AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions030_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241678
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yhdD	152	similar to cell wall-binding protein
#1	yhdE	102	similar to hypothetical proteins
#2	ygxB	30	similar to hypothetical proteins from B. subtilis
#3	yocA	193	similar to transposon-related protein
#4	yojL	300	similar to cell wall-binding protein
#5	yubE	160	similar to N-acetylmuramoyl-L-alanine amidase
#6	yubD	300	similar to multidrug resistance protein
#7	ywtD	140	similar to murein hydrolase
#8	ywsC	300	similar to capsular polyglutamate biosynthesis

Motif 1
GTTTTGCCTTTTTATAAAAATAGCCAAATTATC	0	57	0
AAAAAAAAGGAATTAAAAAACATGCACCCAGCT	1	23	0
TCGATTGAAAAATGAAAAAAAAGGAATTAAAAA	1	37	0
  GAGAATTGATTAGAAAAATAGACAAGAAAGG	4	8	1
TTCCTTAGACTTTCGAAAAACATATCGTGCTTA	4	99	1
TAGTATTTTGTTTCCAAAAATGGCACACAACTG	4	239	0
AAACTGTTTTTTTGCAAAAACAGCTAGTATTTT	4	263	0
ATCCCTAAAGAATTGAAAAATATTAGAAGTGCA	5	74	1
ACACAATCGATTTGAAATAATATTTGATTATAT	6	122	1
CATTCACATAATTATAATAAAATAATATCATTT	6	162	1
AAGGGAGAATATTAGAATGAAAGCTAATGGTAT	6	202	1
GCTTCTTTTGTTTTCAAAAAATGATGTGTTTCG	6	248	1
ATGCTGGGCAAATAAAAAGAGAGTGTCTCATCA	7	28	0
GCATATTCATTCTGTAAAAATATTAAAAAGTCT	7	57	1
TCTCTTAACATATTCAAAAAAATACCGATGTTA	7	87	1
CGATGTTAAAACTGCAAAAAGAGGAGGAGATAA	7	112	1
ACCTTATCACTTTTTAAAAAAATCAAAGAGAAT	8	95	0
GTCCTGCTGTTTTCCAAAAATAGAAAACAGTTT	8	132	1
CAAACTTCTCTTTTGAAAGAGATTTTATACCTA	8	166	0
GATGAATGAATTTACAACAATATAGAAGGAGAT	8	266	1
          ***  ***** **
MAP Score: 26.0441

Motif 2
AAAGGGCATAAAAAAAGAAGGAATCTTAAT 	0	9	0
CCTTTTTATAAAAATAGCCAAATTATCTTAA	0	53	0
CTATTTTTATAAAAAGGCAAAACGATGAGAC	0	67	1
GTGCCGATATAAAAAAGAAACAGCAAATGCA	0	102	1
TCATTGGGGGAAAAAGGAGAACTAAG     	0	136	1
TAATCGATTGAAAAATGAAAAAAAAGGAATT	1	42	0
TAAAACTATGAATAAAGAAAGGTGATACAT 	3	9	0
TACTGCTCCAAACATTGAGGGTGAAACACA 	3	173	1
ATTGATTAGAAAAATAGACAAGAAAGGAGGA	4	14	1
AAGCGAGGGTAAAAATGATGGTTTTCTATTG	4	62	0
AACTTGCTGAAAAATTGACGATAAAACAGTT	4	213	1
TTTTTTTGCAAAAACAGCTAGTATTTTGTTT	4	259	0
TTTCAAGCACAACATAGAAAGCTTGAAAGCT	6	74	0
TTTGTTTTCAAAAAATGATGTGTTTCGCATG	6	254	1
       TTCAAAAAAGAGAGTGTCTGATGA	7	3	1
TGGGCAAATAAAAAGAGAGTGTCTCATCAGA	7	26	0
TACCGATGTTAAAACTGCAAAAAGAGGAGGA	7	109	1
ATATTAAATACAAACAGCAGGGTGTGACTAT	8	28	1
ATATCAGGAGAAAAATGAAAGCGCATTCTCT	8	71	1
GATTTTTTTAAAAAGTGATAAGGTATAAGTC	8	104	1
CTATTTTTGGAAAACAGCAGGACTTATACCT	8	124	0
CTGTTTTCCAAAAATAGAAAACAGTTTGTAG	8	138	1
AATCTCTTTCAAAAGAGAAGTTTGGCTTAGT	8	175	1
AATTTACAACAATATAGAAGGAGATGTCGAA	8	274	1
          **** ******
MAP Score: 19.6069

Motif 3
GCATAAAAAAAGAAGGAATCTTAAT        	0	2	0
CAATAAGGGGGAAAAAGGGCATAAAAAAAGAAG	0	20	0
TCATTGGGGGAAAAAGGAGAACTAAG       	0	136	1
AAAAATGAAAAAAAAGGAATTAAAAAACATGCA	1	30	0
TATGAATAAAGAAAGGTGATACAT         	3	1	0
TTATGACATAAGAGGGTATATCAGACCAAGTAA	3	128	0
ATGTCATAATAAAAAAGGTCATACTGCTCCAAA	3	152	1
AAAATAGACAAGAAAGGAGGAGAAACTGCTTCG	4	24	1
CCAAATGTTTGAAAAGGGTTTAACTTGCTGAAA	4	192	1
TTCGCTCAATGAAAAGGTTTTTACCATGTTT  	5	8	0
TTCATTGAGCGAAAAGGTTTTTATTTTGCAATC	5	28	1
CTAAAGAATTGAAAAATATTAGAAGTGCAAGTA	5	78	1
ACAATATCGGGGAAAAGCTTTCAAGCTTTCTAT	6	59	1
CCCCTGAAAGGGAGAATATTAGAATGAAAGCTA	6	195	1
TTTGAAAACAAAAGAAGCTAATAGATTTTGCAT	6	233	0
TATTCATATAGGAAGGGATGACAAC        	6	285	1
  TTCAAAAAAGAGAGTGTCTGATGAGACACTC	7	8	1
GCAAATAAAAAGAGAGTGTCTCATCAGACACTC	7	21	0
TAAAAATATTAAAAAGTCTCTTAACATATTCAA	7	71	1
AAAACTGCAAAAAGAGGAGGAGATAATAAAA  	7	119	1
CTTCTCTTTTGAAAGAGATTTTATACCTACAAA	8	162	0
          ******* * * *
MAP Score: 5.16327

Motif 4
GAATCCCCCCTACTTGGACTTATCTATA  	2	12	1
ATCAGGTTTTTACTTGGTCTGATATACCCT	3	119	1
CTTAAATAGTTCCTTAGACTTTCGAAAAAC	4	90	1
TTTAGAATTTTACTTGCACTTCTAATATTT	5	91	0
          **********
MAP Score: 0.13251