AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions001_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944239925
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	srfAA	300	surfactin synthetase
#1	srfAC	300	surfactin synthetase
#2	ydaB	210	similar to hypothetical proteins
#3	yhfL	116	similar to long-chain fatty-acid-CoA ligase
#4	yhfU	134	similar to biotin biosynthesis
#5	yjaX	164	similar to 3-oxoacyl- acyl-carrier protein synthase
#6	yjaY	22	similar to 3-oxoacyl- acyl-carrier protein synthase
#7	ylpC	108	ylpC
#8	tdh	265	threonine 3-dehydrogenase
#9	pksC	300	pksC
#10	pksD	300	pksD
#11	pksF	300	pksF
#12	pksG	224	pksG
#13	pksI	39	pksI
#14	pksJ	44	pksJ
#15	pksK	76	polyketide synthase of type I
#16	pksL	300	polyketide synthase of type I
#17	pksN	32	polyketide synthase
#18	pksP	32	polyketide synthase of type I
#19	yngI	43	similar to long-chain acyl-CoA synthetase
#20	yngJ	90	similar to butyryl-CoA dehydrogenase
#21	ynzE	270	ynzE
#22	ppsD	24	peptide synthetase
#23	ppsB	24	peptide synthetase
#24	ppsA	300	peptide synthetase
#25	yogA	127	similar to alcohol dehydrogenase
#26	lcfA	188	long chain acyl-CoA synthetase
#27	ytcI	172	similar to acetate-CoA ligase
#28	acsA	160	acetyl-CoA synthetase
#29	bioW	251	6-carboxyhexanoate-CoA ligase
#30	menE	90	O-succinylbenzoic acid-CoA ligase
#31	menB	34	dihydroxynapthoic acid synthetase
#32	menF	288	menaquinone-specific isochorismate synthase
#33	yukL	87	similar to antibiotic synthetase
#34	yukM	300	similar to antibiotic synthetase
#35	dhbB	27	isochorismatase
#36	dhbE	28	2,3-dihydroxybenzoate-AMP ligase (enterobactin synthetase component E)
#37	dhbC	25	isochorismate synthase
#38	dhbA	193	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
#39	dltA	300	D-alanyl-D-alanine carrier protein ligase (Dcl)

Motif 1
CCATTGCACGGAAAAAGAAGACAAGGAATTC	1	159	1
CCCATCCACAGAAAAACACACGCCAAATTTT	2	29	0
GAGAAACAGAAAAAAACACTCAAGAGCAAAA	3	30	0
CACAATAAATGAAAAACAACCTGTTTGCATT	8	42	0
TTGTCCTTCTGGAAAAGACAGTTCTGTTTAC	8	184	1
TCATTTGAAAGAAAATGAAGCGCATTATCAT	9	33	1
AGAACATAAGAAAAAAGACCCGGATTACATA	9	78	0
GAAAAAAGCAGAAAAACAATGGAGCAAACTG	9	140	1
CATAAATATAAAAAAAGAAGGTTATACAC  	10	281	1
    CCGTTTAAAAATGACAATCAGAACCGT	13	6	1
ATGCGCGGAGAAAAAAGAAGGACAGTGGCAA	16	219	1
TCACTTTTTAAAAAAAGACGACTTAGAAAGC	21	25	0
TGAATTTTTTAAAAAACAAAGGTGAGATTCA	21	85	1
AAATTTGATAAAAAAAGAAACGAAAAATAAA	24	97	1
AAAAAAGCAGAAAAATGACAATAAAAGAAAT	24	235	0
CATATTATGAGAAAAAGAAAGATTTACCTTT	26	96	1
GCAAAAAAAAGAAAAAGAAAGGTAAATCTTT	26	113	0
TTTATATGTAAAAAATGAAAAAGAGTGGGGA	27	46	0
AAAAGAAATCGAAAAAGACCGTTTTGTGTGA	29	15	1
TAAAAGGAAACAAAAAGACCGTTTTCACACA	29	39	0
TTTCAGAAATGAAAAAGAAACAAGCTTAAAT	32	153	0
GACATCCAGCGAAAAAGACTGCTGCGCCTTG	38	136	0
GTATGTTTTTGAAAATGAATCTTTAT     	39	5	0
AGATTAGGGAAAAAATGAAACTTTTTGAGCA	39	57	1
AACCATACATAAAAAACAAAACAAGCAGTAT	39	218	0
          ********* *
MAP Score: 27.2302

