AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i102_Ferric_Transport_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	yclN	300	similar to ferrichrome ABC transporter (permease)
#2	yclQ	21	similar to ferrichrome ABC transporter (binding protein)

Motif number 1

ATTCCTCGTGAAAAATACAAATGTTCTCCTG	1	18	0	AAAAATAAAA	    0.877978	-283
TTTCACGAGGAATAATGTTAGGTTTGCTGAC	1	36	1	AATAATGTAG	    0.944655	-265
TTATAAAGATAAATATGGTAAACAGCCTAAC	1	79	1	AAATATGTAA	    0.969191	-222
TTTTGGGATGGAAAATGGTTAGAATGATTAG	1	111	1	GAAAATGTTA	    0.946847	-190
AATGATTAGTAAAATTGATAAATGACTAGGT	1	133	1	AAAATTGTAA	    0.969191	-168
AATATTCTTTAAAAATATTAACCTAGTCATT	1	153	0	AAAAATATAA	    0.975698	-148
CTAACCCTATAAAAATGGTAATATGTAAATG	1	186	1	AAAAATGTAA	    0.994336	-115
ATATGTAAATGATAATGATAATCAATTACTA	1	206	1	GATAATGTAA	    0.973255	-95
          ******* ***

Masking position 2
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

TAACGCAGGCATACGGTCAGCAAACCTAAC	1	52	0	ATACGGTCAG	    0.969161	-249
ATAAAGATAAATATGGTAAACAGCCTAACG	1	81	1	ATATGGTAAA	    0.947726	-220
TTGGGATGGAAAATGGTTAGAATGATTAGT	1	113	1	AAATGGTTAG	    0.989541	-188
TAAAATTGATAAATGACTAGGTTAATATTT	1	142	1	AAATGACTAG	    0.924551	-159
TACCATTTTTATAGGGTTAGTCAATATTCT	1	176	0	ATAGGGTTAG	    0.966758	-125
AACCCTATAAAAATGGTAATATGTAAATGA	1	188	1	AAATGGTAAT	    0.978637	-113
GGTAATATGTAAATGATAATGATAATCAAT	1	202	1	AAATGATAAT	    0.912874	-99
ACTCAAAACAATATGGCCATATAGTAATTG	1	228	0	ATATGGCCAT	    0.965503	-73
          **********

Masking position 3
Map Score:   9.06679

Number of sites scoring better than the average of aligned sites = 547
Number in coding regions = 431
Number in noncoding regions = 116
Number of orfs with sites within 600 bp upstream = 90
Fraction of orfs with sites within 600 bp upstream = 0.0144555


Motif number 3

TACGGTCAGCAAACCTAACATTATTCCTCG	1	41	0	AAACCTAACA	     0.94784	-260
ATATGGTAAACAGCCTAACGTTTTGGGATG	1	91	1	CAGCCTAACG	    0.988015	-210
AACCATTTTCCATCCCAAAACGTTAGGCTG	1	101	0	CATCCCAAAA	    0.953882	-200
TTTTACTAATCATTCTAACCATTTTCCATC	1	117	0	CATTCTAACC	    0.964192	-184
TGCCTCCTTACATCCTTACAGCAAAAAGAA	1	279	0	CATCCTTACA	    0.986455	-22
          **********

Masking position 8
Map Score:   1.26703

Number of sites scoring better than the average of aligned sites = 325
Number in coding regions = 256
Number in noncoding regions = 69
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


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