AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions041_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242075
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	sdhA	33	succinate dehydrogenase (flavoprotein subunit)
#1	sdhC	292	succinate dehydrogenase (cytochrome b558 subunit)
#2	ysfA	118	ysfA
#3	ysfB	68	similar to hypothetical proteins
#4	ysfC	102	similar to glycolate oxidase subunit
#5	yvfV	174	similar to glycolate oxidase
#6	yvfT	132	similar to two-component sensor histidine kinase [YvfU]
#7	yvfR	283	similar to ABC transporter (ATP-binding protein)

Motif 1
ATATTGGGGATGAGAGAGGGGTTCATC    	5	157	1
AGGATTGCCTAGACACCGGGGTGAGAAAAAA	7	169	1
ATATTATAGCTCAAACAGGGGGGAGGATTAC	1	34	1
GAATCAGGGGTCAAACAGGGGATCGGATATG	6	109	1
TTCGCACTTATCAAACAGGGGGTAAAGTA  	1	273	1
ATGAATTGGAAGATGCAGGAGGAGGATTGCC	7	147	1
AGATTACTAGAGGGAGAGGGGCTATC     	0	17	1
GACGCCCTTTTGAGGGAGGAGTAAAATGAAA	1	179	1
TATACGCAGGAGAGAGGGGAGACAGAT    	1	6	0
CTTTATTAAAAGAATCAGGGGTCAAACAGGG	6	98	1
AATAAAAACATGATGAGGGGGAACGCC    	3	51	1
ATTACATTTTAGAAAAAGGAGCGTTTTAC  	2	99	1
TACAATTGAAAGAAGTGGGGGAAGAGATTTA	1	236	1
      GACATGAAACCGGGTGACAGCGCCC	3	4	1
AAGCGTTTTTTGACAGGGGGATGGGTGAA  	4	83	1
ATAATAAACCAGGTGCAGGGTTAGAATATAC	2	66	1
GCAGTTTAAAAGAAAGAGGACATGGGAGATA	7	106	1
ATCAATGTAAACGATCAGGAGGTGCTCAT  	7	264	1
          *** *******
MAP Score: 25.9488

Motif 2
TATAGCTCAAACAGGGGGGAGGATTACAGAAT	1	38	1
GCGTTTTTTGACAGGGGGATGGGTGAA     	4	85	1
CAGGGGTCAAACAGGGGATCGGATATGGT   	6	113	1
CTAGATTACTAGAGGGAGAGGGGCTATC    	0	15	1
CACTTATCAAACAGGGGGTAAAGTA       	1	277	1
AAAAACATGATGAGGGGGAACGCC        	3	54	1
AATTGAAAGAAGTGGGGGAAGAGATTTAGCAC	1	239	1
TTGCCTAGACACCGGGGTGAGAAAAAAATGAC	7	173	1
TATACGCAGGAGAGAGGGGAGACAGAT     	1	5	0
  GACATGAAACCGGGTGACAGCGCCCGGTTT	3	8	1
CTTTTAATAAAGAGAGGAACGGCATAATCGTA	6	78	0
TGGGGATGAGAGAGGGGTTCATC         	5	161	1
GACGCCCTTTTGAGGGAGGAGTAAAATGAAAT	1	179	1
CACATAATAAACCAGGTGCAGGGTTAGAATAT	2	63	1
AATTGGAAGATGCAGGAGGAGGATTGCCTAGA	7	150	1
          ********  **
MAP Score: 17.6905

Motif 3
   GATAGCCCCTCTCCCTCTAGTAATCTA	0	16	0
  ATCTGTCTCCCCTCTCTCCTGCGTATAT	1	8	1
TTTCATTTTACTCCTCCCTCAAAAGGGCGT	1	180	0
      TTCACCCATCCCCCTGTCAAAAAA	4	88	0
    GATGAACCCCTCTCTCATCCCCAATA	5	158	0
TTATGCCGTTCCTCTCTTTATTAAAAGAAT	6	83	1
          **********
MAP Score: 8.69631

Motif 4
        GATAGCCCCTCTCCCTCTAGTAATCT	0	17	0
       ATCTGTCTCCCCTCTCTCCTGCGTATA	1	3	1
TCATTCTGTAATCCTCCCCCCTGTTTGAGCTATA	1	38	0
CGCGTTTTCTTGACGCCCTTTTGAGGGAGGAGTA	1	168	1
GCTAAATCTCTTCCCCCACTTCTTTCAATTGTAA	1	235	0
      TACTTTACCCCCTGTTTGATAAGTGCGA	1	274	0
  TGTCTATGTGGCGCTCCTTTTTTTAACATGAT	2	8	1
       GTAAAACGCTCCTTTTTCTAAAATGTA	2	101	0
AACCGGGCGCTGTCACCCGGTTTCATGTC     	3	5	0
      GGCGTTCCCCCTCATCATGTTTTTATTA	3	50	0
TAGAAAACTCTTTCCTTCCATTGTCAGAATAGTG	5	72	1
TATACGATTATGCCGTTCCTCTCTTTATTAAAAG	6	76	1
ATCCCCTGTTTGACCCCTGATTCTTTTAATAAAG	6	98	0
CTATCTCCCATGTCCTCTTTCTTTTAAACTGCTG	7	104	0
AAATGACATTTGTCACTCCATCATCATGACACCC	7	198	1
TCCATCATCATGACACCCCATACTAACATCGTCT	7	214	1
          ** * **** ** *
MAP Score: 6.73036

