AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i102_bsub_mtub_100.orf -o102_bsub_mtub_100.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	    0.873677	-283
GTCAGCAAACCTAACATTATTCCTCGTGAAA	1	36	0	CTACATTATT	    0.942551	-265
GTTAGGCTGTTTACCATATTTATCTTTATAA	1	79	0	TTACATATTT	    0.967988	-222
CTAATCATTCTAACCATTTTCCATCCCAAAA	1	111	0	TAACATTTTC	    0.944821	-190
ACCTAGTCATTTATCAATTTTACTAATCATT	1	133	0	TTACAATTTT	    0.967988	-168
AATGACTAGGTTAATATTTTTAAAGAATATT	1	153	1	TTATATTTTT	    0.974743	-148
CATTTACATATTACCATTTTTATAGGGTTAG	1	186	0	TTACATTTTT	    0.994108	-115
TAGTAATTGATTATCATTATCATTTACATAT	1	206	0	TTACATTATC	    0.972206	-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	    0.777899	-282
TGCCTGCGTTATAAAGATAAATATGGTAAA	1	71	1	ATAAAGATAA	    0.887547	-230
GAAAATGGTTAGAATGATTAGTAAAATTGA	1	121	1	AGAATGATTA	    0.939703	-180
GTAAAATTGATAAATGACTAGGTTAATATT	1	141	1	TAAATGACTA	    0.956347	-160
AATATTCTTTAAAAATATTAACCTAGTCAT	1	154	0	AAAAATATTA	    0.838629	-147
TTTTTAAAGAATATTGACTAACCCTATAAA	1	169	1	ATATTGACTA	    0.828554	-132
TAACCCTATAAAAATGGTAATATGTAAATG	1	187	1	AAAATGGTAA	    0.905707	-114
TGGTAATATGTAAATGATAATGATAATCAA	1	201	1	TAAATGATAA	    0.955542	-100
GGCCATATAGTAATTGATTATCATTATCAT	1	214	0	TAATTGATTA	     0.88405	-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

AAAATACAAATGTTCTCCTGAGAAAGA   	1	8	0	TGTTCTCCTG	    0.957353	-293
GAATAATGTTAGGTTTGCTGACCGTATGCC	1	45	1	AGGTTTGCTG	    0.961703	-256
GTTTGCTGACCGTATGCCTGCGTTATAAAG	1	57	1	CGTATGCCTG	    0.980347	-244
CATCCCAAAACGTTAGGCTGTTTACCATAT	1	91	0	CGTTAGGCTG	    0.989518	-210
GAGATACGTTCTTTTTGCTGTAAGGATGTA	1	271	1	CTTTTTGCTG	    0.976979	-30
          **********

Masking position 9
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