AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i016_Pentose_Phosphate_Shunt_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	xylA	300	xylose isomerase
#2	xylB	150	xylulose kinase

Motif number 1

        TCTTTTAATAATAACTTTTGAT	1	3	1	TTTTAATAAT	    0.685297	-298
TGATTTACTTTTTTGACAAAGGTTTGATCA	1	29	1	TTTTGACAAA	    0.766741	-272
TAATTTAAAGATTAAACAAATGGAGTGGAT	1	73	0	ATTAAACAAA	    0.961384	-228
TTGTTTAATCTTTAAATTAAGTATCAACAT	1	84	1	TTTAAATTAA	    0.881831	-217
AACACATTAGATTTAATAAAGGGAAGATTC	1	124	0	ATTTAATAAA	    0.935763	-177
TTCATAAAAAACTAAAAAAAATATTGAAAA	1	152	1	ACTAAAAAAA	    0.859069	-149
GTTATATAAGATGAAAATAAGTTAGTTTGT	1	192	1	ATGAAAATAA	     0.60207	-109
TAGTTTGTTGTTTAAACAAACTAACTTATT	1	207	0	TTTAAACAAA	    0.966392	-94
TACTTACTATATGAAATAAAATGCATCTGT	1	247	1	ATGAAATAAA	    0.907161	-54
AACCATTCACTCTAAATAAATCCTAATTAT	2	106	0	TCTAAATAAA	    0.920161	-45
CTCCTTGCCCTTTTAAAAAACCATTCACTC	2	124	0	TTTTAAAAAA	    0.909313	-27
          **********

Masking position 6
Map Score:   9.64405

Number of sites scoring better than the average of aligned sites = 1608
Number in coding regions = 1190
Number in noncoding regions = 418
Number of orfs with sites within 600 bp upstream = 369
Fraction of orfs with sites within 600 bp upstream = 0.0592676


Motif number 2

TTGATCAGCGATATCCACTTCATCCACTCCAT	1	52	1	ATTCCACTCA	    0.980749	-249
TACATAGCGAATCTTCCCTTTATTAAATCTAA	1	116	1	ATTTCCCTTA	    0.895884	-185
TTAGTTTTTTATGAACACATTAGATTTAATAA	1	135	0	ATAACACTTA	    0.883159	-166
TTCATCTTATATAACCTCGTCAGTATTTTCAA	1	175	0	ATACCTCTCA	    0.960452	-126
       GTGATTTCCCCCTTAAAAATAAATT	1	286	0	ATTCCCCTTA	    0.982339	-15
TCCTGCTATCAATACCAAGTCACTGAATTACC	2	27	1	AAACCAATCA	    0.888512	-124
CAAGTCACTGAATTACCCGTCATGATTCCTTT	2	42	1	AATACCCTCA	    0.981767	-109
TAATTATAGAAGTTACCCGTCATAACAACAAG	2	81	0	AGTACCCTCA	    0.960406	-70
CACTCTAAATAAATCCTAATTATAGAAGTTAC	2	97	0	AATCCTATTA	    0.776534	-54
TGCCCTTTTAAAAAACCATTCACTCTAAATAA	2	117	0	AAAACCATCA	    0.912106	-34
          ** ***** ***

Masking position 10
Map Score:   9.56377

Number of sites scoring better than the average of aligned sites = 1036
Number in coding regions = 842
Number in noncoding regions = 194
Number of orfs with sites within 600 bp upstream = 194
Fraction of orfs with sites within 600 bp upstream = 0.0311597


Motif number 3

AAACCTTTGTCAAAAAAGTAAATCAAAAGT	1	24	0	CAAAAAAGTA	    0.969955	-277
AATTAAGTATCAACATAGTACATAGCGAAT	1	98	1	CAACATAGTA	    0.932617	-203
AATGTGTTCATAAAAAACTAAAAAAAATAT	1	146	1	TAAAAAACTA	    0.962758	-155
TTTGTTGTTTAAACAAACTAACTTATTTTC	1	204	0	AAACAAACTA	     0.96803	-97
TTTGTTTAAACAACAAACTAATAGGTGATG	1	217	1	CAACAAACTA	    0.993711	-84
CCCGTCATAACAACAAGCAATAGGAAAGGA	2	68	0	CAACAAGCAA	    0.923048	-83
CTTGCCCTTTTAAAAAACCATTCACTCTAA	2	121	0	TAAAAAACCA	    0.904331	-30
          **********

Masking position 5
Map Score:   6.83457

Number of sites scoring better than the average of aligned sites = 200
Number in coding regions = 176
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 4

TTTGTCAAAAAAGTAAATCAAAAGTTATTA	1	19	0	AAGTAAATCA	    0.977312	-282
TTCATATAGTAAGTACATCACCTATTAGTT	1	232	0	AAGTACATCA	    0.961931	-69
TATTTTTAAGGGGGAAATCAC         	1	290	1	GGGGAAATCA	    0.983727	-11
GAATCATGACGGGTAATTCAGTGACTTGGT	2	40	0	GGGTAATTCA	     0.97607	-111
          **********

Masking position 5
Map Score:   1.04298

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 35
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 5

          **********

No masking
Map Score:   -2.17836e-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:   -2.17836e-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:   -2.17836e-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