AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions022_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241347
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yhaR	164	similar to 3-hydroxbutyryl-CoA dehydratase
#1	yngG	250	similar to hydroxymethylglutaryl-CoA lyase
#2	yngI	43	similar to long-chain acyl-CoA synthetase
#3	yngJ	90	similar to butyryl-CoA dehydrogenase
#4	ynzE	270	ynzE
#5	yngK	135	alternate gene name: yotA; similar to hypothetical proteins
#6	yngL	110	yngL
#7	ppsD	24	peptide synthetase
#8	ppsB	24	peptide synthetase
#9	ppsA	300	peptide synthetase
#10	mmgB	149	3-hydroxybutyryl-CoA dehydrogenase
#11	mmgA	137	acetyl-CoA acetyltransferase
#12	yqiK	78	similar to glycerophosphodiester phosphodiesterase
#13	yqiH	300	alternate gene name: yzpA; similar to lipoprotein
#14	ysiA	104	similar to transcriptional regulator (TetR/AcrR family)
#15	lcfA	188	long chain acyl-CoA synthetase
#16	yshC	73	similar to DNA polymerase beta
#17	yshA	133	yshA
#18	menB	34	dihydroxynapthoic acid synthetase
#19	menF	288	menaquinone-specific isochorismate synthase
#20	yusL	267	similar to 3-hydroxyacyl-CoA dehydrogenase
#21	yusM	300	similar to proline dehydrogenase

Motif 1
CATATTATGAGAAAAAGAAAGATTTACCTT	15	96	1
GCAAAAAAAAGAAAAAGAAAGGTAAATCTT	15	114	0
TTTCAGAAATGAAAAAGAAACAAGCTTAAA	19	154	0
TTTATATAGTGAAAAAGAAGGGATATCTTG	0	10	0
AAATTTGATAAAAAAAGAAACGAAAAATAA	9	97	1
TGAATGAATGAAAAAAGAAGGCTGCGTCAA	11	39	0
AAGAAGTCAAAAAAAAGGAAGGCGACTTTG	1	169	1
GAAAAGTGTAAAAAAAGGAGATTATTAC  	17	8	0
AAGCGGAATCGTAAAAGAAGTCAAAAAAAA	1	155	1
GAATGTATAGGAGAAAGAAAAAAGTAAGCG	0	124	1
GCTATCAGTGGAGAAAGAAATTTAAGCTTG	19	134	1
TGGAATCGATGAAAATGGAAATCCCGATCG	1	115	1
AAAAATGACAATAAAAGAAATTATATGACT	9	226	0
TATTGACCTTGAAAAATAAAAAGGTTTATT	0	81	1
AAAAAGAAACGAAAAATAAAGAAATAATAC	9	108	1
TCCGCTTACCATAAAAGGAAAACCTCCTAT	19	94	0
CACATAGAGAATAAAAGGAGGTCATCAT  	18	16	1
ATTCTTGATACAAAAAGAAAGACGGACAGA	6	36	0
AAGCCTCCAAGAAAAAGGATGATGTTATCA	6	86	0
TCCTATCATTAAGAAAGGAGGAACAATGA 	2	24	1
  AACATGATGAAAAAGGGGATTTGAATGG	10	8	1
AGGCGACTTTGTAAATGAAGGAGACGTACT	1	188	1
AGAAAAGTCTGAAAATTAAAACTGAA    	3	6	0
GAAGGAAACTATAAAATGAACAGAAACCAA	21	228	0
          **********
MAP Score: 28.3368

