCTGATGGT	2	125	1	AAATAACAGA	    0.970806	-176
TTCCGCCATTAAATATCCAACAGACCATCAGGGT	2	148	0	AAATAACAGA	    0.970806	-153
ATTTATAATAAATTTAACAACAAACTGGGAGCGT	2	255	0	AATTTACAAA	    0.903787	-46
AATTTATTATAAATATGCAACTAATTAGCGCTTT	2	275	1	AAATAACTAA	    0.985349	-26
          *****   * ****

Masking position 9
Map Score:   16.5223

Number of sites scoring better than the average of aligned sites = 402
Number in coding regions = 351
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 2

AGAGATACCAAAAAGTAAATCACAACTATA	1	62	0	AAAAGTAAAT	    0.915571	-97
AAAGAAATCAAAAGATAAAAAAATGTTTGA	1	105	0	AAAGATAAAA	    0.935117	-54
TATTTTTAGTAAAAAGAAATCAAAAGATAA	1	117	0	AAAAAGAAAT	    0.948435	-42
TCTTTTTACTAAAAATAATTAGCTAAAATA	1	130	1	AAAAATAATT	    0.962124	-29
GTTTGTTCTAAAAAACAATTAGCTACAGCT	2	43	0	AAAAACAATT	     0.96847	-258
GTTAACAATGAAAGACAATTTCAAATTCTT	2	80	0	AAAGACAATT	    0.945646	-221
AACAGCATTTAACAACAAAATTGAATAAAA	2	107	1	AACAACAAAA	     0.89087	-194
AAAATTGAATAAAAATAAAAAACAGACCCT	2	123	1	AAAAATAAAA	    0.962195	-178
          **********

Masking position 7
Map Score:   8.20584

Number of sites scoring better than the average of aligned sites = 361
Number in coding regions = 306
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 3

TAGTCTAATGTAAATTCTGTCTTA      	2	5	0	TAAATTCTGT	    0.989087	-296
AGACTAATTTTAAAAGCTGTAGCTAATTGT	2	29	1	TAAAAGCTGT	    0.967471	-272
AAGACAATTTCAAATTCTTTGATTCAGTTT	2	69	0	CAAATTCTTT	    0.886746	-232
ATTTTGTTGTTAAATGCTGTTAACAATGAA	2	98	0	TAAATGCTGT	     0.98989	-203
TTATTTTTATTCAATTTTGTTGTTAAATGC	2	111	0	TCAATTTTGT	    0.885938	-190
          **********

Masking position 4
Map Score:   3.16558

Number of sites scoring better than the average of aligned sites = 39
Number in coding regions = 36
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

TTTAGTTAGTTATTTTGCAAAAAAGGATTAGTT	1	28	1	TTTTTGAAAA	    0.952003	-131
TAGCTAATTATTTTTAGTAAAAAGAAATCAAAA	1	122	0	TTTTAGAAAA	    0.539701	-37
TTACTAAAAATAATTAGCTAAAATACCGTCATA	1	135	1	TATTAGTAAA	    0.916373	-24
AGCTAATTGTTTTTTAGAACAAACTGAATCAAA	2	49	1	TTTTAGAAAA	    0.912166	-252
ATTAGTTGCATATTTATAATAAATTTAACAACA	2	267	0	TTTTATAAAA	    0.952613	-34
          * ***** * ***

Masking position 5
Map Score:   2.64505

Number of sites scoring better than the average of aligned sites = 23
Number in coding regions = 19
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 5

          **********

No masking
Map Score:   -2.24942e-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:   -2.24942e-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:   -2.24942e-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