AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i138_Transmembrane_Transport_11_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	ycdH	187	similar to adhesion protein
#2	ycdI	55	similar to ABC transporter (ATP-binding protein)

Motif number 1

AAGTAGCCCGGCATTTTTAGCCGGGTTTTT	1	17	1	GCATTTTTAG	    0.973551	-171
TTTTAGCCGGGTTTTTTTAGTACATATATT	1	31	1	GTTTTTTTAG	    0.885208	-157
AGAATAAATTTCATTTTCATTTATTTTTCC	1	74	0	TCATTTTCAT	    0.976172	-114
TGACTTCGGTTTATTATGATATAGGATTAC	1	116	1	TTATTATGAT	    0.800638	-72
AAAATCGTTATCATTTTGATTTAAAGTTAC	1	146	1	TCATTTTGAT	    0.983518	-42
GTATATCCCCTCTTTTTCAGTAACTTTAAA	1	165	0	TCTTTTTCAG	    0.984844	-23
GCACACTATTTCTTTGTGAGAAAGGAAGAT	2	32	1	TCTTTGTGAG	    0.971917	-24
          **********

Masking position 9
Map Score:   7.15963

Number of sites scoring better than the average of aligned sites = 1558
Number in coding regions = 1331
Number in noncoding regions = 227
Number of orfs with sites within 600 bp upstream = 240
Fraction of orfs with sites within 600 bp upstream = 0.038548


Motif number 2

CTGCAGGCGGGAAAAATAAATGAAAATGAA	1	65	1	GAAAAATAAA	    0.969487	-123
AAAAATAAATGAAAATGAAATTTATTCTTG	1	76	1	GAAAATGAAA	    0.984988	-112
TTACGTTTTGCAAGAATAAATTTCATTTTC	1	86	0	CAAGAATAAA	    0.965617	-102
TTTATTCTTGCAAAACGTAATGACTTCGGT	1	96	1	CAAAACGTAA	    0.913022	-92
AACTTTAAATCAAAATGATAACGATTTTGT	1	144	0	CAAAATGATA	    0.947067	-44
CTTCCTTTCTCACAAAGAAATAGTGTGCAC	2	30	0	CACAAAGAAA	    0.963667	-26
TGTGAGAAAGGAAGATTAAC          	2	46	1	GAAGATTAAC	    0.867988	-10
          **********

Masking position 5
Map Score:   5.08577

Number of sites scoring better than the average of aligned sites = 1764
Number in coding regions = 1434
Number in noncoding regions = 330
Number of orfs with sites within 600 bp upstream = 335
Fraction of orfs with sites within 600 bp upstream = 0.0538066


Motif number 3

TTATGATATAGGATTACAAAATCGTTATCATT	1	129	1	GGTTACAAAT	    0.976731	-59
TGAAAAAGAGGGGATATACGAT          	1	176	1	GGATATACAT	    0.976668	-12
GCACCCCTCCGGCGCACACTATC         	2	2	0	GGGCACACAT	    0.998575	-54
GCGCCGGAGGGGTGCACACTATTTCTTTGTGA	2	19	1	GGGCACACAT	    0.998575	-37
          ** ****** **

Masking position 6
Map Score:   2.59991

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 37
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

AACCCGGCTAAAAATGCCGGGCTACTTCAA	1	14	0	AAAATGCCGG	    0.995755	-174
TATGTACTAAAAAAACCCGGCTAAAAATGC	1	27	0	AAAAACCCGG	    0.995571	-161
AAAGTTACTGAAAAAGAGGGGATATACGAT	1	168	1	AAAAAGAGGG	     0.98801	-20
          **********

Masking position 4
Map Score:   1.5764

Number of sites scoring better than the average of aligned sites = 251
Number in coding regions = 204
Number in noncoding regions = 47
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:   -3.30951e-14

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:   -3.30951e-14

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:   -3.30951e-14

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