Motif 2
GTTTTCAATATTTTTTATCTTTCTACCGTTCAGT	0	10	0
TAGTCCCACATTTTCTTATTTTGTTCCCCATCCA	2	52	0
TCTTGAGTGTTTTTTTCTGTTTCTCTATAATGGA	3	36	1
TACGGCCGGTTTTTTTGCGTTCATTATGTAAACT	4	31	1
GACATAATAATTACCTGCATTTATTGTATAACCA	4	82	1
GTACTAATTCTATCCTATTTTTTTTCACATGGCA	5	73	0
GCAAACAGGTTGTTTTTCATTTATTGTGATATTT	8	45	1
TATATCTCCTGATCCTTTATTCCTCAATGGAAAA	9	111	1
GCTCCATTGTTTTTCTGCTTTTTTCCATTGAGGA	9	131	0
TTCACATATGTCTTTTCCATTTATTAATTTCATT	10	190	1
ATAACCTTCTTTTTTTATATTTATGACGGCTATT	10	272	0
ATACTTCAAAGATTCTCTGTTTATCCATAATGCG	11	78	0
CAGTGCTACCGCTTTTTCTTTCATTAATAAATTT	12	114	0
       GATGCTTCTGTATTTCTTCCCTTACTC	15	59	0
GATTTGCCACTGTCCTTCTTTTTTCTCCGCGCAT	16	219	0
     TCATTGTTCCTCCTTTCTTAATGATAGGA	19	24	0
CATGTGAATCTCACCTTTGTTTTTTAAAAAATTC	21	86	0
GTTTCTCTTCGATTTTATTTTTATTTAGTACTAG	21	168	0
TTAATCGGACTAATTTTCTTTTGTGCATCATTC 	24	9	0
ATTATTTCTTTATTTTTCGTTTCTTTTTTTATCA	24	102	0
TTATTGTCATTTTTCTGCTTTTTTCTACATTTTC	24	242	1
GATTTACCTTTCTTTTTCTTTTTTTTGCCGTCCA	26	116	1
GTATCCCCACTCTTTTTCATTTTTTACATATAAA	27	43	1
ATATTCATATTCTTCTCAATTTTTAAAATATAAA	28	90	0
      ATGATGACCTCCTTTTATTCTCTATGTG	31	16	0
GAATATAGGAGGTTTTCCTTTTATGGTAAGCGGA	32	90	1
TAAGCTTGTTTCTTTTTCATTTCTGAAATTAGGT	32	156	1
          * **** * *** *
MAP Score: 26.8121

