AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i113_ecoli_bsub_300.orf -o113_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	yflD	100	yflD
#2	yflA	124	similar to aminoacid carrier protein
#3	yrbD	300	similar to sodium/proton-dependent alanine carrier protein

Motif number 1

  TGTTACACTCCTTTTTTCCGATCCAGTT	1	9	1	TCCTTTTTTC	    0.990145	-92
TTGGATACGTTCGTTTTTTCTATCGTTTCG	1	43	0	TCGTTTTTTC	    0.986399	-58
ATAAAAGCCATCCTTTTTATGTTCCAAGTT	2	38	1	TCCTTTTTAT	    0.956858	-87
AAAAACATAAACCTTTTGACATAGAACTTG	2	62	0	ACCTTTTGAC	    0.958291	-63
   CCCATCACCCTTTTTTCGTTTATGAAT	2	108	0	CCCTTTTTTC	    0.959141	-17
GATTGCTTTATCCTTTATATACGGTTTGAC	3	57	1	TCCTTTATAT	    0.832478	-244
TCCTTTATATACGGTTTGACTGAACTAGGC	3	67	1	ACGGTTTGAC	    0.877017	-234
TCGACTACGCTGCGTTTTTCTACAGAGGCA	3	137	0	TGCGTTTTTC	    0.821243	-164
TCGATACGCCGCGTTTTTTCTTTTTCCCTT	3	163	1	GCGTTTTTTC	    0.944273	-138
ATTTCTACAATCGATTTGTCACATTATATG	3	218	0	TCGATTTGTC	    0.943133	-83
TAGAAATAGTTCGATTAGACCAAAATCCTT	3	241	1	TCGATTAGAC	    0.787952	-60
TAGACCAAAATCCTTTTTATACATGTATTC	3	256	1	TCCTTTTTAT	    0.956858	-45
          **********

Masking position 5
Map Score:   14.4695

Number of sites scoring better than the average of aligned sites = 1186
Number in coding regions = 999
Number in noncoding regions = 187
Number of orfs with sites within 600 bp upstream = 213
Fraction of orfs with sites within 600 bp upstream = 0.0342114


Motif number 2

TTTCGCTCGAACTGGATCGGAAAAAAGGAGTG	1	16	0	ACTGATGGAA	    0.947469	-85
AGTTCGAGCGAAACGATAGAAAAAACGAACGT	1	35	1	AAAGATGAAA	    0.983059	-66
AACACGAATCAGCAGATTAGAAAAGTGAAAAT	1	76	1	AGCGATAGAA	     0.90287	-25
AATCATTTCCCATAGATGGAAAAACATAAACC	2	79	0	CATGATGAAA	    0.870211	-46
       ATAAGATGAACGGAACAAATGATGA	3	4	1	AGAGAAGGAA	    0.976013	-297
TGAACGGAACAAATGATGAAAAGCATTTCAAT	3	17	1	AAAGATAAAA	    0.929934	-284
AGCAATCACAAAATGATTGAAATGCTTTTCAT	3	32	0	AAAGATGAAA	    0.983059	-269
ATCAATAAGAAGAGGAAGGGAAAAAGAAAAAA	3	176	0	AGAGAAGGAA	    0.976013	-125
          *** *** ****

Masking position 6
Map Score:   5.91292

Number of sites scoring better than the average of aligned sites = 275
Number in coding regions = 235
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 3

AAGGATGGCTTTTATCAATCGCCATCCTGCAGAC	2	19	0	TACAATCCCA	    0.991313	-106
TGTCAAAAGGTTTATGTTTTTCCATCTATGGGAA	2	71	1	TAGTTTTCCA	    0.900578	-54
TTTTCGTTTATGAATCATTTCCCATAGATGGAAA	2	89	0	TACATTTCCA	    0.986615	-36
ATATAAAGGATAAAGCAATCACAAAATGATTGAA	3	43	0	TACAATCCAA	     0.95626	-258
TGAAGGATTTTATAACAATTGCCATAAGTTTGCC	3	107	1	TACAATTCCA	    0.992768	-194
TTTGGTCTAATCGAACTATTTCTACAATCGATTT	3	231	0	TACTATTCTA	    0.928396	-70
          *  * ***** ***

Masking position 9
Map Score:   1.96982

Number of sites scoring better than the average of aligned sites = 180
Number in coding regions = 172
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

          **********

No masking
Map Score:   1.3033e-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 5

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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