AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i188_ecoli_bsub_300.orf -o188_ecoli_bsub_300.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	menD	88	2-oxoglutarate decarboxylase; SHCHC synthase
#2	menF	300	isochorismate hydroxymutase 2, menaquinone biosynthesis
#3	menB	34	dihydroxynapthoic acid synthetase
#4	menF	288	menaquinone-specific isochorismate synthase

Motif number 1

CGGTATCAATATTGCGGCTAAGTATAAGGA	1	60	0	ATTGCGGCTA	     0.98719	-29
GCCTCACATTATACGGGGTACTACAAAAAA	2	35	0	ATACGGGGTA	    0.930467	-266
GTCGCAAGAGATTCCGGCGACACCCGGCAT	2	130	1	ATTCCGGCGA	    0.965662	-171
GATAACCCGAATGCCGGGTGTCGCCGGAAT	2	140	0	ATGCCGGGTG	    0.992407	-161
TGCCAGTAGAATTGCGGGTATGTTTGCTGA	2	223	0	ATTGCGGGTA	    0.993264	-78
ACTTTCATAAATGGCGGGTGGAGGAATATA	4	68	1	ATGGCGGGTG	    0.992477	-221
          **********

Masking position 2
Map Score:   6.69844

Number of sites scoring better than the average of aligned sites = 262
Number in coding regions = 242
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 2

CTCCCTACACCGGGGTACTGCATTTTTTTTG	2	11	1	CGGGTACTGC	    0.991544	-290
TCACATTATACGGGGTACTACAAAAAAAATG	2	31	0	CGGGTACTAC	    0.975394	-270
GAGAGGTCCGCGTGCAATCACTTACTACGGC	2	75	1	CGTGAATCAC	    0.921466	-226
AACCCGAATGCCGGGTGTCGCCGGAATCTCT	2	136	0	CCGGTGTCGC	    0.972224	-165
ACCCGGCATTCGGGTTATCGATATTCCTTTC	2	151	1	CGGGTATCGA	    0.984734	-150
CGACGTAAAACGGGTAATCGCGCCCAGGACG	2	280	0	CGGGAATCGC	    0.995441	-21
          **** ******

Masking position 4
Map Score:   3.90689

Number of sites scoring better than the average of aligned sites = 717
Number in coding regions = 670
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 3

ACACCGGGGTACTGCATTTTTTTTGTAGTACCCC	2	17	1	ACTGCTTTTT	    0.962356	-284
TGGAAAATCTACTGCGCCATTTGTCGCAAGAGAT	2	108	1	ACTGCCTTTT	    0.856591	-193
GGTTATCGATATTCCTTTCCCTCTCAAAGACGCT	2	163	1	ATTCCTCCTT	    0.811924	-138
   ATGATGACCTCCTTTTATTCTCTATGTGAAT	3	14	0	CCTCCTATTT	    0.925577	-21
  TGTGATCGCCTCGTTTCTCTGTGATGCATACC	4	9	1	CCTCGTTCTT	    0.953263	-280
AAAAGGAAAACCTCCTATATTCCTCCACCCGCCA	4	79	0	CCTCCATTCT	    0.802394	-210
GTCCAAATGGCCTGCCTTACCTATTATAAACCTA	4	186	0	CCTGCTCCTT	    0.991437	-103
GGCCATTTGGACTGCATGATCTGTGTTTGACACA	4	208	1	ACTGCTTCTT	    0.983563	-81
ATACCATACACCTGTGTCTCCTTTGTGTCAAACA	4	231	0	CCTGTTCCTT	    0.919035	-58
  GAGACATTCCTCCATAATCCTTAAAATGCTTT	4	267	0	CCTCCTTCCT	    0.983702	-22
          ***** *  *** *

Masking position 3
Map Score:   4.50652

Number of sites scoring better than the average of aligned sites = 818
Number in coding regions = 709
Number in noncoding regions = 109
Number of orfs with sites within 600 bp upstream = 123
Fraction of orfs with sites within 600 bp upstream = 0.0197559


Motif number 4

TCGATATTCCTTTCCCTCTCAAAGACGCTT	2	168	1	TTTCCCTCTC	    0.981979	-133
GATGACCTCCTTTTATTCTCTATGTGAATG	3	13	0	TTTTATTCTC	    0.894713	-22
TATAGGAGGTTTTCCTTTTATGGTAAGCGG	4	94	1	TTTCCTTTTA	    0.911405	-195
CAAGCTTAAATTTCTTTCTCCACTGATAGC	4	135	0	TTTCTTTCTC	    0.987374	-154
TTTAAGCTTGTTTCTTTTTCATTTCTGAAA	4	155	1	TTTCTTTTTC	    0.971994	-134
          **********

Masking position 7
Map Score:   1.52526

Number of sites scoring better than the average of aligned sites = 165
Number in coding regions = 126
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


Motif number 5

TATGAATCGGTAATGATGCGACTCATTA  	1	9	0	TAATGATGCG	    0.931206	-80
AAAAATAGATTATTGATATGAATCGGTAAT	1	25	0	TATTGATATG	    0.887709	-64
TTAGCCGCAATATTGATACCGGACAAACTC	1	69	1	TATTGATACC	    0.983632	-20
TCAAAGACGCTTTTGATGCCTTGAGCTGGC	2	186	1	TTTTGATGCC	    0.978389	-115
CTTAAAATGCTTTTAATACCATACACCTGT	4	250	0	TTTTAATACC	    0.889336	-39
          **********

Masking position 6
Map Score:   0.368121

Number of sites scoring better than the average of aligned sites = 359
Number in coding regions = 327
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 6

          **********

No masking
Map Score:   1.40931e-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:   1.40931e-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:   1.40931e-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