Motif 3
ACCAGACTAGAAATGAAAACGTAAAACACGT	21	211	0
GACGGCAAAAAAAAGAAAAAGAAAGGTAAAT	26	117	0
TATATGTAAAAAATGAAAAAGAGTGGGGATA	27	44	0
CTAATTTCAGAAATGAAAAAGAAACAAGCTT	32	157	0
ATGGATAAGAAAGAGAAAATGCGTTGCACAT	0	242	1
GGGGAACAAAATAAGAAAATGTGGGACTATT	2	57	1
TAATAAGAGGATAAGAAAATGTAGAAAAAAG	24	259	0
TGTTCATATTATGAGAAAAAGAAAGATTTAC	26	92	1
GAAAAGACATATGTGAAAAAGTAAAGGAGAT	10	176	0
TGAAATTAATAAATGGAAAAGACATATGTGA	10	191	0
GACGGAGAATAGATGGAAAAGCTTGCGAAAA	26	13	1
ATTTATTAATGAAAGAAAAAGCGGTAGCACT	12	116	1
AAACTCATTTGAAAGAAAATGAAGCGCATTA	9	29	1
AGAGTATGGTATATGGAAAGGAGGCGT    	5	6	0
GCTACAGTCGAGGAGGAAATGGAACGGTTTA	1	103	1
AAAGATGTGAAGGAGGAAACGAT        	20	77	1
ATATCACAATAAATGAAAAACAACCTGTTTG	8	46	0
AAGAAGCTTCAGAAGAAAAGCTCTAT     	16	284	1
AGACCGTTTTGTGTGAAAACGGTCTTTTTGT	29	30	1
GTCTGTATTGAAAAGAAAACAGCTTGGACCG	30	47	0
AATAATTCCAAAATGAAATAGTTTTACAAGT	2	105	1
     CTGTAAAAAGAAATCGAAAAAGACCG	29	5	1
ATAACAGAACATAAGAAAAAAGACCCGGATT	9	83	0
ATATGTAAAGATATGAAAATACAATTAATGA	25	93	1
CGCTTACCATAAAAGGAAAACCTCCTATATT	32	91	0
CAAGCAGACCAGGTGAAAAGAGTAAGGGAAG	15	40	1
TAAATTTTGCAGGTGAAATGGAGGCAGCGTG	14	23	1
ATATATTGCCATGTGAAAAAAAATAGGATAG	5	67	1
GGTGAGGTAAGGAAGAAAATCTAACAAATTA	2	157	1
GCAGTTGGTTAAAAGGAAACAAAAAGACCGT	29	48	0
CTAAGCCATTATGTGAAATTGTAAA      	27	4	0
TGAAACAGCTGTATGAAAAACCCGCTGTCAA	39	156	1
GAGCTATCCGGGGTGAAAAACATCGGTGAAT	11	264	1
GGTATTCGCGGTGTGAAAACCATACATAAAA	39	235	0
AAATACTATCGGGAGAAAATATCACAATAAA	8	64	0
TTAGAGCGAAGAAAGGAATTGATGAT     	38	177	1
GCAGCGATTGAAATGAAATTAATAAATGGAA	10	204	0
AAATGACAATAAAAGAAATTATATGACTATA	24	223	0
ATGCATGGAAATGAGAAATCCAATAGCCGTC	10	251	1
TTGAAAAGGTGTGTGGAATTG          	23	13	1
AAAGAGTAAGGGAAGAAATACAGAAGCATC 	15	56	1
          ********* *
MAP Score: 25.8274

Motif 4
TGCTCCTACAATGAGAAGGAGTTTGAAAGAG	1	73	1
TGTTACAAAGATGTGAAGGAGGAAACGAT  	20	71	1
TATGTAAAAAATGAAAAAGAGTGGGGATACC	27	42	0
AGTATGGTATATGGAAAGGAGGCGT      	5	4	0
GAAAAACGTGATGGGAAAGAAGCTTCAGAAG	16	268	1
TGTTCATATTATGAGAAAAAGAAAGATTTAC	26	92	1
GAAAAGACATATGTGAAAAAGTAAAGGAGAT	10	176	0
AATTTCAGAAATGAAAAAGAAACAAGCTTAA	32	155	0
GCTGATATGGATAAGAAAGAGAAAATGCGTT	0	236	1
TTATTCCTCAATGGAAAAAAGCAGAAAAACA	9	127	1
TTTATTCTCTATGTGAATGAG          	31	0	0
       GAAATGAGAAGGACGGCTTTCTAA	21	3	1
AAATTAATAAATGGAAAAGACATATGTGAAA	10	189	0
ATATATTGCCATGTGAAAAAAAATAGGATAG	5	67	1
AACAACATGCATGGAAATGAGAAATCCAATA	10	245	1
TAAATTTAAGATATAAAGGAGTCTTCCCTA 	5	144	1
      CTGAATTTAAAGGAGGTTCATGAGA	37	4	1
TTGAAAACTCATTTGAAAGAAAATGAAGCGC	9	25	1
AAATGTCTGTATTGAAAAGAAAACAGCTTGG	30	51	0
CATTTTTTACATATAAAAAAGGACCAGCGGC	27	60	1
          *** *******
MAP Score: 18.1929