Motif 5
TATGTGGCGCTCCTTTTTTTAACATGATGT	2	14	1
 GTAAAACGCTCCTTTTTCTAAAATGTAAT	2	99	0
TGGAAGGCTTTGCTTTTTTTCTTTTACAAT	4	46	1
ATTATGCCGTTCCTCTCTTTATTAAAAGAA	6	82	1
ATCTCCCATGTCCTCTTTCTTTTAAACTGC	7	106	0
          **********
MAP Score: 3.58119

Motif 6
AGTACTAGATTACTAGAGGGAGAGGGGCTATC   	0	11	1
TATACGCAGGAGAGAGGGGAGACAGAT        	1	2	0
ATTATAGCTCAAACAGGGGGGAGGATTACAGAATG	1	36	1
GACGCCCTTTTGAGGGAGGAGTAAAATGAAATTGT	1	179	1
TGCTTACAATTGAAAGAAGTGGGGGAAGAGATTTA	1	232	1
CGCACTTATCAAACAGGGGGTAAAGTA        	1	275	1
   GACATGAAACCGGGTGACAGCGCCCGGTTTTT	3	7	1
CTTATATAATAAAAACATGATGAGGGGGAACGCC 	3	44	1
AAGCGTTTTTTGACAGGGGGATGGGTGAA      	4	83	1
TATACTGCACTCCTGGGAGATCGGGAGTGTTTTTG	5	13	1
ACCTGATCATATATTGGGGATGAGAGAGGGGTTCA	5	147	1
ATCAGGGGTCAAACAGGGGATCGGATATGGT    	6	111	1
GCAGTTTAAAAGAAAGAGGACATGGGAGATAGAAA	7	106	1
GAGATAGAAAAGATGGATGAATTGGAAGATGCAGG	7	131	1
ATGAATTGGAAGATGCAGGAGGAGGATTGCCTAGA	7	147	1
TTGCCTAGACACCGGGGTGAGAAAAAAATGACATT	7	173	1
ATTGATTGTAAAATGACGGAGAAGACGATGTTAGT	7	235	0
AATGTAAACGATCAGGAGGTGCTCAT         	7	267	1
          * * ******   **
MAP Score: 2.81541

Motif 7
   GATAGCCCCTCTCCCTCTAGTAATCTA	0	16	0
        ATCTGTCTCCCCTCTCTCCTGC	1	2	1
CATTCTGTAATCCTCCCCCCTGTTTGAGCT	1	41	0
TTTCATTTTACTCCTCCCTCAAAAGGGCGT	1	180	0
TGTGCTAAATCTCTTCCCCCACTTCTTTCA	1	242	0
        TACTTTACCCCCTGTTTGATAA	1	280	0
  TGTCTATGTGGCGCTCCTTTTTTTAACA	2	8	1
        GGCGTTCCCCCTCATCATGTTT	3	56	0
      TTCACCCATCCCCCTGTCAAAAAA	4	88	0
   CCATATACTGCACTCCTGGGAGATCGG	5	7	1
AAAAACACTCCCGATCTCCCAGGAGTGCAG	5	17	0
    GATGAACCCCTCTCTCATCCCCAATA	5	158	0
TATACGATTATGCCGTTCCTCTCTTTATTA	6	76	1
   ACCATATCCGATCCCCTGTTTGACCCC	6	115	0
GTCTAGGCAATCCTCCTCCTGCATCTTCCA	7	153	0
          **********
MAP Score: 2.62281

Motif 8
GCAGGAGAGAGGGGAGACAGAT         	1	1	0
GCCCTTTTGAGGGAGGAGTAAAATGAAATTG	1	182	1
TGAAAGAAGTGGGGGAAGAGATTTAGCACAT	1	242	1
TTTTATTATATAAGAAAAAAACCGGGCGCTG	3	27	0
AGCCTTCCATGGAGAAACATACAAAAAATGA	4	24	0
TTCTGACAATGGAAGGAAAGAGTTTTCTAGG	5	70	0
GATCATATATTGGGGATGAGAGAGGGGTTCA	5	151	1
GAATTCCTTCGGGAAAATAGATATTGCCTTT	6	18	0
CAGAAAGATATAAGGGAAAAACCCGAATTCC	6	42	0
TGACATTCATAGAAAGATACACTCTTCAAAC	7	73	0
CACAGCAGTTTAAAAGAAAGAGGACATGGGA	7	102	1
AAAGAGGACATGGGAGATAGAAAAGATGGAT	7	118	1
CCTAGACACCGGGGTGAGAAAAAAATGACAT	7	176	1
TCATGATGATGGAGTGACAAATGTCATTTTT	7	196	0
          ******* ***
MAP Score: 0.515962