Motif 2
 CAAGATATCCCTTCTTTTTCACTATATAA	0	9	1
CCAAATAAACCTTTTTATTTTTCAAGGTCA	0	84	0
TATGCGCTTACTTTTTTCTTTCTCCTATAC	0	128	0
AGTCGCCTTCCTTTTTTTTGACTTCTTTTA	1	166	0
TCTAAGTCGTCTTTTTTTAAAAAGTGATTT	4	29	1
TGAATCTCACCTTTGTTTTTTAAAAAATTC	4	86	0
TGCTTTAGGACTTTTTTCGTTTATTTAGTG	5	25	1
CTCTGTCCGTCTTTCTTTTTGTATCAAGAA	6	35	1
ATAACATCATCCTTTTTCTTGGAGGCTTCT	6	88	1
TTTTTCGTTTCTTTTTTTATCAAATTTCCG	9	94	0
AGTATTATTTCTTTATTTTTCGTTTCTTTT	9	109	0
ATTTTTATAACATTTTTTTTGAATATAGTA	9	135	0
CTTTTATTGTCATTTTTCTGCTTTTTTCTA	9	239	1
CATTTTTCTGCTTTTTTCTACATTTTCTTA	9	249	1
ATTCAAATCCCCTTTTTCATCATGTT    	10	6	0
TTTGACGCAGCCTTCTTTTTTCATTCATTC	11	38	1
TGATGTTTGGCTTTTATCTTTGACCAGAAT	13	265	0
AAAGGTAAATCTTTCTTTTTCTCATAATAT	15	97	0
AAAGATTTACCTTTCTTTTTCTTTTTTTTG	15	113	1
CTTTCTTTTTCTTTTTTTTGCCGTCCATCT	15	123	1
GTAATAATCTCCTTTTTTTACACTTTTCGC	17	10	1
GAAATTTAAGCTTGTTTCTTTTTCATTTCT	19	150	1
ATGAAATGCGCTTTTTTCATCGCGAGCAAA	21	100	1
          **********
MAP Score: 21.3769

Motif 3
TTAGCATACAAATGGCAGGAAACCTGTGGAAAGTCCA	1	31	1
AAAGAAGTCAAAAAAAAGGAAGGCGACTTTGTAAATG	1	168	1
GCGACTTTGTAAATGAAGGAGACGTACTGCTCGAACT	1	190	1
CTCCTTTCTTAATGATAGGAAAGCGTTTACATTT   	2	7	0
TTGGGACAGGAAACGATGGTAAACCGCTGAATTTTTT	4	58	1
ATTTTTTAAAAAACAAAGGTGAGATTCACATGAATAT	4	88	1
CTCTTATTATGAGAACTGGAGGGAATCCG        	9	281	1
AATTAGAAAAAATTAGCGGAAAGAAGCAACTTTTTAT	13	90	0
TTATCTTTCTAACAACAGGAAATGATCGGGTCGTATA	13	168	1
GGGGACGGAGAATAGATGGAAAAGCTTGCGAAAATAC	15	10	1
AAAAAAAGAAAAAGAAAGGTAAATCTTTCTTTTTCTC	15	104	0
CGAAAAGTGTAAAAAAAGGAGATTATTAC        	17	2	0
AGTGTATCATAACAGCGGGAGGCTCGTCTTTCCATTC	17	50	1
TCACATAGAGAATAAAAGGAGGTCATCAT        	18	15	1
GCGGGTGGAGGAATATAGGAGGTTTTCCTTTTATGGT	19	80	1
TCCTTTGTCGAAATAACGGAAGGCGGCATTTGAGATT	21	163	1
AATGAACAGAAACCAAAGGAGGATCACAATGGATAAT	21	207	0
TTTTGAAGATGACGGCGGGAGGGAGTCGG        	21	281	1
          **  *  *****   **
MAP Score: 15.3773

Motif 4
     CAAGATATCCCTTCTTTTTCACTAT	0	5	1
AAACTTTATGTTTCCATTCAAACAATATGC	0	38	1
ATTCAAACAATATGCATTTTTCAGTATCTA	0	53	1
TTCTTTCTCCTATACATTCCCCGCCATCCC	0	113	0
GCGCTTACTTTTTTCTTTCTCCTATACATT	0	125	0
GGCCAGGAGGTAGCCATTTTGGAATCGATG	1	96	1
ACGATCGGGATTTCCATTTTCATCGATTCC	1	116	0
CAGTACGTCTCCTTCATTTACAAAGTCGCC	1	189	0
GTGTTTTACGTTTTCATTTCTAGTCTGGTT	4	213	1
AAGTGTCCCTTATCCATTCTTGATACAAAA	6	51	0
TCTGCTTTTTTCTACATTTTCTTATCCTCT	9	255	1
ATTTGTTTGATTTCCATTCAAATCCCCTTT	10	21	0
TTCTAACAACTATTCATTTT          	11	0	0
CAGCCTTCTTTTTTCATTCATTCATGCCCG	11	45	1
CCTAAAGTTTTCTCCATTATACTTATTTTG	12	43	0
AGCAACTTTTTATTCATTTTAAAAAATTTG	13	73	0
CTTTACAAATTCTCCATTCTGGTCAAAGAT	13	250	1
AATGAATGACTATTCATTCATAATTTCATG	14	61	0
AATGAATAGTCATTCATTTCTATAGGAAGG	14	73	1
TTACCTTTCTTTTTCTTTTTTTTGCCGTCC	15	119	1
   GTAATAATCTCCTTTTTTTACACTTTT	17	7	1
GAGGCTCGTCTTTCCATTCATTTAATAAAC	17	68	1
   CGTTTCTCCTCCATTCCGCGAGAATCC	17	116	0
ATATAGGAGGTTTTCCTTTTATGGTAAGCG	19	92	1
GCTTGTTTCTTTTTCATTTCTGAAATTAGG	19	159	1
CGGACCGGCATCTCCCTTTACGCTCGCCGC	20	109	1
TGCTGCTGATTATCCATTGTGATCCTCCTT	21	199	1
CTTTGGTTTCTGTTCATTTTATAGTTTCCT	21	226	1
          **********
MAP Score: 9.50828

