AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i223_Pseudouridylate_Synthase_ecoli_reg_100.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	yciL	210	orf, hypothetical protein
#2	yjbC	211	orf, hypothetical protein

Motif number 1

AGAACTTACATCTGACTCACTGATAGTAAA	1	130	0	TCTGACTCAC	    0.997414	-81
AGATGTAAGTTCTGACTCACTGTTGCACAA	1	147	1	TCTGACTCAC	    0.997414	-64
TCCCGTGATTTCTTACTAACCGGAGAAGTA	2	11	0	TCTTACTAAC	    0.989179	-201
GAATTTAACCACTTACTGACATGGCTCACG	2	57	1	ACTTACTGAC	    0.981692	-155
          **********

Masking position 5
Map Score:   5.90407

Number of sites scoring better than the average of aligned sites = 24
Number in coding regions = 19
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

ATCTTTATGGTTAAAGCTTGTTTCGATTAA	1	22	0	TTAAAGCTTG	    0.847685	-189
CATAAAGATAGTGTAGTATGTTGCGCCTCA	1	43	1	GTGTAGTATG	    0.862206	-168
AGTCGTTTACTTAAGGCCTGAAGAGTTCAA	1	94	1	TTAAGGCCTG	    0.978572	-117
CTCACTGATAGTAAAGTCTGTTTGAACTCT	1	115	0	GTAAAGTCTG	    0.975152	-96
TGAGTCAGATGTAAGTTCTGACTCACTGTT	1	141	1	GTAAGTTCTG	    0.926137	-70
AAGAAATCACGGGAGGCATGCTACCACTGC	2	27	1	GGGAGGCATG	    0.975345	-185
GTGCGACATCGTGAGCCATGTCAGTAAGTG	2	66	0	GTGAGCCATG	     0.96719	-146
          **********

Masking position 9
Map Score:   2.58876

Number of sites scoring better than the average of aligned sites = 1055
Number in coding regions = 943
Number in noncoding regions = 112
Number of orfs with sites within 600 bp upstream = 121
Fraction of orfs with sites within 600 bp upstream = 0.0194346


Motif number 3

GCATATCAGACGCCTGGGAAGGCGACACCA	1	179	1	CGCCTGGGAA	    0.991063	-32
AGGCATGCTACCACTGCGAATTTAACCACT	2	40	1	CCACTGCGAA	    0.980165	-172
TCGCACATTGCTTCTGGAAAGTGATTTGAG	2	90	1	CTTCTGGAAA	    0.978054	-122
CGAATTCAAGCCAATGGAAATAACAAATAG	2	127	1	CCAATGGAAA	    0.959207	-85
     AAATTCTCCTGTAAAAAACGGAATA	2	197	0	CTCCTGTAAA	    0.968596	-15
          **********

Masking position 5
Map Score:   1.82876

Number of sites scoring better than the average of aligned sites = 402
Number in coding regions = 374
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 4

AACATACTACACTATCTTTATGGTTAAAGC	1	35	0	ACTATCTTTA	    0.947301	-176
AACAGACTTTACTATCAGTGAGTCAGATGT	1	123	1	ACTATCAGTG	     0.94804	-88
GTAAGTTCTGACTCACTGTTGCACAAAAGC	1	151	1	ACTCACTGTT	    0.933386	-60
TCATGAGCGAACTATTTGTTATTTCCATTG	2	138	0	ACTATTTGTT	    0.978444	-74
TTCGCTCATGACTATTTTTTATCAACCCAA	2	157	1	ACTATTTTTT	    0.952725	-55
          **********

Masking position 3
Map Score:   0.763767

Number of sites scoring better than the average of aligned sites = 127
Number in coding regions = 109
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 5

          **********

No masking
Map Score:   -7.57849e-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:   -7.57849e-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:   -7.57849e-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