AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i061_ecoli_bsub_100.orf -o061_ecoli_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -x5 -e 
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 =  	0.47
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	yffG	205	putative oxidoreductase, Fe-S subunit
#2	gltB	300	glutamate synthase, large subunit
#3	gltA	146	glutamate synthase (large subunit)

Motif number 1

GATTTTTTGTGGAGAAGACGCGT         	1	2	0	GGGAAACGCG	    0.978913	-204
ATTGCGTTTCAGCGAACTGGAACATTAATGAT	1	31	0	AGGAATGGAA	    0.855259	-175
CCGACTTACAGGGGAATCGGCAATGTTCATGT	1	127	0	GGGAACGGCA	    0.993189	-79
TTATCTTTAAGGCTAAAAGGGAAGTCGTTAGA	2	49	0	GGTAAAGGGA	    0.965823	-252
AGCTGATACAGGTCAAATGGCAAGCTTATTGG	2	139	0	GGCAATGGCA	    0.971012	-162
CGGTTAATACGGTGAAGAGGGGATCTCAATTA	2	238	0	GGGAAAGGGG	    0.996448	-63
GATGCGAAAAGGACAACAAGGGGGCGAATCGG	2	269	1	GGCAAAAGGG	    0.917231	-32
ACAACAAGGGGGCGAATCGGAGGCGCGCGT  	2	281	1	GGGAACGGAG	    0.991702	-20
GAAATTGATCGGGGGAGAGGAATT        	3	133	1	GGGGAAGGAA	    0.970035	-14
          ** *** *****

Masking position 6
Map Score:   9.22915

Number of sites scoring better than the average of aligned sites = 744
Number in coding regions = 690
Number in noncoding regions = 54
Number of orfs with sites within 600 bp upstream = 57
Fraction of orfs with sites within 600 bp upstream = 0.00915516


Motif number 2

ATCTGCCACAGTTTATAGCGAAATAGTTAC	1	86	1	GTTTATAGCG	    0.988469	-120
TTTCGCATCGGTTAATACGGTGAAGAGGGG	2	248	0	GTTAATACGG	     0.95716	-53
ATTATATATTGTTTATATCGTTTTGAAAAC	3	58	1	GTTTATATCG	    0.969184	-89
AACCTACAATGATTATAGAGTTGTTAGATT	3	85	1	GATTATAGAG	    0.937759	-62
ATCAATTTCCGATAATACCGGTCATAAAAT	3	112	0	GATAATACCG	    0.976635	-35
          **********

Masking position 5
Map Score:   2.569

Number of sites scoring better than the average of aligned sites = 120
Number in coding regions = 105
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 3

CAGGGGAATCGGCAATGTTCATGTGCCCAG	1	121	0	GGCAATGTTC	    0.939489	-85
TTATTGGTACAGAAATGTGCTTTAGCGCAA	2	116	0	AGAAATGTGC	    0.927836	-185
CAGGTCAAATGGCAAGCTTATTGGTACAGA	2	133	0	GGCAAGCTTA	    0.953986	-168
CAACTTATCGGGAAAGCTGATACAGGTCAA	2	155	0	GGAAAGCTGA	    0.972572	-146
CCGATAAGTTGGAAATCCGCTGGAAGCTTT	2	174	1	GGAAATCCGC	    0.950889	-127
CTGCTCATCCAGAAAGCTTCCAGCGGATTT	2	186	0	AGAAAGCTTC	    0.968226	-115
AAATATGATGAGCAGGCTGCTCATCCAGAA	2	202	0	AGCAGGCTGC	    0.958992	-99
          **********

Masking position 4
Map Score:   4.12858

Number of sites scoring better than the average of aligned sites = 1359
Number in coding regions = 1269
Number in noncoding regions = 90
Number of orfs with sites within 600 bp upstream = 86
Fraction of orfs with sites within 600 bp upstream = 0.013813


Motif number 4

TTAACACACCTTTATGACAGTCAGGAATTG	2	11	1	TTTATGACAG	    0.898964	-290
AGAGAAACAGTCAATTCCTGACTGTCATAA	2	22	0	TCAATTCCTG	    0.948637	-279
AAAATCCATTTTAATTTCAGTCATTTAATA	2	79	1	TTAATTTCAG	     0.93322	-222
AGAGGGGATCTCAATTACTGCATAAATATG	2	225	0	TCAATTACTG	    0.969218	-76
GTTGTTAGATTTTATGACCGGTATTATCGG	3	104	1	TTTATGACCG	    0.932262	-43
TCTCCCCCGATCAATTTCCGATAATACCGG	3	121	0	TCAATTTCCG	     0.97142	-26
          **********

Masking position 5
Map Score:   1.63266

Number of sites scoring better than the average of aligned sites = 369
Number in coding regions = 317
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 63
Fraction of orfs with sites within 600 bp upstream = 0.0101189


Motif number 5

GAATAAGTAACTATTTCGCTATAAACTGTGG	1	91	0	CTTTTCGCTA	    0.990573	-115
CAGGAATTGACTGTTTCTCTAACGACTTCCC	2	32	1	CTTTTCTCTA	    0.985492	-269
TTAATAAAGAATTTTGCGCTAAAGCACATTT	2	103	1	ATTTGCGCTA	    0.976138	-198
TTTTGAGATTCTTTTGATCTAAATTATATAT	3	36	1	CTTTGATCTA	    0.963566	-111
          ** ********

Masking position 5
Map Score:   0.114963

Number of sites scoring better than the average of aligned sites = 24
Number in coding regions = 16
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 6

          **********

No masking
Map Score:   -1.36181e-12

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:   -1.36181e-12

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:   -1.36181e-12

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