Motif 5
CATAAGAATTAAAAGCTGATATGGATAAGAAAGAGAA	0	222	1
GATAAGAAAGAGAAAATGCGTTGCACATGTTCACTGC	0	245	1
ATTGCACGGAAAAAGAAGACAAGGAATTCACACCAAG	1	161	1
TTTAACCCAAAAAAGATAACTTGTAAAACTATTTCAT	2	117	0
TCCATTATAGAGAAACAGAAAAAAACACTCAAGAGCA	3	33	0
AACTTAAATTAAAAATCAGTTGACATAATAATTACCT	4	61	1
CCATGTGAAAAAAAATAGGATAGAATTAGTACCTGAT	5	75	1
         AAAAAGGTGAGGTGCACACAAG      	6	1	1
ATCTGTCTTGAAAAATGGGCGGAAATTTTTTTTGAAA	8	143	0
CTCATTTGAAAGAAAATGAAGCGCATTATCATGATAT	9	32	1
CTCAATGGAAAAAAGCAGAAAAACAATGGAGCAAACT	9	133	1
GACATATGTGAAAAAGTAAAGGAGATTCAACTTGGAA	10	165	0
ATAAATATAAAAAAAGAAGGTTATACAC         	10	282	1
ACTTTTTAAAAAAAGACGACTTAGAAAGCCGTCCTTC	21	17	0
AGTACTAAATAAAAATAAAATCGAAGAGAAACACGTA	21	170	1
TAACCAGACTAGAAATGAAAACGTAAAACACGTCCTG	21	207	0
GAAATTTGATAAAAAAAGAAACGAAAAATAAAGAAAT	24	96	1
AAGAAAATGTAGAAAAAAGCAGAAAAATGACAATAAA	24	241	0
GGCAAAAAAAAGAAAAAGAAAGGTAAATCTTTCTTTT	26	108	0
TTTTATATGTAAAAAATGAAAAAGAGTGGGGATACCC	27	41	0
TTTATATTTTAAAAATTGAGAAGAATATGAATATATA	28	90	1
      CTGTAAAAAGAAATCGAAAAAGACCGTTTTG	29	4	1
GCAGTTGGTTAAAAGGAAACAAAAAGACCGTTTTCAC	29	42	0
TTCTATTGACAGAAACAGGAGAGAATAATATATTCTA	29	96	1
GAAATGAAAAAGAAACAAGCTTAAATTTCTTTCTCCA	32	142	0
TGATTGTCGAAAAAACGGGAAGGGAATTTTTGATATG	39	109	1
          *****  **   * * *
MAP Score: 14.727

Motif 6
CAGGAAAGCACAAACCGGCCGTTTCTGATC	1	45	0
    CCATCAAAAACCGGTCTGCCATACGG	4	6	1
TGAACGCAAAAAAACCGGCCGTATGGCAGA	4	24	0
TTTAGAAGATCAATCAGGTTGTGATCAATT	5	118	0
TTGCATTACGCAAACAGGTTGAGAATGCTT	8	19	0
TTGCGTAATGCAAACAGGTTGTTTTTCATT	8	36	1
        TTCAATCCGGTCCTTCTCTGCT	12	212	0
ATTATACATAAATACAGGCTCTTTCCGTAA	27	133	0
CGTTTTCACACAAAACGGTCTTTTTCGATT	29	21	0
TATGGTGCTTCAATCCGGTCTCGCCGCTTA	34	10	1
TAGAGGTGCTCAATCCGGCTCGTTCGCGTG	34	257	1
GTGGACATGTCATACAGGCTTTTATTTGAT	39	187	1
TCACACCGCGAATACCGGTTCATATATTTA	39	250	1
          **********
MAP Score: 11.493

