AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions028_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241553
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	lmrB	39	drug-export protein
#1	lmrA	216	transcriptional regulator
#2	mdr	112	multidrug-efflux transporter
#3	yfiU	110	similar to multidrug-efflux transporter
#4	yhbI	159	similar to transcriptional regulator (MarR family)
#5	yhbJ	35	yhbJ
#6	yhcA	40	similar to multidrug resistance protein
#7	ylbK	180	similar to hypothetical proteins

Motif 1
CCATATGATGATTAATCATTGTACATTTTATCT	1	28	1
TCATTGTACATTTTATCTATTCAGTCAAAAGAT	1	43	1
AGAAAAGCTGACTGATCTTTTGACTGAATAGAT	1	57	0
TCTCTCAGTATTTTTTGTTGTCATATCCTTCTT	1	87	1
ATCCTTCTTTTTTTGTCTTTTCATACAATGAAT	1	111	1
CATACAATGAATTTTTCTTGACAATTGATGATT	1	132	1
TTTCTTGACAATTGATGATTGAATCAAGATAAT	1	145	1
CAGTCACTATATTTTTGATTGCAATTCAGTAAG	1	182	1
ATGATAATAGTTTGATTGTTGAATATCTCGATT	2	47	0
GGGAGCAGGCTTTTTTTATTTGACATTTAGTTC	3	38	1
CTTGAAATATATTATTCATTTTAAATGAACTAA	3	64	0
TTTCAGGGCTTTTTTTTATTTAATAAAAGCAAG	4	21	1
TCGCAAGCGTTTTCTTGCTTTTATTAAATAAAA	4	34	0
AGAAAAAGAAATTTTTCCTTTGACAAATCTTCT	4	79	1
ACAAATCTTCTTTCATTTATTAATATTTTATCT	4	101	1
TTTATTAATATTTTATCTTGTGAACTATTATTG	4	116	1
GACAACCTCCTTTCATGGTTTGATGACTGATCT	6	13	0
TCATACATTATTTTATCATGATATACATGTCAT	7	39	0
TGATAAAATAATGTATGATGTAAAACGGCCAAG	7	54	1
ACCTGTCCTCTTGATTCTTTGTACTAATATACG	7	91	1
          *** *** *** *
MAP Score: 20.2955

Motif 2
CTCTATCAACTGCATGTAGTATGTCGTTTTTT         	0	1	0
TCTCCTTACATCCATATGATGATTAATCATTGTACATTTTA	1	17	1
AAGATCAGTCAGCTTTTCTCTCAGTATTTTTTGTTGTCATA	1	71	1
TGTTGTCATATCCTTCTTTTTTTGTCTTTTCATACAATGAA	1	102	1
CTGACAGTCCTCCCTATAAAATCGAGTTTATCTGGATAATC	2	10	1
    TTGTTCTACCTCCTCTTACTTTTCTATGTAAGTTCTG	2	85	0
   TGAAAAGCCCATTTCAGGGCTTTTTTTTATTTAATAAA	4	7	1
AAGGAAAAATTTCTTTTTCTCCCGTATTTTTTTCGCAAGCG	4	58	0
AAAGAAATTTTTCCTTTGACAAATCTTCTTTCATTTATTAA	4	83	1
TATCATGATATACATGTCATTGGGCATTTTTAGCATCGGGG	7	18	0
GGCCAAGCAGTACCTGTCCTCTTGATTCTTTGTACTAATAT	7	80	1
CTGCCTGAATTCCCTGTATACCGAATTCTATGGTCTAAACT	7	137	0
          * * * *      *  *****
MAP Score: 12.9968

Motif 3
TCTCTCAGTATTTTTTGTTGTCATATCCTTCTTTTTTTG	1	87	1
GTCATATCCTTCTTTTTTTGTCTTTTCATACAATGAATT	1	106	1
CATACAATGAATTTTTCTTGACAATTGATGATTGAATCA	1	132	1
AGTCACTATATTTTTGATTGCAATTCAGTAAGGTGGGAA	1	183	1
GAGCAGGCTTTTTTTATTTGACATTTAGTTCATTTAAAA	3	40	1
AACTCCTTTTAGTTCACTTGAAATATATTATTCATTTTA	3	74	0
TTTTCTCCCGTATTTTTTTCGCAAGCGTTTTCTTGCTTT	4	46	0
AAAAAGAAATTTTTCCTTTGACAAATCTTCTTTCATTTA	4	81	1
TTTATTAATATTTTATCTTGTGAACTATTATTGAGGAAT	4	116	1
          * **   *** **  *  *
MAP Score: 10.6786

