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

Motif number 1

TGCATGTGCCAAGAGGTGATCGC       	1	4	0	AAGAGGTGAT	    0.981781	-297
CATTGTCATAAAGAGGTGATGCGAACATGA	1	32	1	AAGAGGTGAT	    0.981781	-269
TTGTTCTCAGCAAAGCTGCTGTTTACCAGA	1	71	0	CAAAGCTGCT	    0.925452	-230
TTTGCTGAGAACAAGCTGCATTCGGTGAGG	1	87	1	ACAAGCTGCA	     0.95937	-214
GGAAGTCGTGAAGAGGTGAACACAGTGGTC	1	174	0	AAGAGGTGAA	    0.990361	-127
GGAGGATGAAAAAAGAAGGAAGTCGTGAAG	1	191	0	AAAAGAAGGA	    0.889599	-110
TGCGTTGTACAATAGCTGGAGGATGAAAAA	1	208	0	AATAGCTGGA	    0.961377	-93
AACGTAAGCAAAAAGGTACACCAATAGGTA	1	258	0	AAAAGGTACA	     0.94172	-43
TTTAGCGAATAAAAGGAGGAAAGCC     	1	286	1	AAAAGGAGGA	    0.981163	-15
          **********

Masking position 4
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

CAGAGCACGGTTATCATGTTCGCATCACCTC	1	44	0	TTTCATGTTC	    0.974292	-257
CGAGTTTGCTTTCAAAACCTCACCGAATGCA	1	103	0	TTAAAACCTC	    0.959733	-198
CAGGCGAAGGTTTTCAAGCTCGGCCGTGTAT	1	137	0	TTTCAAGCTC	    0.991893	-164
TGTTCACCTCTTCACGACTTCCTTCTTTTTT	1	182	1	TTACGACTTC	    0.961342	-119
CTTCCTTCTTTTTTCATCCTCCAGCTATTGT	1	199	1	TTTCATCCTC	    0.992024	-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

        GCGATCACCTCTTGGCACATGC	1	3	1	GATCACCTCT	     0.96218	-298
CGGTTATCATGTTCGCATCACCTCTTTATG	1	38	0	GTTCGCATCA	    0.982182	-263
CCGTGCTCTGGTAAACAGCAGCTTTGCTGA	1	65	1	GTAAACAGCA	    0.941014	-236
AATGCAGCTTGTTCTCAGCAAAGCTGCTGT	1	79	0	GTTCTCAGCA	    0.983188	-222
AGACCACTGTGTTCACCTCTTCACGACTTC	1	173	1	GTTCACCTCT	    0.990396	-128
TCCAGCTATTGTACAACGCATAAATCGGAC	1	218	1	GTACAACGCA	    0.961664	-83
          **********

Masking position 9
Map Score:   4.8177

Number of sites scoring better than the average of aligned sites = 633
Number in coding regions = 563
Number in noncoding regions = 70
Number of orfs with sites within 600 bp upstream = 73
Fraction of orfs with sites within 600 bp upstream = 0.011725


Motif number 4

TTTATGACAATGCATGTGCCAAGAGGTGAT	1	14	0	TGCATGTGCC	    0.944725	-287
GAGCACGGTTATCATGTTCGCATCACCTCT	1	43	0	ATCATGTTCG	    0.974432	-258
AGGTTTTGAAAGCAAACTCGTTTATACACG	1	114	1	AGCAAACTCG	    0.942131	-187
GGCGAAGGTTTTCAAGCTCGGCCGTGTATA	1	136	0	TTCAAGCTCG	    0.988491	-165
TCCTTCTTTTTTCATCCTCCAGCTATTGTA	1	201	1	TTCATCCTCC	    0.969247	-100
          **********

Masking position 4
Map Score:   0.381324

Number of sites scoring better than the average of aligned sites = 583
Number in coding regions = 541
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


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


Motif number 7

          **********

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