Motif 7
ATGAAAATACAATTAATGAGGAGGCAGACAGC    	25	105	1
CTTTCCTATCATTAAGAAAGGAGGAACAATGA    	19	21	1
GATGTTACAAAGATGTGAAGGAGGAAACGAT     	20	69	1
TAAATTTTGCAGGTGAAATGGAGGCAGCGTG     	14	23	1
ACTTTCATAAATGGCGGGTGGAGGAATATAGGAGGT	32	67	1
TCTTCTATTGACAGAAACAGGAGAGAATAATATATT	29	94	1
ATTGAGGAATAAAGGATCAGGAGATATAACAGAACA	9	103	0
ACTGCTTATAAAGATTAGGGGAGGTATGACAAT   	0	277	1
TCCTCTTATTATGAGAACTGGAGGGAATCCG     	24	279	1
AAAGCATTTTAAGGATTATGGAGGAATGTCTC    	32	266	1
CATTAAAATAATCCCTTGAGGAGAGAGCGCATTATG	11	51	1
       AAAATCGTGACAGGAGACATGAAC     	22	3	1
TATAACAAGAATTTTTCAAGGAGGATTGTAC     	8	244	1
ATTCACATAGAGAATAAAAGGAGGTCATCAT     	31	13	1
ATAATTTGGTATTCTTAAAGAAGGCATGTATTTTTG	28	36	0
TGTGCTAAAAATACTATCGGGAGAAAATATCACAAT	8	67	0
GTATTTATGTATAATGGGTGGAGAAAGTGAGGAG  	27	148	1
AGAGTATGGTATATGGAAAGGAGGCGT         	5	1	0
GATCTCTAAAATCGAAAGGGGAGGTTTT        	26	170	1
ACGCAAGGGAATTACAGAAGGCGGGAGCGAAACAT 	1	275	1
GTGATTGTCGAAAAAACGGGAAGGGAATTTTTGATA	39	108	1
CCGCCATTGCACGGAAAAAGAAGACAAGGAATTCAC	1	156	1
ACATATGTGAAAAAGTAAAGGAGATTCAACTTGGAA	10	165	0
AGGGCGAGAAATGATGCAAGAAGAAACTTTTTATAG	29	206	1
CGTCATAAATATAAAAAAAGAAGGTTATACAC    	10	278	1
CCAGGTGAAAAGAGTAAGGGAAGAAATACAGAAGCA	15	48	1
          *    * ******* *
MAP Score: 10.7428

Motif 8
AGCTACAGTCGAGGAGGAAATGGAACGGTTT	1	102	1
TGAAATGGACGAGATGGGAGATATCTTTGAC	1	219	1
CTCTATAATGGAGAAGAAAGCTTGGCTTCAA	3	58	1
ATTCACTTAAGGGGTGGGAGA          	3	105	1
ATAATCCCTTGAGGAGAGAGCGCATTATGGA	11	58	1
TGAGCTATCCGGGGTGAAAAACATCGGTGAA	11	263	1
TATCCAATGCGCGGAGAAAAAAGAAGGACAG	16	213	1
ATTGAAAAACGTGATGGGAAAGAAGCTTCAG	16	265	1
  CCATTTCTGAGGTGGAAGAACATCTTAAA	17	8	1
TACAATTAATGAGGAGGCAGACAGC      	25	112	1
          GGGGACGGAGAATAGATGGAA	26	0	1
TGTATAATGGGTGGAGAAAGTGAGGAG    	27	155	1
TAAATGGCGGGTGGAGGAATATAGGAGGTTT	32	74	1
TTTGCTATCAGTGGAGAAAGAAATTTAAGCT	32	131	1
TCGAAAAAACGGGAAGGGAATTTTTGATATG	39	115	1
CGATTTCTAATTGGAGAGAGAATAACT    	39	283	1
          * *********
MAP Score: 7.11277

