AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i341_weak2_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	ybiT	218	putative ATP-binding component of a transport system
#2	ygiM	241	orf, hypothetical protein
#3	cca	63	tRNA nucleotidyl transferase

Motif number 1

GATTTTGTGCCTGGCAGGCCATTGGGTTGAGA	1	20	1	CTGGCAGCAT	    0.921139	-199
TCACTGTGAGCTGGAATGAACTTATAATGCGC	1	69	0	CTGGAAGACT	    0.973709	-150
CCAGCTCACAGTGAAATCAGATGTGTACGAAA	1	87	1	GTGAAACAAT	    0.922366	-132
TGCCATAAGTCTGAAAGAAGATCCTGCTCCTC	1	158	0	CTGAAAAAAT	    0.916708	-61
 AGGCGTATCCTGAAAAGAGATATGACAAACC	1	198	0	CTGAAAGAAT	    0.965702	-21
CGTCACTTATGTGACATAACCGATAAGTAAAG	2	14	0	GTGACAAACG	     0.94006	-228
ATACTATCTACTGACAAAAAAGATCGCATTAA	2	59	0	CTGACAAAAG	    0.950036	-183
GTTTGAAGCAGTGGCAAGACCTGACACAGAGG	2	136	1	GTGGCAGACT	     0.98335	-106
AACGATAGTAGTGGCATCAGTGTCGCTACGCA	2	191	0	GTGGCACATG	    0.871728	-51
GTCATGGAAAGTGGAACGATAGTAGTGGCATC	2	205	0	GTGGAAGAAG	    0.979857	-37
          ****** ** **

Masking position 6
Map Score:   9.68964

Number of sites scoring better than the average of aligned sites = 1076
Number in coding regions = 994
Number in noncoding regions = 82
Number of orfs with sites within 600 bp upstream = 96
Fraction of orfs with sites within 600 bp upstream = 0.0154192


Motif number 2

GTTAAGCGAGATTTTGTGCCTGGCAGGCCA	1	11	1	ATTTTGTGCC	    0.990872	-208
GAATGAACTTATAATGCGCTTCCAATACTC	1	58	0	ATAATGCGCT	    0.835976	-161
ACGAAATCACATTTTTTGCCTTTGGCTTGA	1	113	1	ATTTTTTGCC	    0.967335	-106
GACTTATGGCATAATGCGCGGTTTGTCATA	1	179	1	ATAATGCGCG	    0.883094	-40
TTCATCGTCACTTATGTGACATAACCGATA	2	21	0	CTTATGTGAC	    0.895868	-221
TTAATGCGATCTTTTTTGTCAGTAGATAGT	2	59	1	CTTTTTTGTC	    0.790137	-183
AGTAGATAGTATTTTGCGCCAAATTGCCAT	2	79	1	ATTTTGCGCC	    0.994226	-163
CTGCTTCAAACTTTTACGCCCGTCAAATTG	2	117	0	CTTTTACGCC	    0.963113	-125
          **********

Masking position 5
Map Score:   6.2201

Number of sites scoring better than the average of aligned sites = 1784
Number in coding regions = 1613
Number in noncoding regions = 171
Number of orfs with sites within 600 bp upstream = 197
Fraction of orfs with sites within 600 bp upstream = 0.0316415


Motif number 3

TGCCTGGCAGGCCATTGGGTTGAGAATATTAG	1	27	1	GCCATTGTTG	    0.991184	-192
CACATTTTTTGCCTTTGGCTTGAGTGTAGACC	1	120	1	GCCTTTGTTG	    0.983675	-99
CGCGCATTATGCCATAAGTCTGAAAGAAGATC	1	167	0	GCCATAGCTG	    0.989556	-52
AAAAAAGATCGCATTAAGTTCGCCGTTCATCG	2	44	0	GCATTAGTCG	    0.923333	-198
CCGTTGCATGGCAATTTGGCGCAAAATACTAT	2	84	0	GCAATTGCGC	    0.965217	-158
CATGCAACGGGCAATTTGACGGGCGTAAAAGT	2	106	1	GCAATTGCGG	    0.991806	-136
          ****** * ***

Masking position 5
Map Score:   3.43718

Number of sites scoring better than the average of aligned sites = 491
Number in coding regions = 452
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 4

GGCTTGAGTGTAGACCTTAAGCGAGGAGCAGGA	1	136	1	TAGACTAACG	    0.986739	-83
CGCATTAAGTTCGCCGTTCATCGTCACTTATGT	2	34	0	TCGCCTCACG	    0.997945	-208
TTGCGCCAAATTGCCATGCAACGGGCAATTTGA	2	92	1	TTGCCTCACG	    0.994414	-150
CGCAAAGCATTCGACATCAATCGGAATCCTCTG	2	162	0	TCGACTAACG	    0.995097	-80
          ***** * ** **

Masking position 7
Map Score:   1.1429

Number of sites scoring better than the average of aligned sites = 138
Number in coding regions = 132
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 5

TGCCTGGCAGGCCATTGGGTTGAGAATATT	1	27	1	GCCATTGGGT	     0.98105	-192
CACATTTTTTGCCTTTGGCTTGAGTGTAGA	1	120	1	GCCTTTGGCT	    0.973072	-99
         GGCCTTTACTTATCGGTTATG	2	2	1	GCCTTTACTT	    0.975507	-240
GTCAGGTCTTGCCACTGCTTCAAACTTTTA	2	131	0	GCCACTGCTT	    0.992847	-111
CGACACTGATGCCACTACTATCGTTCCACT	2	198	1	GCCACTACTA	    0.949303	-44
          **********

Masking position 6
Map Score:   2.13576

Number of sites scoring better than the average of aligned sites = 455
Number in coding regions = 422
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 6

          **********

No masking
Map Score:   1.23167e-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:   1.23167e-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:   1.23167e-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