AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i302_mixed17_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	ybfT	218	similar to glucosamine-6-phosphate isomerase
#2	nagA	181	N-acetylglucosamine-6-phosphate deacetylase

Motif number 1

GATTGCATACAGAATGGGGAGAATGAA   	1	8	0	AGAATGGGGA	    0.939369	-211
GTCTCAATGAAAAAGAACGGATTGCATACA	1	27	0	AAAAGAACGG	    0.954386	-192
AATTTGTTATAAAAGAAGGATACAAATCTT	1	85	0	AAAAGAAGGA	    0.955479	-134
TGACAGTTTGATAAGGGCGGTGCTAAATTC	1	130	1	ATAAGGGCGG	    0.972823	-89
GGCAGCCCGGAACAGGAGGAACATATC   	2	8	0	AACAGGAGGA	    0.961423	-174
CAGATTTTATAAAAGGGGGGAAAACACCTC	2	91	1	AAAAGGGGGG	    0.995782	-91
CACTAGTCTGAAAAAGAGTAAAATAAAGGT	2	134	1	AAAAAGAGTA	    0.740821	-48
TTCAAATTCCAGAAAGGCGGATCATCT   	2	165	1	AGAAAGGCGG	    0.963814	-17
          **********

Masking position 4
Map Score:   7.28354

Number of sites scoring better than the average of aligned sites = 1737
Number in coding regions = 1117
Number in noncoding regions = 620
Number of orfs with sites within 600 bp upstream = 627
Fraction of orfs with sites within 600 bp upstream = 0.100707


Motif number 2

AGAAGGATACAAATCTTTCATATTGGGAGGGC	1	70	0	AAATCTTATA	    0.937916	-149
TAATTTCTGAAAATTTGTTATAAAAGAAGGAT	1	94	0	AAATTGTATA	    0.989593	-125
AAATTTTCAGAAATTAATATTGACAGTTTGAT	1	110	1	AAATTATTTG	    0.889965	-109
GGGCGGTGCTAAATTCGTAATGACAAGTATCA	1	144	1	AAATTGTATG	    0.987444	-75
CAAGTATCATAAATTGGTCATAACAAATATGG	1	167	1	AAATTGTATA	    0.989594	-52
CCCTTTTATAAAATCTGTTTTAGGTTCAAGCC	2	76	0	AAATCGTTTA	    0.976875	-106
          ***** ** ***

Masking position 8
Map Score:   5.19096

Number of sites scoring better than the average of aligned sites = 128
Number in coding regions = 109
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 3

GCATACAGAATGGGGAGAATGAA       	1	4	0	TGGGGAGAAT	    0.967077	-215
TTCATATTGGGAGGGCAAATGGTATTATGG	1	56	0	GAGGGCAAAT	    0.957552	-163
GCCCGGAACAGGAGGAACATATC       	2	4	0	GGAGGAACAT	    0.986112	-178
TTTATAAAAGGGGGGAAAACACCTCAGCTG	2	96	1	GGGGGAAAAC	    0.991576	-86
ATTCCAGAAAGGCGGATCATCT        	2	170	1	GGCGGATCAT	    0.976553	-12
          **********

Masking position 9
Map Score:   0.849423

Number of sites scoring better than the average of aligned sites = 347
Number in coding regions = 261
Number in noncoding regions = 86
Number of orfs with sites within 600 bp upstream = 107
Fraction of orfs with sites within 600 bp upstream = 0.017186


Motif number 4

ACAAATCTTTCATATTGGGAGGGCAAATGG	1	64	0	CATATTGGGA	    0.912217	-155
TCTTTTATAACAAATTTTCAGAAATTAATA	1	99	1	CAAATTTTCA	    0.942544	-120
CCGCCCTTATCAAACTGTCAATATTAATTT	1	120	0	CAAACTGTCA	      0.9424	-99
TTGTCATTACGAATTTAGCACCGCCCTTAT	1	140	0	GAATTTAGCA	    0.887377	-79
TTGTTATGACCAATTTATGATACTTGTCAT	1	163	0	CAATTTATGA	    0.955878	-56
ACAATACTTTCATTTTATCACTTTCGGGCT	2	50	1	CATTTTATCA	    0.956926	-132
          **********

Masking position 6
Map Score:   0.0700314

Number of sites scoring better than the average of aligned sites = 717
Number in coding regions = 629
Number in noncoding regions = 88
Number of orfs with sites within 600 bp upstream = 93
Fraction of orfs with sites within 600 bp upstream = 0.0149374


Motif number 5

          **********

No masking
Map Score:   6.84553e-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:   6.84553e-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 7

          **********

No masking
Map Score:   6.84553e-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