Motif 5
GTAGCCATTTTGGAATCGATGAAAATGGAA	1	105	1
TTTTCTTGTCAGGGAATGATTATAGAACTC	3	30	1
GATGTGAAGGAGGAAACGAT          	3	80	1
ATTTTGGGACAGGAAACGATGGTAAACCGC	4	55	1
CTAACCAGACTAGAAATGAAAACGTAAAAC	4	215	0
AAGGGACACTTGGGAATGATAACATCATCC	6	70	1
TTGATAAAAAAAGAAACGAAAAATAAAGAA	9	101	1
ATGACAATAAAAGAAATTATATGACTATAT	9	222	0
TTCTAACAACAGGAAATGATCGGGTCGTAT	13	174	1
TTCCTTCCTATAGAAATGAATGACTATTCA	14	75	0
TTTCTATAGGAAGGAACGATGAACA     	14	89	1
CCGGAGGTGAAGGGAATGGTACGAGAGAAA	20	166	0
CCCAGTCTGAAGGAAACTATAAAATGAACA	21	236	0
          **********
MAP Score: 8.6636

Motif 6
TTTATATAGTGAAAAAGAAGGGATATCTTG 	0	9	0
AGGTTTATTTGGGGATGGCGGGGAATGTATA	0	102	1
CGGTTAGCATACAAATGGCAGGAAACCTGTG	1	28	1
AAGAAGTCAAAAAAAAGGAAGGCGACTTTGT	1	169	1
AGGCGACTTTGTAAATGAAGGAGACGTACTG	1	188	1
TCCTATCATTAAGAAAGGAGGAACAATGA  	2	24	1
     GAAATGAGAAGGACGGCTTTCTAAGT	4	5	1
AGATTCACATGAATATGGAGGCGGTGTTTGG	4	109	1
TTGATACAAAAAGAAAGACGGACAGAGAATG	6	31	0
AAGCCTCCAAGAAAAAGGATGATGTTATCAT	6	85	0
TCTTATTATGAGAACTGGAGGGAATCCG   	9	282	1
TCCAGAGGCCGCGGAGGCAGGA         	10	137	1
TGAATAGTTGTTAGAAGGAGGCTGTTTGACG	11	14	1
TGAATGAATGAAAAAAGAAGGCTGCGTCAAA	11	38	0
GCTTTGAAACGGGCATGAATGAATGAAAAAA	11	53	0
TAAAGACAACGCGAATGCAGGCGAGCAAGTT	13	224	0
CATATTATGAGAAAAAGAAAGATTTACCTTT	15	96	1
CAAAAAAAAGAAAAAGAAAGGTAAATCTTTC	15	112	0
CTCTAAAATCGAAAGGGGAGGTTTT      	15	173	1
AGCGAAAAGTGTAAAAAAAGGAGATTATTAC	17	10	0
GTGTATCATAACAGCGGGAGGCTCGTCTTTC	17	51	1
CACATAGAGAATAAAAGGAGGTCATCAT   	18	16	1
GAGAACTTTCATAAATGGCGGGTGGAGGAAT	19	63	1
TTTAAGGATTATGGAGGAATGTCTC      	19	273	1
CATTACGGCGGCGGAAAACGGACAAGTCAAA	20	72	0
GAGCGTAAAGGGAGATGCCGGTCCGACTCAG	20	103	0
ACTTAAGCCCGGAGGTGAAGGGAATGGTACG	20	173	0
TATGAAGCCTATAAAAGTCGGGCAACTTAAG	20	197	0
TGTCGAAATAACGGAAGGCGGCATTTGAGAT	21	168	1
ATGAACAGAAACCAAAGGAGGATCACAATGG	21	212	0
CAGGTGTTTTGAAGATGACGGCGGGAGGGAG	21	275	1
          * *********
MAP Score: 6.44067

