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

Motif number 1

   GATAGCCCCTCTCCCTCTAGTAATCTAG	1	16	0	CCCTCCCTCT	    0.995773	-18
    ATCTGTCTCCCCTCTCTCCTGCGTATA	2	7	1	CTCCCTCTCT	    0.996621	-286
TTCTGTAATCCTCCCCCCTGTTTGAGCTATA	2	39	0	CTCCCCCTGT	    0.998998	-254
TTTCATTTTACTCCTCCCTCAAAAGGGCGTC	2	180	0	CTCTCCCTCA	    0.993748	-113
TGCTAAATCTCTTCCCCCACTTCTTTCAATT	2	240	0	CTCCCCCACT	    0.997879	-53
      TACTTTACCCCCTGTTTGATAAGTG	2	278	0	TTCCCCCTGT	    0.993556	-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

TTTCTTGCTTAATTTTTCATAAGAATTACAG	2	75	0	AATTTTCATA	    0.917139	-218
GAAAAATTTTATTTTATCAATATATATTTCT	2	101	0	ATTTATCAAT	    0.957217	-192
GATAAAATAAAATTTTTCAATCAACTAATCA	2	114	1	AATTTTCAAT	    0.982742	-179
TTTTTCAATCAACTAATCAATTCGGAAAATT	2	126	1	AATAATCAAT	    0.957535	-167
TCAATTCGGAAAATTATAATTTATGTACGCG	2	142	1	AATTATAATT	    0.859393	-151
GAGTAAAATGAAATTGTCAATAAATCTTAAT	2	198	1	AATTGTCAAT	    0.980088	-95
GCACATTTCGCACTTATCAAACAGGGGGTAA	2	268	1	CATTATCAAA	    0.936008	-25
          ** ********

Masking position 9
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

AAACAGGGGGGAGGATTACAGAATGATCCT	2	47	1	GAGGATTACA	    0.923581	-246
AATTTTTCATAAGAATTACAGGATCATTCT	2	66	0	AAGAATTACA	    0.966308	-227
TAATTCTTATGAAAAATTAAGCAAGAAATA	2	78	1	GAAAAATTAA	    0.775575	-215
AAAATTAAGCAAGAAATATATATTGATAAA	2	90	1	AAGAAATATA	    0.936734	-203
TAGTTGATTGAAAAATTTTATTTTATCAAT	2	111	0	AAAAATTTTA	    0.893338	-182
AATCAATTCGGAAAATTATAATTTATGTAC	2	140	1	GAAAATTATA	    0.945312	-153
AAGATTTATTGACAATTTCATTTTACTCCT	2	196	0	GACAATTTCA	      0.9281	-97
GAAGTGGGGGAAGAGATTTAGCACATTTCG	2	248	1	AAGAGATTTA	    0.797286	-45
          **********

Masking position 2
Map Score:   3.77093

Number of sites scoring better than the average of aligned sites = 1002
Number in coding regions = 833
Number in noncoding regions = 169
Number of orfs with sites within 600 bp upstream = 171
Fraction of orfs with sites within 600 bp upstream = 0.0274655


Motif number 4

CCCCTCTCCCTCTAGTAATCTAGTACTC  	1	9	0	TCTAGTAATC	    0.981091	-25
TACAGGATCATTCTGTAATCCTCCCCCCTG	2	50	0	TTCTGTAATC	    0.921471	-243
TACAGAATGATCCTGTAATTCTTATGAAAA	2	63	1	TCCTGTAATT	    0.921471	-230
AATTTTTCAATCAACTAATCAATTCGGAAA	2	124	1	TCAACTAATC	    0.973845	-169
CAAAAGGGCGTCAAGAAAACGCGTACATAA	2	162	0	TCAAGAAAAC	    0.945458	-131
AATGAAATTGTCAATAAATCTTAATAAAGT	2	204	1	TCAATAAATC	    0.930864	-89
          **********

Masking position 7
Map Score:   2.4657

Number of sites scoring better than the average of aligned sites = 682
Number in coding regions = 624
Number in noncoding regions = 58
Number of orfs with sites within 600 bp upstream = 71
Fraction of orfs with sites within 600 bp upstream = 0.0114038


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