AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i232_formulase_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	def	129	peptide deformylase
#2	sun	45	orf, hypothetical protein
#3	HI0622	300	polypeptide deformylase (def)
#4	HI0623	92	methionyl-tRNA formyltransferase (fmt)

Motif number 1

GCTGTCAATCAGAGGGGGATTTGTCTAGAAT	1	64	1	AGGGGGGATT	    0.989602	-66
CGGGCTTAGAAGAGTGGACTA          	2	1	0	AGGTGGACTA	    0.966051	-45
ACGCCCGGCAAGACCGGGCTTAGAAGAGTGG	2	15	0	AGCCGGGCTT	    0.972485	-31
TGCCGATGGTAGTGTGGGGTTTCCCCATGTG	3	35	1	AGGTGGGGTT	    0.995265	-266
GGGTAGAATTTTAGTGGGATTATAGCACAGC	3	262	0	TTGTGGGATT	    0.863163	-39
CTTGTTTTTAAGGGTAGAATTTTAGTGGGAT	3	273	0	AGGTAGAATT	    0.873695	-28
     AACGTAGGGTGGGCTTTAGCCAGCAA	4	6	1	AGGTGGGCTT	     0.99891	-87
ATTTCAAAAAACGGTGGGCTTAAGCCCACCC	4	39	1	ACGTGGGCTT	    0.993452	-54
GATAGGAAGTAGGGTGGGCTTAAGCCCACCG	4	50	0	AGGTGGGCTT	     0.99891	-43
          ** ********

Masking position 10
Map Score:   17.7666

Number of sites scoring better than the average of aligned sites = 143
Number in coding regions = 124
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 2

ATGCTGTCAATCAGAGGGGGATTTGTCTAGA	1	62	1	TAGAGGGGGA	    0.930737	-68
ACCGGGCTTAGAAGAGTGGACTA        	2	3	0	GAGAGTGGAC	    0.986058	-43
AATGCCGATGGTAGTGTGGGGTTTCCCCATG	3	33	1	GAGTGTGGGG	    0.984608	-268
TTTCCCCATGTGAGAGTAGGGCACCGCCAGG	3	54	1	TAGAGTAGGG	    0.947089	-247
CTCTTGTTTTTAAGGGTAGAATTTTAGTGGG	3	275	0	TAGGGTAGAA	    0.845357	-26
       AACGTAGGGTGGGCTTTAGCCAGC	4	4	1	GAGGGTGGGC	    0.998436	-89
TCATTTCAAAAAACGGTGGGCTTAAGCCCAC	4	37	1	AACGGTGGGC	    0.952955	-56
TTGATAGGAAGTAGGGTGGGCTTAAGCCCAC	4	52	0	GAGGGTGGGC	    0.998436	-41
          * *********

Masking position 3
Map Score:   10.4152

Number of sites scoring better than the average of aligned sites = 325
Number in coding regions = 289
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 3

AAGCAGCCTTAGCAATCTTTGCGATTGGTC	1	28	1	AGCAATCTTT	    0.991699	-102
GAATAGAAGAAATAATCTTTCTAACTCCTG	1	91	1	AATAATCTTT	    0.935095	-39
TCAATAAGTAAGTAATTTTTCAACTCATAT	3	203	1	AGTAATTTTT	    0.935095	-98
GGCTTTAGCCAGCAATCATTTCAAAAAACG	4	22	1	AGCAATCATT	     0.97769	-71
          **********

Masking position 5
Map Score:   1.847

Number of sites scoring better than the average of aligned sites = 54
Number in coding regions = 48
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 4

     CCTTATCTCCCTGCCATAAGCAGCC	1	6	1	TCTCCCTGCC	    0.936167	-124
TCTAGACAAATCCCCCTCTGATTGACAGCA	1	63	0	TCCCCCTCTG	    0.965467	-67
GTGTGGGGTTTCCCCATGTGAGAGTAGGGC	3	46	1	TCCCCATGTG	    0.979451	-255
AAACAGAAGGACCCCGTGTCGAAAGATATG	3	113	1	ACCCCGTGTC	    0.979515	-188
AAAAGCTAAAACCCCATATCTTTCGACACG	3	127	0	ACCCCATATC	    0.981076	-174
TAGGAATGTGACTTCATATGAGTTGAAAAA	3	218	0	ACTTCATATG	    0.839052	-83
AGCCCACCCTACTTCCTATCAATTACCATA	4	61	1	ACTTCCTATC	    0.915017	-32
          **********

Masking position 7
Map Score:   3.86326

Number of sites scoring better than the average of aligned sites = 326
Number in coding regions = 264
Number in noncoding regions = 62
Number of orfs with sites within 600 bp upstream = 74
Fraction of orfs with sites within 600 bp upstream = 0.0118856


Motif number 5

GGGTTTTAGCTTTTGGGAATTTATTCATTA	3	143	1	TTTTGGGAAT	    0.974986	-158
AATTACTTACTTATTGAAAATTAAAATTAG	3	190	0	TTATTGAAAA	    0.875578	-111
AATAAAACATTTATAGGAATGTGACTTCAT	3	231	0	TTATAGGAAT	    0.953579	-70
AGCCCACCGTTTTTTGAAATGATTGCTGGC	4	29	0	TTTTTGAAAT	    0.941006	-64
ATGTTCTACGTTATGGTAATTGATAGGAAG	4	72	0	TTATGGTAAT	    0.953579	-21
          **********

Masking position 4
Map Score:   1.18419

Number of sites scoring better than the average of aligned sites = 84
Number in coding regions = 63
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 6

          **********

No masking
Map Score:   -8.85746e-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:   -8.85746e-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:   -8.85746e-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