AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions039_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241985
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	appD	191	oligopeptide ABC transporter (ATP-binding protein)
#1	appA	87	oligopeptide ABC transporter (oligopeptide-binding protein)
#2	dppA	128	dipeptide ABC transporter
#3	dinG	125	ATP-dependent helicase
#4	yvyE	216	alternate gene name: yvhK; similar to hypothetical proteins

Motif 1
TAATATTACATTTATCCTAAAAAATTCTTGAT	0	37	1
ATAATATTGAATTATCGAAAAATTTTATAGTT	0	95	0
ATCAATTACATTTATAATAAAAATATATGACA	4	31	0
ATTCTAACAAATTATATTAAAAAAAGAGGAAA	2	75	0
AAGCAATCCCTTTATTCAGAAATAATAAATAA	0	123	0
GAATGCGTATATTCTAGAAAAAAACATTTTTA	4	91	1
ATTATGTCGAATTATAATGAAAGAATGCGTAT	4	69	1
AAGGGATTGCTTTCTCTTGAAAACGTTTGACA	0	143	1
ATATTCATAATTTAGTAAAAAAGGAGGAGCGT	2	105	1
AAGAGTAGATAGTATATAAAAATGTTTTTTTC	4	107	0
TATCGGGGGTTTTCTTTTAAGATTTTGAGAGT	3	25	1
TTTTAAGATTTTGAGAGTAAAACGGTTTTGCC	3	39	1
          *****  *****
MAP Score: 11.5275

Motif 2
ATTTTTCCTCTTTTTTTAATATAATTTGTTAGAA	2	72	1
AATATACGCATTCTTTCATTATAATTCGACATAA	4	70	0
TAAAAATGTTTTTTTCTAGAATATACGCATTCTT	4	89	0
ATCGGGGGTTTTCTTTTAAGATTTTGAGAGTAAA	3	26	1
AAAATCAAGAATTTTTTAGGATAAATGTAATATT	0	38	0
GAAAAAAACATTTTTATATACTATCTACTCTTTA	4	107	1
GAAATGTTCGTTCTTCTAGGCTGTTGTTTATGTA	1	46	0
TGAAAGAGGATTCTTTTTTTATCACTGAATGATT	2	15	1
TTTGTGCGTATTTTGGTATCATAAAGAGTAGATA	4	128	0
TGTATAGGCAGTCTTTTATGCTTAGCAGGAGGGT	4	184	1
AAAATTCTTGATTTTGCAAAATGATTGTAATAAT	0	57	1
CGTTGTCATATATTTTTATTATAAATGTAATTGA	4	28	1
CGCTCCTCCTTTTTTACTAAATTATGAATATTCT	2	102	0
AAATTTTATAGTTGTATATTATTACAATCATTTT	0	74	0
CCTATACAAATTCGTACAGTCTTTAGAATTTTTG	4	158	0
          ***** **  ** *
MAP Score: 11.0785

Motif 3
ATAATGGAATTTCATTAATAATATTACATTTATCCTAAAAAAT	0	19	1
AAAAAACATTTTTATATACTATCTACTCTTTATGATACCAAAA	4	109	1
TTAATATAATTTGTTAGAATATTCATAATTTAGTAAAAAAGGA	2	87	1
TATTACAATCATTTTGCAAAATCAAGAATTTTTTAGGATAAAT	0	46	0
      ATCCTTGAAAGAGGATTCTTTTTTTATCACTGAATGA	2	4	1
TTTTTCGATAATTCAATATTATTTATTATTTCTGAATAAAGGG	0	105	1
GATTGTAATAATATACAACTATAAAATTTTTCGATAATTCAAT	0	79	1
CCTATACAAATTCGTACAGTCTTTAGAATTTTTGTGCGTATTT	4	149	0
TTTCCCAGTTATATTGCATTTTTCCTCTTTTTTTAATATAATT	2	55	1
AAAATGTTTTTTTCTAGAATATACGCATTCTTTCATTATAATT	4	78	0
GAAATGTTCGTTCTTCTAGGCTGTTGTTTATGTAGTGTGCATA	1	37	0
          **  *  *  **      *** *
MAP Score: 8.00513

Motif 4
AAAATTTTATAGTTGTATATTATTACAATCATT	0	76	0
TCTGAATAAAGGGATTGCTTTCTCTTGAAAACG	0	135	1
CGTTCTTCTAGGCTGTTGTTTATGTAGTGTGCA	1	39	0
TCCTTGAAAGAGGATTCTTTTTTTATCACTGAA	2	11	1
CCCCCGATAAAGGGGGCTTTTCTT         	3	1	0
CCCCTTTATCGGGGGTTTTCTTTTAAGATTTTG	3	19	1
GCAAGAATTGAGGTGTCCATTTTA         	3	111	1
TAATGAAAGAATGCGTATATTCTAGAAAAAAAC	4	83	1
TAGAATTTTTGTGCGTATTTTGGTATCATAAAG	4	136	0
AATTTGTATAGGCAGTCTTTTATGCTTAGCAGG	4	180	1
          *** ** **** *
MAP Score: 2.38757

Motif 5
AATAATATTACATTTATCCTAAAAAATTCTTGATTTTGCA	0	35	1
TTTTATAGTTGTATATTATTACAATCATTTTGCAAAATCA	0	65	0
AAATAATATTGAATTATCGAAAAATTTTATAGTTGTATAT	0	89	0
TAAAGGGATTGCTTTCTCTTGAAAACGTTTGACAACAAGA	0	141	1
AGATTTTTCCCAGTTATATTGCATTTTTCCTCTTTTTTTA	2	50	1
CCTTTATCGGGGGTTTTCTTTTAAGATTTTGAGAGTAAAA	3	21	1
CTCCGTCACGGCGTTGTCATATATTTTTATTATAAATGTA	4	17	1
AAATTATGTCGAATTATAATGAAAGAATGCGTATATTCTA	4	67	1
          *  ** ** *  **   * *
MAP Score: 2.13424