AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i113_Amino_Acid_Transport_4_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

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	    0.989924	-92
TTGGATACGTTCGTTTTTTCTATCGTTTCG	1	43	0	TCGTTTTTTC	    0.986095	-58
ATAAAAGCCATCCTTTTTATGTTCCAAGTT	2	38	1	TCCTTTTTAT	    0.955922	-87
AAAAACATAAACCTTTTGACATAGAACTTG	2	62	0	ACCTTTTGAC	    0.957385	-63
   CCCATCACCCTTTTTTCGTTTATGAAT	2	108	0	CCCTTTTTTC	    0.958252	-17
GATTGCTTTATCCTTTATATACGGTTTGAC	3	57	1	TCCTTTATAT	    0.829324	-244
TCCTTTATATACGGTTTGACTGAACTAGGC	3	67	1	ACGGTTTGAC	    0.874576	-234
TCGACTACGCTGCGTTTTTCTACAGAGGCA	3	137	0	TGCGTTTTTC	    0.817925	-164
TCGATACGCCGCGTTTTTTCTTTTTCCCTT	3	163	1	GCGTTTTTTC	    0.943081	-138
ATTTCTACAATCGATTTGTCACATTATATG	3	218	0	TCGATTTGTC	    0.941917	-83
TAGAAATAGTTCGATTAGACCAAAATCCTT	3	241	1	TCGATTAGAC	    0.784178	-60
TAGACCAAAATCCTTTTTATACATGTATTC	3	256	1	TCCTTTTTAT	    0.955922	-45
          **********

Masking position 5
Map Score:   14.4695

Number of sites scoring better than the average of aligned sites = 2456
Number in coding regions = 2110
Number in noncoding regions = 346
Number of orfs with sites within 600 bp upstream = 348
Fraction of orfs with sites within 600 bp upstream = 0.0558946


Motif number 2

CACTCCTTTTTTCCGATCCAGTTCGAGCGAAA	1	16	1	TTCCATCAGT	    0.947164	-85
ACGTTCGTTTTTTCTATCGTTTCGCTCGAACT	1	35	0	TTTCATCTTT	    0.982956	-66
ATTTTCACTTTTCTAATCTGCTGATTCGTGTT	1	76	0	TTCTATCGCT	    0.902332	-25
GGTTTATGTTTTTCCATCTATGGGAAATGATT	2	79	1	TTTCATCATG	    0.869519	-46
TCATCATTTGTTCCGTTCATCTTAT       	3	4	0	TTCCTTCTCT	    0.975869	-297
ATTGAAATGCTTTTCATCATTTGTTCCGTTCA	3	17	0	TTTTATCTTT	    0.929534	-284
ATGAAAAGCATTTCAATCATTTTGTGATTGCT	3	32	1	TTTCATCTTT	    0.982956	-269
TTTTTTCTTTTTCCCTTCCTCTTCTTATTGAT	3	176	1	TTCCTTCTCT	    0.975869	-125
          **** *** ***

Masking position 7
Map Score:   5.91292

Number of sites scoring better than the average of aligned sites = 717
Number in coding regions = 613
Number in noncoding regions = 104
Number of orfs with sites within 600 bp upstream = 115
Fraction of orfs with sites within 600 bp upstream = 0.0184709


Motif number 3

AAGGATGGCTTTTATCAATCGCCATCCTGCAGAC	2	19	0	TACAATCCCA	    0.992534	-106
TGTCAAAAGGTTTATGTTTTTCCATCTATGGGAA	2	71	1	TAGTTTTCCA	    0.913413	-54
TTTTCGTTTATGAATCATTTCCCATAGATGGAAA	2	89	0	TACATTTCCA	    0.988484	-36
ATATAAAGGATAAAGCAATCACAAAATGATTGAA	3	43	0	TACAATCCAA	    0.962217	-258
TGAAGGATTTTATAACAATTGCCATAAGTTTGCC	3	107	1	TACAATTCCA	     0.99378	-194
TTTGGTCTAATCGAACTATTTCTACAATCGATTT	3	231	0	TACTATTCTA	    0.936252	-70
          *  * ***** ***

Masking position 9
Map Score:   1.96982

Number of sites scoring better than the average of aligned sites = 143
Number in coding regions = 127
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


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