AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i133_Transmembrane_Transport_7_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	ywcB	300	alternate gene name: ipa-32r

Motif number 1

       GCGATCACCTCTTGGCACATGCA	1	4	1	ATCACCTCTT	    0.977871	-297
TCATGTTCGCATCACCTCTTTATGACAATG	1	32	0	ATCACCTCTT	    0.977871	-269
TCTGGTAAACAGCAGCTTTGCTGAGAACAA	1	71	1	AGCAGCTTTG	    0.910557	-230
CCTCACCGAATGCAGCTTGTTCTCAGCAAA	1	87	0	TGCAGCTTGT	    0.950926	-214
GACCACTGTGTTCACCTCTTCACGACTTCC	1	174	1	TTCACCTCTT	     0.98827	-127
CTTCACGACTTCCTTCTTTTTTCATCCTCC	1	191	1	TCCTTCTTTT	    0.868551	-110
TTTTTCATCCTCCAGCTATTGTACAACGCA	1	208	1	TCCAGCTATT	    0.953354	-93
TACCTATTGGTGTACCTTTTTGCTTACGTT	1	258	1	TGTACCTTTT	    0.929826	-43
     GGCTTTCCTCCTTTTATTCGCTAAA	1	286	0	TCCTCCTTTT	    0.977123	-15
          **********

Masking position 7
Map Score:   11.1392

Number of sites scoring better than the average of aligned sites = 1678
Number in coding regions = 1384
Number in noncoding regions = 294
Number of orfs with sites within 600 bp upstream = 311
Fraction of orfs with sites within 600 bp upstream = 0.0499518


Motif number 2

GAGGTGATGCGAACATGATAACCGTGCTCTG	1	44	1	GAACATGAAA	    0.971893	-257
TGCATTCGGTGAGGTTTTGAAAGCAAACTCG	1	103	1	GAGGTTTTAA	    0.956037	-198
ATACACGGCCGAGCTTGAAAACCTTCGCCTG	1	137	1	GAGCTTGAAA	    0.991122	-164
AAAAAAGAAGGAAGTCGTGAAGAGGTGAACA	1	182	0	GAAGTCGTAA	    0.957788	-119
ACAATAGCTGGAGGATGAAAAAAGAAGGAAG	1	199	0	GAGGATGAAA	    0.991265	-102
          ******** **

Masking position 2
Map Score:   2.44455

Number of sites scoring better than the average of aligned sites = 471
Number in coding regions = 396
Number in noncoding regions = 75
Number of orfs with sites within 600 bp upstream = 62
Fraction of orfs with sites within 600 bp upstream = 0.00995824


Motif number 3

CATGTGCCAAGAGGTGATCGC         	1	2	0	GAGGTGATCG	    0.919765	-299
ATAAAGAGGTGATGCGAACATGATAACCGT	1	39	1	GATGCGAACA	    0.853686	-262
TTACCAGAGCACGGTTATCATGTTCGCATC	1	49	0	ACGGTTATCA	    0.932631	-252
CAGCAAAGCTGCTGTTTACCAGAGCACGGT	1	64	0	GCTGTTTACC	    0.895201	-237
CAGCAGCTTTGCTGAGAACAAGCTGCATTC	1	80	1	GCTGAGAACA	    0.902197	-221
TGCATTCGGTGAGGTTTTGAAAGCAAACTC	1	103	1	GAGGTTTTGA	    0.816649	-198
TTCAAGCTCGGCCGTGTATAAACGAGTTTG	1	126	0	GCCGTGTATA	    0.790947	-175
AAGACAGGCGAAGGTTTTCAAGCTCGGCCG	1	142	0	AAGGTTTTCA	    0.896366	-159
TCTTTAGACCACTGTGTTCACCTCTTCACG	1	168	1	ACTGTGTTCA	    0.960274	-133
TCCGATTTATGCGTTGTACAATAGCTGGAG	1	217	0	GCGTTGTACA	    0.936328	-84
          **********

Masking position 4
Map Score:   3.3998

Number of sites scoring better than the average of aligned sites = 4501
Number in coding regions = 4080
Number in noncoding regions = 421
Number of orfs with sites within 600 bp upstream = 357
Fraction of orfs with sites within 600 bp upstream = 0.0573402


Motif number 4

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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