Motif 7
GTTTTATATAGTGAAAAAGAAGGGATATCTTG    	0	6	0
AAAGAAGTCAAAAAAAAGGAAGGCGACTTTGTAAAT	1	168	1
GCGACTTTGTAAATGAAGGAGACGTACTGCTCGAAC	1	190	1
TGTTACAAAGATGTGAAGGAGGAAACGAT       	3	71	1
       GAAATGAGAAGGACGGCTTTCTAAGTCGT	4	3	1
ATTTTTTAAAAAACAAAGGTGAGATTCACATGAATA	4	88	1
ATTCACATGAATATGGAGGCGGTGTTTGGACATTTA	4	111	1
AATTAGTCCGATTAAAAAGTAGTGTATAAGACCTTA	9	28	1
    AACATGATGAAAAAGGGGATTTGAATGGAAAT	10	6	1
ATGAATAGTTGTTAGAAGGAGGCTGTTTGACGCAGC	11	13	1
AAAGCCAAACATCAGGAAGAGGTGGTCAT       	13	281	1
AAAAAAAGAAAAAGAAAGGTAAATCTTTCTTTTTCT	15	105	0
ATCTGCTATAATGATAAGGTGGATCTCTAAAATCGA	15	149	1
GGATCTCTAAAATCGAAAGGGGAGGTTTT       	15	169	1
CGAAAAGTGTAAAAAAAGGAGATTATTAC       	17	3	0
TATTAAATGAATGGAAAGACGAGCCTCCCGCTGTTA	17	59	0
TCACATAGAGAATAAAAGGAGGTCATCAT       	18	15	1
TTGTCGAAATAACGGAAGGCGGCATTTGAGATTGCT	21	167	1
AATGAACAGAAACCAAAGGAGGATCACAATGGATAA	21	208	0
ATAACTCCCAGTCTGAAGGAAACTATAAAATGAACA	21	236	0
          **  ***** **   *
MAP Score: 5.86681

Motif 8
AGGTTTATTTGGGGATGGCGGGGAATGTATA	0	102	1
AGTCAAAAAAAAGGAAGGCGACTTTGTAAAT	1	173	1
CGACTTTGTAAATGAAGGAGACGTACTGCTC	1	191	1
TCCTATCATTAAGAAAGGAGGAACAATGA  	2	24	1
GTTACAAAGATGTGAAGGAGGAAACGAT   	3	72	1
TTCACATGAATATGGAGGCGGTGTTTGGACA	4	112	1
GTGATGTAATGGGGGAGAAGAAACAGA    	5	118	1
 AGCGGATTAGCGGACAGAGGCCATTCTCTG	6	9	1
AAAAAGAAAGACGGACAGAGAATGGCCTCTG	6	24	0
AATCATGGTAGCTGGCGCAGGTCAGATGGGG	10	48	1
CGCAGGTCAGATGGGGAGCGGAATTGCTCAA	10	63	1
ATGTGAATCCAGAGGCCGCGGAGGCAGGA  	10	130	1
TGAATAGTTGTTAGAAGGAGGCTGTTTGACG	11	14	1
TTAATCCTAGAGTGGAGCCGACAAAATAAGT	12	22	1
AGACAACGCGAATGCAGGCGAGCAAGTTCCA	13	221	0
          GGGGACGGAGAATAGATGGAA	15	0	1
ATTATAGCAGATGGACGGCAAAAAAAAGAAA	15	130	0
ATTCTCGCGGAATGGAGGAGAAACG      	17	118	1
TTCATAAATGGCGGGTGGAGGAATATAGGAG	19	70	1
TGTCGAAATAACGGAAGGCGGCATTTGAGAT	21	168	1
GTGTTTTGAAGATGACGGCGGGAGGGAGTCG	21	278	1
ATGACGGCGGGAGGGAGTCGG          	21	289	1
          * *********
MAP Score: 1.85648