AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions025_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241419
 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	appB	75	oligopeptide ABC transporter (permease)
#3	oppB	107	oligopeptide ABC transporter (permease)
#4	dppA	128	dipeptide ABC transporter

Motif 1
AGCTCCCCTTTCCCCCCTCTTGTTGTCAAAC	0	167	0
    TAGATATTCCCCCTCTTGAAATGTTCG	1	70	0
GAAAACGCTCTCCCTCCCCTTTAAGGGAAAT	2	10	0
GGAGAGCGTTTTCTCCCTCTTCTGTTTTTAA	2	28	1
GTAGTGTGCATACCCCCTCTCAAAGCTGTGC	1	18	0
        GCTAGCTCCCCTTTCCCCCCTCT	0	178	0
      ATACTTGTCCCCCTTTACTTTCCTT	2	60	0
TTATATTGCATTTTTCCTCTTTTTTTAATAT	4	63	1
ATATGGGGCTTTTCTCCCCATATACCTTGAG	3	33	0
TGATTGAGATTTTTCCCAGTTATATTGCATT	4	44	1
ATAAAGGGATTGCTTTCTCTTGAAAACGTTT	0	140	1
          * *********
MAP Score: 23.757

Motif 2
CTAGCTCCCCTTTCCCCCCTCTTGTTGTCAAA	0	168	0
ATGTAGTGTGCATACCCCCTCTCAAAGCTGTG	1	19	0
      TAGATATTCCCCCTCTTGAAATGTTC	1	71	0
GAAAACGCTCTCCCTCCCCTTTAAGGGAAAT 	2	9	0
AGGGAGAGCGTTTTCTCCCTCTTCTGTTTTTA	2	26	1
      ATACTTGTCCCCCTTTACTTTCCTTA	2	59	0
TATGGGGCTTTTCTCCCCATATACCTTGAGGT	3	31	0
ATGATTGAGATTTTTCCCAGTTATATTGCATT	4	43	1
TTATATTGCATTTTTCCTCTTTTTTTAATATA	4	63	1
          ** ******* *
MAP Score: 13.9122

Motif 3
TTTATCCTAAAAAATTCTTGATTTTGCAAAATGATTGTAAT	0	47	1
AATTATCGAAAAATTTTATAGTTGTATATTATTACAATCAT	0	77	0
AAATTTTTCGATAATTCAATATTATTTATTATTTCTGAATA	0	102	1
CCCCTCTTGAAATGTTCGTTCTTCTAGGCTGTTGTTTATGT	1	47	0
TGTCCCCCTTTACTTTCCTTATTAAAAACAGAAGAGGGAGA	2	39	0
AGCCCCATATACCTTTCTTACTGATGGAGTATAAAAATGTA	3	54	1
TCCTTGAAAGAGGATTCTTTTTTTATCACTGAATGATTGAG	4	11	1
GTTATATTGCATTTTTCCTCTTTTTTTAATATAATTTGTTA	4	62	1
AATTTGTTAGAATATTCATAATTTAGTAAAAAAGGAGGAGC	4	94	1
          *   *** *  ** *  *  *
MAP Score: 7.80584

Motif 4
ATCCTAAAAAATTCTTGATTTTGCAAAATGATTGT	0	50	1
AACTATAAAATTTTTCGATAATTCAATATTATTTA	0	95	1
AATATTATTTATTATTTCTGAATAAAGGGATTGCT	0	119	1
AATAAAGGGATTGCTTTCTCTTGAAAACGTTTGAC	0	139	1
CTTCTAGGCTGTTGTTTATGTAGTGTGCATACCCC	1	33	0
TCCCTCTTCTGTTTTTAATAAGGAAAGTAAAGGGG	2	41	1
CCCATATACCTTTCTTACTGATGGAGTATAAAAAT	3	57	1
AAGAGGATTCTTTTTTTATCACTGAATGATTGAGA	4	18	1
ACGCTCCTCCTTTTTTACTAAATTATGAATATTCT	4	102	0
          *** ** ** * * *
MAP Score: 0.966584