Motif 4
ATGATTAATCATCATATGGATGTAAGGAGAGAAATA	1	11	0
GAAGGATATGACAACAAAAAATACTGAGAGAAAAGC	1	82	0
TTGTATGAAAAGACAAAAAAAGAAGGATATGACAAC	1	103	0
CTGACAGTCCTCCCTATAAAATCGAGTTTATCTGGA	2	10	1
TATCAGAACTTACATAGAAAAGTAAGAGGAGGTAGA	2	82	1
ACTAAATGTCAAATAAAAAAAGCCTGCTCCCGCAGT	3	33	0
TCTTGCTTTTATTAAATAAAAAAAAGCCCTGAAATG	4	19	0
GCTTTTTTTTATTTAATAAAAGCAAGAAAACGCTTG	4	28	1
AGAAAACGCTTGCGAAAAAAATACGGGAGAAAAAGA	4	52	1
CAAGATAAAATATTAATAAATGAAAGAAGATTTGTC	4	100	0
ATCAGTCATCAAACCATGAAAGGAGGTTGTCTTAG 	6	15	1
GACATGTATATCATGATAAAATAATGTATGATGTAA	7	41	1
CTCGTATATTAGTACAAAGAATCAAGAGGACAGGTA	7	90	0
GGTTCAGTTTAGACCATAGAATTCGGTATACAGGGA	7	132	1
TAGAATTCGGTATACAGGGAATTCAGGCAGGAGGTT	7	148	1
          *    ******* * *
MAP Score: 9.81512

Motif 5
ATACAATGAATTTTTCTTGACAATTGATGATTG	1	133	1
AATTGATGATTGAATCAAGATAATAGACCAGTC	1	154	1
TAAAATCGAGTTTATCTGGATAATCGAGATATT	2	26	1
TGTAAGTTCTGATATCATGATAATAGTTTGATT	2	63	0
ATGAATAATATATTTCAAGTGAACTAAAAGGAG	3	78	1
TTATTAATATTTTATCTTGTGAACTATTATTGA	4	117	1
CTATTATTGAGGAATGAGGTGAAAAGGAG    	4	140	1
CAATGACATGTATATCATGATAAAATAATGTAT	7	37	1
GATAAAATAATGTATGATGTAAAACGGCCAAGC	7	55	1
          * ***** ** **
MAP Score: 8.52761

Motif 6
CTTTTCTCTCAGTATTTTTTGTTGTCATATCCTT	1	83	1
TTGTTGTCATATCCTTCTTTTTTTGTCTTTTCAT	1	101	1
TTTTCATACAATGAATTTTTCTTGACAATTGATG	1	128	1
TATAGTGACTGGTCTATTATCTTGATTCAATCAT	1	159	0
TTCAACAATCAAACTATTATCATGATATCAGAAC	2	57	1
CTGCGGGAGCAGGCTTTTTTTATTTGACATTTAG	3	34	1
TTGTCAAAGGAAAAATTTCTTTTTCTCCCGTATT	4	71	0
TCCTTTGACAAATCTTCTTTCATTTATTAATATT	4	94	1
TTCATTTATTAATATTTTATCTTGTGAACTATTA	4	112	1
   CTAAGACAACCTCCTTTCATGGTTTGATGAC	6	19	0
TACATCATACATTATTTTATCATGATATACATGT	7	42	0
          *  ** ** *****
MAP Score: 5.69368

Motif 7
AGATAAAATGTACAATGATTAATCATCATA	1	31	0
TGTCTTTTCATACAATGAATTTTTCTTGAC	1	124	1
AACTCGATTTTATAGGGAGGACTGTCAG  	2	8	0
CATAGAAAAGTAAGAGGAGGTAGAACAA  	2	94	1
TTAGTTCATTTAAAATGAATAATATATTTC	3	64	1
TCAAGTGAACTAAAAGGAGTTGACGAAA  	3	92	1
TTTTATTTAATAAAAGCAAGAAAACGCTTG	4	34	1
CATCAAACCATGAAAGGAGGTTGTCTTAG 	6	21	1
CGTATATTAGTACAAAGAATCAAGAGGACA	7	94	0
GAATTCGGTATACAGGGAATTCAGGCAGGA	7	150	1
          **********
MAP Score: 3.7652