AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i102_Ferric_Transport_bsub_reg_300.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

CAGGAGAACATTTGTATTTTTCACGAGGAAT	1	18	1	TTTTATTTTT	    0.875148	-283
GTCAGCAAACCTAACATTATTCCTCGTGAAA	1	36	0	CTACATTATT	    0.943272	-265
GTTAGGCTGTTTACCATATTTATCTTTATAA	1	79	0	TTACATATTT	      0.9684	-222
CTAATCATTCTAACCATTTTCCATCCCAAAA	1	111	0	TAACATTTTC	    0.945515	-190
ACCTAGTCATTTATCAATTTTACTAATCATT	1	133	0	TTACAATTTT	      0.9684	-168
AATGACTAGGTTAATATTTTTAAAGAATATT	1	153	1	TTATATTTTT	    0.975071	-148
CATTTACATATTACCATTTTTATAGGGTTAG	1	186	0	TTACATTTTT	    0.994186	-115
TAGTAATTGATTATCATTATCATTTACATAT	1	206	0	TTACATTATC	    0.972566	-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

AGGAGAACATTTGTATTTTTCACGAGGAAT	1	19	1	TTGTATTTTT	    0.772761	-282
TTTACCATATTTATCTTTATAACGCAGGCA	1	71	0	TTATCTTTAT	     0.88457	-230
TCAATTTTACTAATCATTCTAACCATTTTC	1	121	0	TAATCATTCT	    0.938009	-180
AATATTAACCTAGTCATTTATCAATTTTAC	1	141	0	TAGTCATTTA	      0.9551	-160
ATGACTAGGTTAATATTTTTAAAGAATATT	1	154	1	TAATATTTTT	    0.834645	-147
TTTATAGGGTTAGTCAATATTCTTTAAAAA	1	169	0	TAGTCAATAT	    0.824323	-132
CATTTACATATTACCATTTTTATAGGGTTA	1	187	0	TTACCATTTT	    0.903157	-114
TTGATTATCATTATCATTTACATATTACCA	1	201	0	TTATCATTTA	     0.95428	-100
ATGATAATGATAATCAATTACTATATGGCC	1	214	1	TAATCAATTA	    0.881512	-87
          **********

Masking position 8
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	     0.95577	-293
GGCATACGGTCAGCAAACCTAACATTATTC	1	45	0	CAGCAAACCT	    0.960274	-256
CTTTATAACGCAGGCATACGGTCAGCAAAC	1	57	0	CAGGCATACG	      0.9796	-244
ATATGGTAAACAGCCTAACGTTTTGGGATG	1	91	1	CAGCCTAACG	    0.989118	-210
TACATCCTTACAGCAAAAAGAACGTATCTC	1	271	0	CAGCAAAAAG	    0.976106	-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