AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions025_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246945
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	appB	130	oligopeptide transport system permease protein
#1	era	300	GTP-binding protein Era
#2	appB	166	oligopeptide transport system permease protein
#3	hypothetical	300	hypothetical protein

Motif 1
GCAATCCCCTGAAAAATTAAGCTTAGATCGG	0	11	1
CAGTTACAGAAAAAATTCCCCTTTTTGTGCT	0	79	1
AAAGATACCCAAAAAATCAATATCACCATGA	1	57	1
CAACCAGAGGAAAAAGTCAAGGAGGTAAACT	1	202	0
GAAAAACGTTAAAAACTCCACTGAGTTAATC	1	232	0
AATCAAGCCTAAAAATTCCTTAGTTTATGGA	1	273	0
        TGAAAAAATCAAGCCTAAAAATT	1	287	0
TATTGACTAGGAAAAATCCCCAGATAGGATC	2	117	1
ACTGCCCAGGGAAAAATTCACTTTCAACCCC	3	146	1
GAAGTTTTGTGAAAATTCTCCTTTGCAAAGG	3	183	1
TCGTACCATTGAAAAATCTATCGGAATTCCT	3	211	0
          ***** *****
MAP Score: 12.3292

Motif 2
TATCACAAAAGTTTAAGCTGTCAGTTACAGAAA	0	58	1
CGTGGTATTGGTTTCGGCGGTAACGC       	1	3	0
TCTTTTTAGCTATGCGGCTGTAGGAGCGTGGTA	1	29	0
ATTCCACAAGGGCCAAGATGAAGGATTACCGAA	1	105	1
CATATTTTTTTGTCAAGCTGGCAAGCCGTTTTC	1	160	1
GCAAGCCGTTTTCCAGGCGGATAGTTTACCTCC	1	180	1
AGAGGAAAAAGTCAAGGAGGTAAACTATCCGCC	1	195	0
GTTTATGGAGGGTCAAGCGGAAAAACGTTAAAA	1	249	0
GCCTTTTCTTGGTGCAGATGCCGATCGCCAGGG	2	76	0
AACTTCGCTATGCAAGGCAGTGGCAACCAACAA	3	52	1
GTGATAGAGAGAAAAGGCGGTTGAGTATATCAT	3	102	0
TGGGCAGTCAGTCTAGGGTGTGATAGAGAGAAA	3	121	0
    GGTAATGGTTAGGCTGTCATCCAAAAACT	3	281	0
          *** ******  *
MAP Score: 7.20419

Motif 3
CCGATCTAAGCTTAATTTTTCAGGGGATTG	0	12	0
TAACTGACAGCTTAAACTTTTGTGATAGGC	0	55	0
TCATGGTGATATTGATTTTTTGGGTATCTT	1	58	0
AATCCTTCATCTTGGCCCTTGTGGAATCCC	1	102	0
AGTTTACCTCCTTGACTTTTTCCTCTGGTT	1	202	1
CGTTTTTCCGCTTGACCCTCCATAAACTAA	1	255	1
AATTTTTAGGCTTGATTTTTTCA       	1	287	1
TCAATATAGCCTAAGCCTTTTCTTGGTGCA	2	93	0
AGGAATTCCGATAGATTTTTCAATGGTACG	3	211	1
CATCCAAAAACTTGGTCTTTAACCTAGTCC	3	263	0
          **********
MAP Score: 5.87116

Motif 4
TCTAAGCTTAATTTTTCAGGGGATTGCC    	0	6	0
CCTCCTTGACTTTTTCCTCTGGTTGATTAACT	1	208	1
GTTTTTAACGTTTTTCCGCTTGACCCTCCATA	1	247	1
CGAGGACCCATTGCTCCCTGGCGATCGGCATC	2	61	1
TATCTGGGGATTTTTCCTAGTCAATATAGCCT	2	111	0
TGAAAGTGAATTTTTCCCTGGGCAGTCAGTCT	3	140	0
TTTTGTGAAAATTCTCCTTTGCAAAGGAATTC	3	187	1
ATTCCGATAGATTTTTCAATGGTACGACGCTT	3	215	1
          *******  ***
MAP Score: 5.69685

Motif 5
ATCTCGCATAGCCTATCACAAAAGTTTAAGCT	0	45	1
TCCTACAGCCGCATAGCTAAAAAGATACCCAA	1	37	1
CCAAGAAAAGGCTTAGGCTATATTGACTAGGA	2	97	1
AGGCTATATTGACTAGGAAAAATCCCCAGATA	2	111	1
CGTCTTATATGCCCATGATATACTCAACCGCC	3	88	1
TAGACTGACTGCCCAGGGAAAAATTCACTTTC	3	139	1
GATTTTCTCGGACTAGGTTAAAGACCAAGTTT	3	254	1
          *******  ***
MAP Score: 4.39943

Motif 6
CTAAGCTTAATTTTTCAGGGGATTGCC      	0	4	0
TGGCAAGCCGTTTTCCAGGCGGATAGTTTACCT	1	178	1
CCTCCTTGACTTTTTCCTCTGGTTGATTAACTC	1	208	1
GTTTTTAACGTTTTTCCGCTTGACCCTCCATAA	1	247	1
TATCTGGGGATTTTTCCTAGTCAATATAGCCTA	2	110	0
GAAAGTGAATTTTTCCCTGGGCAGTCAGTCTAG	3	138	0
GAAAATTCTCCTTTGCAAAGGAATTCCGATAGA	3	193	1
TTCCGATAGATTTTTCAATGGTACGACGCTTTT	3	216	1
GGTACGACGCTTTTCCAAAGATTTTCTCGGACT	3	235	1
          *******  ** *
MAP Score: 2.85222