AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions041_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242068
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	sdhA	33	succinate dehydrogenase (flavoprotein subunit)
#1	sdhC	292	succinate dehydrogenase (cytochrome b558 subunit)
#2	ysfC	102	similar to glycolate oxidase subunit
#3	yvfV	174	similar to glycolate oxidase

Motif 1
GTTTTTTGACAGGGGGATGGGTGAA      	2	87	1
TTGAAAGAAGTGGGGGAAGAGATTTAGCACA	1	241	1
AGATTACTAGAGGGAGAGGGGCTATC     	0	17	1
GACGCCCTTTTGAGGGAGGAGTAAAATGAAA	1	179	1
ATATTGGGGATGAGAGAGGGGTTCATC    	3	157	1
TATACGCAGGAGAGAGGGGAGACAGAT    	1	6	0
ACTGCACTCCTGGGAGATCGGGAGTGTTTTT	3	16	1
TATAGCTCAAACAGGGGGGAGGATTACAGAA	1	38	1
CTTATCAAACAGGGGGTAAAGTA        	1	279	1
CTCCCTCAAAAGGGCGTCAAGAAAACGCGTA	1	166	0
ATTCTGACAATGGAAGGAAAGAGTTTTCTAG	3	71	0
          ******* ***
MAP Score: 18.5192

Motif 2
   GATAGCCCCTCTCCCTCTAGTAATCTA	0	16	0
    ATCTGTCTCCCCTCTCTCCTGCGTAT	1	6	1
TTCTGTAATCCTCCCCCCTGTTTGAGCTAT	1	39	0
TTTCATTTTACTCCTCCCTCAAAAGGGCGT	1	180	0
TGCTAAATCTCTTCCCCCACTTCTTTCAAT	1	240	0
      TACTTTACCCCCTGTTTGATAAGT	1	278	0
  TTCACCCATCCCCCTGTCAAAAAACGCT	2	84	0
    GATGAACCCCTCTCTCATCCCCAATA	3	158	0
          **********
MAP Score: 15.1346

Motif 3
TCAAACAGGGGGGAGGATTACAGAATGATCCTG	1	44	1
GAAAAATTAAGCAAGAAATATATATTGATAAAA	1	87	1
TATAATTTATGTACGCGTTTTCTTGACGCCCTT	1	155	1
TCTTTCAATTGTAAGCACTTTATTAAGATTTAT	1	216	0
AAGAAGTGGGGGAAGAGATTTAGCACATTTCGC	1	245	1
ACAATAGATTGAAAGCGTTTTTTGACAGGGGGA	2	71	1
GATCTCCCAGGAGTGCAGTATATGG        	3	2	0
CTGGGAGATCGGGAGTGTTTTTGATATGCCACA	3	25	1
ACAATGGAAGGAAAGAGTTTTCTAGGGATATTT	3	63	0
TCAGAATAGTGTACGATATTCATATAGTTATTT	3	95	1
TTGGGGATGAGAGAGGGGTTCATC         	3	160	1
          * *** * *****
MAP Score: 8.87705

Motif 4
  GATAGCCCCTCTCCCTCTAGTAATCTAG	0	15	0
          ATCTGTCTCCCCTCTCTCCT	1	0	1
TCTGTCTCCCCTCTCTCCTGCGTATATTAT	1	11	1
TTCTGTAATCCTCCCCCCTGTTTGAGCTAT	1	39	0
TTTCATTTTACTCCTCCCTCAAAAGGGCGT	1	180	0
TGTGCTAAATCTCTTCCCCCACTTCTTTCA	1	242	0
CCCTAGAAAACTCTTTCCTTCCATTGTCAG	3	69	1
 GATGAACCCCTCTCTCATCCCCAATATAT	3	155	0
          **********
MAP Score: 7.69979

Motif 5
TAGATTACTAGAGGGAGAGGGGCTATC   	0	16	1
GCTCAAACAGGGGGGAGGATTACAGAATGA	1	42	1
ACGCCCTTTTGAGGGAGGAGTAAAATGAAA	1	180	1
TCGCACTTATCAAACAGGGGGTAAAGTA  	1	274	1
TTTTTTGACAGGGGGATGGGTGAA      	2	88	1
TATTGGGGATGAGAGAGGGGTTCATC    	3	158	1
          **********
MAP Score: 6.30188

Motif 6
AAACAGGGGGGAGGATTACAGAATGATCCT	1	46	1
AATTTTTCATAAGAATTACAGGATCATTCT	1	65	0
GCGTCAAGAAAACGCGTACATAAATTATAA	1	154	0
CCTTTTGAGGGAGGAGTAAAATGAAATTGT	1	184	1
AAGATTTATTGACAATTTCATTTTACTCCT	1	195	0
         AGAGAGTTTCAGTTTCATTTT	2	1	1
CCTGTCAAAAAACGCTTTCAATCTATTGTA	2	70	0
CCCGATCTCCCAGGAGTGCAGTATATGG  	3	8	0
GGGGATGAGAGAGGGGTTCATC        	3	162	1
          **********
MAP Score: 5.20806

Motif 7
TAGATTACTAGAGGGAGAGGGGCTATC    	0	16	1
TAATATACGCAGGAGAGAGGGGAGACAGAT 	1	9	0
TAGCTCAAACAGGGGGGAGGATTACAGAATG	1	40	1
CAATTGAAAGAAGTGGGGGAAGAGATTTAGC	1	238	1
TTTTTGACAGGGGGATGGGTGAA        	2	89	1
CTGCACTCCTGGGAGATCGGGAGTGTTTTTG	3	17	1
ATCATATATTGGGGATGAGAGAGGGGTTCAT	3	152	1
          ***** *****
MAP Score: 1.06763