AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i135_Transmembrane_Transport_9_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	yuxL	107	similar to acylaminoacyl-peptidase
#2	hom	200	homoserine dehydrogenase
#3	yutH	152	yutH

Motif number 1

CAGCGGAGGGCGCTTTTTTTTGCTGGAGATA	1	35	1	CCTTTTTTTT	    0.945274	-73
TAAATAAAAACTCCTTTATCTCCAGCAAAAA	1	51	0	CCCTTTATCT	    0.954978	-57
    ATTCATCTCCTCCTTTTTACATGTATT	1	91	0	CCCTCCTTTT	    0.963578	-17
TATAAGCCCGCTCCTGTTTTGACAAGACATC	2	99	0	CCCTGTTTTG	    0.976759	-102
GTTGAGTTAACAATTGTCTTTTCCAAGAGGA	2	155	1	CATTGTCTTT	    0.765683	-46
  AAAAACTCCACCTTTCTTTTGATTGTCCT	2	182	0	CCCTTTCTTT	    0.988503	-19
GAGAAGTTTACGACTTTTTCTTGCGCCTTCT	3	53	1	CACTTTTTCT	    0.944229	-100
CTTTTTCTTGCGCCTTCTTCGGATTAAAATA	3	66	1	CCCTTCTTCG	    0.971962	-87
       GATCACCTGCCTGTTGAATTAGGG	3	139	0	CCCTGCCTGT	    0.962146	-14
          * *********

Masking position 5
Map Score:   7.61522

Number of sites scoring better than the average of aligned sites = 1661
Number in coding regions = 1256
Number in noncoding regions = 405
Number of orfs with sites within 600 bp upstream = 449
Fraction of orfs with sites within 600 bp upstream = 0.0721169


Motif number 2

AAAACGAAATACATGTAAAAAGGAGGAGAT	1	84	1	ACATGTAAAA	     0.88014	-24
TTCTAATTATTTTTGTCAGATTTTCTCC  	2	9	0	TTTTGTCAGA	    0.902758	-192
AAATAAAGAATCTTGTCATATCAATGCGTT	2	38	1	TCTTGTCATA	    0.960315	-163
CCTAATGATGTCTTGTCAAAACAGGAGCGG	2	93	1	TCTTGTCAAA	    0.989413	-108
TTGATTGTCCTCTTGGAAAAGACAATTGTT	2	163	0	TCTTGGAAAA	    0.951674	-38
TTTTGTATAAACTAGTAAAAAAGATTGGGT	3	18	0	ACTAGTAAAA	    0.880193	-135
TTCTCAAGCATTTTGTATAAACTAGTAAAA	3	28	0	TTTTGTATAA	    0.816838	-125
          **********

Masking position 10
Map Score:   3.99231

Number of sites scoring better than the average of aligned sites = 757
Number in coding regions = 632
Number in noncoding regions = 125
Number of orfs with sites within 600 bp upstream = 144
Fraction of orfs with sites within 600 bp upstream = 0.0231288


Motif number 3

GCTTTTTTTTGCTGGAGATAAAGGAGTTTT	1	46	1	GCTGGAGATA	    0.940243	-62
GACATCATTAGGCTGAATTTTGCGAATGTA	2	75	0	GGCTGAATTT	    0.956386	-126
TATATGTCTGTGTTGAGTTAACAATTGTCT	2	144	1	TGTTGAGTTA	    0.963264	-57
TCAAAAGAAAGGTGGAGTTTTT        	2	189	1	GGTGGAGTTT	     0.98494	-12
GTCATACACAGCCGGAATTATGAATACATA	3	95	0	GCCGGAATTA	     0.97112	-58
ATCACCTGCCTGTTGAATTAGGGCTCATCA	3	132	0	TGTTGAATTA	    0.943425	-21
          **********

Masking position 6
Map Score:   3.13213

Number of sites scoring better than the average of aligned sites = 333
Number in coding regions = 278
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 57
Fraction of orfs with sites within 600 bp upstream = 0.00915516


Motif number 4

          **********

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 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