Motif 9
CTACAGTCGAGGAGGAAATGGAACGGTTTA	1	104	1
AATTACAGAAGGCGGGAGCGAAACAT    	1	284	1
AATCCCTTGAGGAGAGAGCGCATTATGGAT	11	60	1
GAATGTCTTTGGCGGAACGGCATACCTTGA	12	36	1
CAGGTGAAATGGAGGCAGCGTG        	14	32	1
GCTCTGAGCAGGAGAAACCGTGTTCTCTGA	16	116	0
AGCCATTGACGGCGGAACAGGATGCAGTAA	16	173	1
CATTAAGAAAGGAGGAACAATGA       	19	30	1
AAGATGTGAAGGAGGAAACGAT        	20	78	1
ATAGCAAGCAGGTGAGAGCGC         	25	1	0
CAATTAATGAGGAGGCAGACAGC       	25	114	1
TATAATGGGTGGAGAAAGTGAGGAG     	27	157	1
TGCTATCAGTGGAGAAAGAAATTTAAGCTT	32	133	1
TTGACACAAAGGAGACACAGGTGTATGGTA	32	233	1
GTCAATAAGCGGCGAGACCGGATTGAAGCA	34	15	0
ACAGACATCCAGCGAAAAAGACTGCTGCGC	38	140	0
          **********
MAP Score: 2.68447

Motif 10
GTTTTCAATATTTTTTATCTTTCTACCGTTCA	0	12	0
CCAAAATTGGTTTCTTATTAGGGTGGGGTCTT	0	57	1
AGCGGCCATCTGTTTTTTGATTGGAAGCACTG	0	149	1
AAACCGGCCGTTTCTGATCATGCCGCTGAAGC	1	32	0
GTGAATTCCTTGTCTTCTTTTTCCGTGCAATG	1	160	0
AGTCCCACATTTTCTTATTTTGTTCCCCATCC	2	53	0
CACTCAGGGCTTTTTGCTCTTGAGTGTTTTTT	3	19	1
TGCTCTTGAGTGTTTTTTTCTGTTTCTCTATA	3	33	1
TTTTAGCTCATTTCTGATTTTGTATATTCGCT	8	109	0
AATCCGGGTCTTTTTTCTTATGTTCTGTTATA	9	83	1
CTCCATTGTTTTTCTGCTTTTTTCCATTGAGG	9	132	0
TCGATGTTCTTTGCTGATCCTGTTATCATGTT	10	56	1
TGCCACATTATTTTTTGTGCTGTTCGGAGATG	21	246	1
ATAGTATTATTTCTTTATTTTTCGTTTCTTTT	24	109	0
AAAAATTTAATGTTTTTTATTGTACTTTAAAA	24	159	1
AGTCATATAATTTCTTTTATTGTCATTTTTCT	24	226	1
TATTGTCATTTTTCTGCTTTTTTCTACATTTT	24	243	1
AGCGGGAATCTTTTTGTTAATTGGTCTTATAT	26	57	1
AAGATTTACCTTTCTTTTTCTTTTTTTTGCCG	26	114	1
ATCCCCACTCTTTTTCATTTTTTACATATAAA	27	45	1
AAATCGATCCTTTCTTCTATTGACAGAAACAG	29	82	1
TGATACTGCTTGTTTTGTTTTTTATGTATGGT	39	216	1
          ****** * ***
MAP Score: 1.07923

Motif 11
ACGGCCGGTTTGTGCTTTCCTGCTCCTACAAT	1	53	1
AAATTTGGCGTGTGTTTTTCTGTGGATGGGGA	2	30	1
TGCTCTTGAGTGTTTTTTTCTGTTTCTCTATA	3	33	1
TAAACAGAACTGTCTTTTCCAGAAGGACAAAA	8	182	0
ATAGAGTCGATGTTCTTTGCTGATCCTGTTAT	10	50	1
TTTTCACATATGTCTTTTCCATTTATTAATTT	10	188	1
AAGCGATGAATGTCTTTGGCGGAACGGCATAC	12	29	1
TTTATCACCATGTGGTTTACGGACAAAATGTC	16	45	1
ACGTACAGGACGTGTTTTACGTTTTCATTTCT	21	202	1
CATTATTTTTTGTGCTGTTCGGAGATGCT   	21	251	1
CTGCATGATCTGTGTTTGACACAAAGGAGACA	32	218	1
          ******** * *
MAP Score: 0.486321