AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i133_Transmembrane_Transport_7_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	yjcH	88	orf, hypothetical protein
#2	BIME214	34	BIME
#3	acs	300	acetyl-CoA synthetase

Motif number 1

ATGGGAGAAGGTTAACGCTCGGGTAACCCTTGCC	1	15	0	GTTAATGGGT	    0.989598	-74
GTGGTTATTTGTTACACATAGGGGC         	3	2	0	GTTACTGGGG	    0.990767	-299
TAAAGACAACATTCACAGTGTGGTTATTTGTTAC	3	21	0	ATTCATTGGT	    0.887109	-280
ACAAAAGTTGATTAATTCTTTGAGGAACATGCAG	3	129	0	ATTAATTGAG	    0.924153	-172
TGGCAGTTTTGTTTAGTATTTGGGCGACAGATCA	3	216	0	GTTTATTGGG	    0.986159	-85
TGGCATAAGCGTTAAATGTAGGGGTATTGGCAGT	3	243	0	GTTAATGGGG	    0.997141	-58
CTTGTAGGATGTTAATAATATGTGGCATAAGCGT	3	265	0	GTTAATTGTG	    0.978107	-36
          *****   * ****

Masking position 9
Map Score:   5.32221

Number of sites scoring better than the average of aligned sites = 183
Number in coding regions = 152
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 2

ACGCTCGGGTAACCCTTGCCGAAT       	1	4	0	AACCTTGCCG	    0.992748	-85
CCCGAGCGTTAACCTTCTCCCATAAGGGAGC	1	26	1	AACCTCTCCC	    0.982031	-63
        CCCACAATTGCCCGATGCGAGTC	2	3	1	CACATTGCCC	    0.972364	-32
         AAACCGTTACCGACTCGCATCG	2	23	0	AACCTTACCG	    0.988644	-12
GATTAAAGACAACATTCACAGTGTGGTTATT	3	27	0	AACATCACAG	    0.896611	-274
GCTGACCTTCAAAAATTACCCTGCCGTTTAT	3	164	1	AAAATTACCC	    0.904147	-137
CTTTTGCGTGATCTGTCGCCCAAATACTAAA	3	208	1	ATCTTCGCCC	    0.919001	-93
          **** ******

Masking position 6
Map Score:   3.77229

Number of sites scoring better than the average of aligned sites = 1304
Number in coding regions = 1179
Number in noncoding regions = 125
Number of orfs with sites within 600 bp upstream = 111
Fraction of orfs with sites within 600 bp upstream = 0.0178285


Motif number 3

GTGGTATTTTACATGCACTTACAATTGATT	3	54	0	ACATGCACTT	    0.979951	-247
ATGCAGTTATGCATGCTGTTGAAAAAGAGG	3	105	0	GCATGCTGTT	    0.986282	-196
TCTTTGAGGAACATGCAGTTATGCATGCTG	3	117	0	ACATGCAGTT	    0.976846	-184
TCAAAAATTACCCTGCCGTTTATTTGCACA	3	172	1	CCCTGCCGTT	     0.98288	-129
          **********

Masking position 4
Map Score:   2.21941

Number of sites scoring better than the average of aligned sites = 137
Number in coding regions = 122
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 4

AGATTCTCCAGAGGTAATGTAGGGATTGTT	1	66	0	GAGGTAATGT	    0.959069	-23
CATTCACAGTGTGGTTATTTGTTACACATA	3	16	0	GTGGTTATTT	    0.952417	-285
TAACTCTAAAGTGGTATTTTACATGCACTT	3	64	0	GTGGTATTTT	    0.952416	-237
TGAGGAACATGCAGTTATGCATGCTGTTGA	3	113	0	GCAGTTATGC	    0.927317	-188
TCACGCAAAAGTAGAATTGTGCAAATAAAC	3	189	0	GTAGAATTGT	    0.902801	-112
AGGGGTATTGGCAGTTTTGTTTAGTATTTG	3	228	0	GCAGTTTTGT	    0.975685	-73
          **********

Masking position 8
Map Score:   1.84886

Number of sites scoring better than the average of aligned sites = 721
Number in coding regions = 666
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 58
Fraction of orfs with sites within 600 bp upstream = 0.00931577


Motif number 5

CTGACTAACTCTAAAGTGGTATTTTACATG	3	69	0	CTAAAGTGGT	    0.965105	-232
CATGCTGTTGAAAAAGAGGAAGATACTGAC	3	94	0	AAAAAGAGGA	    0.946207	-207
AGGTCAGCAACAAAAGTTGATTAATTCTTT	3	142	0	CAAAAGTTGA	    0.984783	-159
ACAGATCACGCAAAAGTAGAATTGTGCAAA	3	194	0	CAAAAGTAGA	    0.984788	-107
          **********

Masking position 5
Map Score:   0.970882

Number of sites scoring better than the average of aligned sites = 122
Number in coding regions = 103
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 6

          **********

No masking
Map Score:   -7.64954e-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:   -7.64954e-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 8

          **********

No masking
Map Score:   -7.64954e-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