AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i111_Amino_Acid_Transport_2_bsub_reg_100.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	yknW	109	yknW
#2	ytrD	29	similar to cytochrome c oxidase subunit
#3	ytrA	300	similar to transcriptional regulator (GntR family)

Motif number 1

      TATGAAAAGCCTTCAATATTGAAGG	1	5	1	AAAAGCTTCA	    0.984291	-105
ATAAATTTCCAAAAACCTTCAATATTGAAGG	1	20	0	AAAAACTTCA	     0.98698	-90
GAAGGATATCAAAAAGTTTCATGTTTTTCTA	1	51	0	AAAAAGTTCA	    0.986948	-59
TTTTTGTAAAAAAAGGATTGACTTTGTGAGT	3	15	1	AAAAGGTTGA	    0.944141	-286
TTAATACAATAAATACTTTGACTCACAAAGT	3	35	0	AAATACTTGA	    0.722004	-266
TGAAACATAAAAAACGAAACAAACGTAACGT	3	141	1	AAAACGAACA	    0.822844	-160
GAAAAAAAGAACAAGCGATCACAGATGCCGC	3	185	0	ACAAGCATCA	    0.909177	-116
TTTGCCATTCAAAACCGATCATCACAAGAAC	3	218	0	AAAACCATCA	     0.97336	-83
TTGAATGGCAAAAAAGTATAATTGATCATTT	3	237	1	AAAAAGATAA	    0.863528	-64
TTTTATAGATAAAAATGATCAATTATACTTT	3	249	0	AAAAATATCA	    0.908981	-52
TTTTTATCTATAAAAGGTTCAGATCGTATAG	3	265	1	TAAAAGTTCA	    0.903488	-36
          ****** ****

Masking position 3
Map Score:   12.9744

Number of sites scoring better than the average of aligned sites = 1071
Number in coding regions = 902
Number in noncoding regions = 169
Number of orfs with sites within 600 bp upstream = 174
Fraction of orfs with sites within 600 bp upstream = 0.0279473


Motif number 2

CTTTTTGATATCCTTCCCGTACTATTTGTTAGA	1	66	1	TCTTCCCTAT	     0.99127	-44
    CTCACTTCCCTCCAAACCTAAGGCATTTC	2	11	0	TCCTCCAACT	    0.980399	-19
ATAAATACTTTGACTCACAAAGTCAATCCTTTT	3	25	0	TACTCACAAT	    0.903228	-276
TATAGTGTATTACTTCAATTAGTACACTTAATA	3	60	0	TCTTCAATAT	    0.928393	-241
GTTTCATAACTGCCTCCCTTAATGTCAATATAT	3	114	0	TCCTCCCTAT	    0.994431	-187
         TTACTTCCCTACTTTCTATACGAT	3	287	0	TCTTCCCACT	    0.989489	-14
          * ****** ** *

Masking position 5
Map Score:   3.01938

Number of sites scoring better than the average of aligned sites = 253
Number in coding regions = 172
Number in noncoding regions = 81
Number of orfs with sites within 600 bp upstream = 84
Fraction of orfs with sites within 600 bp upstream = 0.0134918


Motif number 3

TTTATTAGAAAAACATGAAACTTTTTGATA	1	46	1	AAACATGAAA	    0.968854	-64
AATCCTTTTTTTACAAAAAAACG       	3	4	0	TTACAAAAAA	    0.922202	-297
AGTACACTTAATACAATAAATACTTTGACT	3	43	0	ATACAATAAA	    0.870722	-258
CTATAGACACTAATATAAAATCATTTATAT	3	88	1	TAATATAAAA	    0.756865	-213
GGCAGTTATGAAACATAAAAAACGAAACAA	3	133	1	AAACATAAAA	    0.974068	-168
ATCATCACAAGAACAAGAAAAAAAGAACAA	3	202	0	GAACAAGAAA	    0.915082	-99
TGAACCTTTTATAGATAAAAATGATCAATT	3	256	0	ATAGATAAAA	    0.868686	-45
          **********

Masking position 5
Map Score:   2.98419

Number of sites scoring better than the average of aligned sites = 1359
Number in coding regions = 965
Number in noncoding regions = 394
Number of orfs with sites within 600 bp upstream = 386
Fraction of orfs with sites within 600 bp upstream = 0.0619981


Motif number 4

ATTTCCAAAAACCTTCAATATTGAAGGCTT	1	17	0	ACCTTCAATA	    0.979854	-93
ATTTTATATTAGTGTCTATAGTGTATTACT	3	79	0	AGTGTCTATA	     0.96296	-222
TGCCTCCCTTAATGTCAATATATAAATGAT	3	107	0	AATGTCAATA	    0.924468	-194
TACGATCTGAACCTTTTATAGATAAAAATG	3	263	0	ACCTTTTATA	    0.930336	-38
TTACTTCCCTACTTTCTATACGATCTGAAC	3	281	0	ACTTTCTATA	    0.984746	-20
          **********

Masking position 5
Map Score:   1.86452

Number of sites scoring better than the average of aligned sites = 92
Number in coding regions = 80
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 5

          **********

No masking
Map Score:   -5.51791e-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:   -5.51791e-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:   -5.51791e-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