AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i102_bsub_mtub_300.orf -o102_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -x5 -e 
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 =  	0.55
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	yclN	300	similar to ferrichrome ABC transporter (permease)
#2	yclQ	21	similar to ferrichrome ABC transporter (binding protein)

Motif number 1

CAGGAGAACATTTGTATTTTTCACGAGGAAT	1	18	1	TTTTATTTTT	    0.893266	-283
GTCAGCAAACCTAACATTATTCCTCGTGAAA	1	36	0	CTACATTATT	    0.952046	-265
GTTAGGCTGTTTACCATATTTATCTTTATAA	1	79	0	TTACATATTT	    0.973397	-222
CTAATCATTCTAACCATTTTCCATCCCAAAA	1	111	0	TAACATTTTC	    0.953959	-190
ACCTAGTCATTTATCAATTTTACTAATCATT	1	133	0	TTACAATTTT	    0.973397	-168
AATGACTAGGTTAATATTTTTAAAGAATATT	1	153	1	TTATATTTTT	    0.979035	-148
CATTTACATATTACCATTTTTATAGGGTTAG	1	186	0	TTACATTTTT	    0.995126	-115
TAGTAATTGATTATCATTATCATTTACATAT	1	206	0	TTACATTATC	     0.97692	-95
          *** *******

Masking position 6
Map Score:   10.8836

Number of sites scoring better than the average of aligned sites = 820
Number in coding regions = 622
Number in noncoding regions = 198
Number of orfs with sites within 600 bp upstream = 209
Fraction of orfs with sites within 600 bp upstream = 0.0335689


Motif number 2

ATTCCTCGTGAAAAATACAAATGTTCTCCT	1	19	0	AAAAATACAA	     0.76359	-282
TGCCTGCGTTATAAAGATAAATATGGTAAA	1	71	1	ATAAAGATAA	    0.879209	-230
GAAAATGGTTAGAATGATTAGTAAAATTGA	1	121	1	AGAATGATTA	    0.934946	-180
GTAAAATTGATAAATGACTAGGTTAATATT	1	141	1	TAAATGACTA	     0.95284	-160
AATATTCTTTAAAAATATTAACCTAGTCAT	1	154	0	AAAAATATTA	    0.827495	-147
TTTTTAAAGAATATTGACTAACCCTATAAA	1	169	1	ATATTGACTA	     0.81674	-132
TAACCCTATAAAAATGGTAATATGTAAATG	1	187	1	AAAATGGTAA	    0.898558	-114
TGGTAATATGTAAATGATAATGATAATCAA	1	201	1	TAAATGATAA	    0.951993	-100
GGCCATATAGTAATTGATTATCATTATCAT	1	214	0	TAATTGATTA	    0.876902	-87
          **********

Masking position 3
Map Score:   5.57845

Number of sites scoring better than the average of aligned sites = 2197
Number in coding regions = 1759
Number in noncoding regions = 438
Number of orfs with sites within 600 bp upstream = 438
Fraction of orfs with sites within 600 bp upstream = 0.0703501


Motif number 3

   TCTTTCTCAGGAGAACATTTGTATTTT	1	8	1	CAGGAGAACA	    0.952457	-293
GGCATACGGTCAGCAAACCTAACATTATTC	1	45	0	CAGCAAACCT	    0.957284	-256
CTTTATAACGCAGGCATACGGTCAGCAAAC	1	57	0	CAGGCATACG	    0.978031	-244
ATATGGTAAACAGCCTAACGTTTTGGGATG	1	91	1	CAGCCTAACG	    0.988275	-210
TACATCCTTACAGCAAAAAGAACGTATCTC	1	271	0	CAGCAAAAAG	    0.974275	-30
          **********

Masking position 2
Map Score:   1.0385

Number of sites scoring better than the average of aligned sites = 774
Number in coding regions = 715
Number in noncoding regions = 59
Number of orfs with sites within 600 bp upstream = 59
Fraction of orfs with sites within 600 bp upstream = 0.00947639


Motif number 4

          **********

No masking
Map Score:   -5.09159e-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:   -5.09159e-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:   -5.09159e-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