AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i026_Fumarate_Reductase_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	sdhA	33	succinate dehydrogenase (flavoprotein subunit)
#2	sdhC	292	succinate dehydrogenase (cytochrome b558 subunit)

Motif number 1

   GATAGCCCCTCTCCCTCTAGTAATCTAG	1	16	0	CCCTCCCTCT	    0.995439	-18
    ATCTGTCTCCCCTCTCTCCTGCGTATA	2	7	1	CTCCCTCTCT	    0.996354	-286
TTCTGTAATCCTCCCCCCTGTTTGAGCTATA	2	39	0	CTCCCCCTGT	    0.998918	-254
TTTCATTTTACTCCTCCCTCAAAAGGGCGTC	2	180	0	CTCTCCCTCA	    0.993254	-113
TGCTAAATCTCTTCCCCCACTTCTTTCAATT	2	240	0	CTCCCCCACT	     0.99771	-53
      TACTTTACCCCCTGTTTGATAAGTG	2	278	0	TTCCCCCTGT	    0.993047	-15
          ** ********

Masking position 6
Map Score:   14.4132

Number of sites scoring better than the average of aligned sites = 83
Number in coding regions = 55
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 2

CTGTAATTCTTATGAAAAATTAAGCAAGAAA	2	75	1	TATGAAAATT	    0.905789	-218
AGAAATATATATTGATAAAATAAAATTTTTC	2	101	1	ATTGATAAAT	    0.951203	-192
TGATTAGTTGATTGAAAAATTTTATTTTATC	2	114	0	ATTGAAAATT	    0.980309	-179
AATTTTCCGAATTGATTAGTTGATTGAAAAA	2	126	0	ATTGATTATT	    0.951478	-167
CGCGTACATAAATTATAATTTTCCGAATTGA	2	142	0	AATTATAATT	    0.841724	-151
ATTAAGATTTATTGACAATTTCATTTTACTC	2	198	0	ATTGACAATT	    0.977139	-95
TTACCCCCTGTTTGATAAGTGCGAAATGTGC	2	268	0	TTTGATAATG	    0.927015	-25
          ******** **

Masking position 5
Map Score:   5.09479

Number of sites scoring better than the average of aligned sites = 469
Number in coding regions = 377
Number in noncoding regions = 92
Number of orfs with sites within 600 bp upstream = 102
Fraction of orfs with sites within 600 bp upstream = 0.0163829


Motif number 3

CCCTCTCCCTCTAGTAATCTAGTACTC   	1	8	0	CTAGTAATCT	    0.965551	-26
AAAAATTAAGCAAGAAATATATATTGATAA	2	89	1	CAAGAAATAT	    0.962415	-204
ATTTTTCAATCAACTAATCAATTCGGAAAA	2	125	1	CAACTAATCA	    0.932237	-168
AAAAGGGCGTCAAGAAAACGCGTACATAAA	2	161	0	CAAGAAAACG	    0.959732	-132
ATGAAATTGTCAATAAATCTTAATAAAGTG	2	205	1	CAATAAATCT	     0.97105	-88
          **********

Masking position 6
Map Score:   1.16983

Number of sites scoring better than the average of aligned sites = 267
Number in coding regions = 234
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 4

AACAGGGGGGAGGATTACAGAATGATCCTG	2	48	1	AGGATTACAG	    0.994797	-245
ATTTTTCATAAGAATTACAGGATCATTCTG	2	65	0	AGAATTACAG	     0.99232	-228
          **********

Masking position 5
Map Score:   0.00453881

Number of sites scoring better than the average of aligned sites = 7
Number in coding regions = 5
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 5

          **********

No masking
Map Score:   6.91659e-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:   6.91659e-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:   6.91659e-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