AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i118_ecoli_bsub_100.orf -o118_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	queA	92	synthesis of queuine in tRNA; probably S-adenosylmethionine:tRNA ribosyltransferase-isomerase
#2	tgt	55	tRNA-guanine transglycosylase
#3	yajC	22	orf, hypothetical protein
#4	secD	27	protein secretion; membrane protein, part of the channel
#5	secF	125	protein-export membrane protein

Motif number 1

TCTAGTGCCGGGGCGCTCTCCCTGCAACCTTTA	1	36	0	GGGCGCTCCT	    0.993879	-57
GAGAGCGCCCCGGCACTAGACTACCCGCCTCTT	1	49	1	CGGCACTCTA	    0.997494	-44
     TTCCGCGGCGCTGGTTTAAAACGTTGGA	2	6	1	CGGCGCTTTA	    0.994545	-50
         ACGGTGCTGATCTAGTCGAAAACG	5	2	1	CGGTGCTCTA	    0.994537	-124
TAGTCGAAAACGGCGCTAAACAAACTTATGATA	5	23	1	CGGCGCTCAA	     0.99786	-103
TGACCTTCTTGGTCACTTCACCAAATTTATCAG	5	98	0	GGTCACTCCA	     0.97201	-28
          *******   ***

Masking position 7
Map Score:   8.83674

Number of sites scoring better than the average of aligned sites = 548
Number in coding regions = 522
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 2

CCGGGGCGCTCTCCCTGCAACCTTTACCCC	1	32	0	CTCCCTGCAA	    0.986599	-61
GCAGGGAGAGCGCCCCGGCACTAGACTACC	1	44	1	CGCCCCGGCA	    0.939306	-49
CGGCACTAGACTACCCGCCTCTTATTTTAG	1	59	1	CTACCCGCCT	    0.978498	-34
TTTAAACCAGCGCCGCGGAA          	2	1	0	CGCCGCGGAA	    0.699466	-55
          **********

Masking position 4
Map Score:   2.13551

Number of sites scoring better than the average of aligned sites = 568
Number in coding regions = 517
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 58
Fraction of orfs with sites within 600 bp upstream = 0.00931577


Motif number 3

       TAAATTTCCCTCATTATTAATA 	3	10	0	ATTTCCCTCA	    0.941732	-13
       GGCAATTCCCTTAGGGAAAAATT	4	15	0	AATTCCCTTA	     0.90339	-13
TAATCGTGACAATTGGCTCATTTGTTGTGC	5	56	0	AATTGGCTCA	    0.970453	-70
AATTGTCACGATTAAGCTGAAAGACGCTGA	5	72	1	ATTAAGCTGA	    0.928852	-54
ATTAAGCTGAAAGACGCTGATAAATTTGGT	5	82	1	AAGACGCTGA	    0.978495	-44
GACGCTGATAAATTTGGTGAAGTGACCAAG	5	94	1	AATTTGGTGA	     0.90339	-32
TGAAGTGACCAAGAAGGTCATGAAA     	5	111	1	AAGAAGGTCA	    0.894971	-15
          **********

Masking position 1
Map Score:   1.37775

Number of sites scoring better than the average of aligned sites = 1558
Number in coding regions = 1388
Number in noncoding regions = 170
Number of orfs with sites within 600 bp upstream = 205
Fraction of orfs with sites within 600 bp upstream = 0.0329264


Motif number 4

TTATATTCTATCCAAAAGGGGGTAAAGGTT	1	14	1	TCCAAAAGGG	    0.995642	-79
TTAAAATTTTTCCCTAAGGGAATTGCC   	4	11	1	TCCCTAAGGG	    0.981318	-17
GCTGATCTAGTCGAAAACGGCGCTAAACAA	5	16	1	TCGAAAACGG	    0.988881	-110
          **********

Masking position 6
Map Score:   1.3644

Number of sites scoring better than the average of aligned sites = 9
Number in coding regions = 6
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 5

          **********

No masking
Map Score:   -2.17836e-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:   -2.17836e-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:   -2.17836e-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