AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions025_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246959
 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
CCGATCTAAGCTTAATTTTTCAGGGGATTGC	0	11	0
AGCACAAAAAGGGGAATTTTTTCTGTAACTG	0	79	0
TCATGGTGATATTGATTTTTTGGGTATCTTT	1	57	0
AGTTTACCTCCTTGACTTTTTCCTCTGGTTG	1	202	1
GATTAACTCAGTGGAGTTTTTAACGTTTTTC	1	232	1
TCCATAAACTAAGGAATTTTTAGGCTTGATT	1	273	1
AATTTTTAGGCTTGATTTTTTCA        	1	287	1
GATCCTATCTGGGGATTTTTCCTAGTCAATA	2	117	0
CGGGGTTGAAAGTGAATTTTTCCCTGGGCAG	3	147	0
CCTTTGCAAAGGAGAATTTTCACAAAACTTC	3	183	0
AGGAATTCCGATAGATTTTTCAATGGTACGA	3	211	1
          ***** *****
MAP Score: 13.3076

Motif 2
ACCGCCGAAACCAATACCACGCTCCTACAGCCG	1	15	1
AAAAAGATACCCAAAAAATCAATATCACCATGA	1	55	1
GCCAGCTTGACAAAAAAATATGTTGGGTTAACC	1	149	0
AAAAATCAAGCCTAAAAATTCCTTAGTTTATGG	1	274	0
CAGTTCCTGTCAAACAAATACGTTCCTAACCTT	2	19	1
GGCATCTGCACCAAGAAAAGGCTTAGGCTATAT	2	87	1
TTGAGGAAAACAAATAACTTCGCTATGCAAGGC	3	37	1
GCAGTGGCAACCAACAAAAACGTCTTATATGCC	3	68	1
AGGCTGTCATCCAAAAACTTGGTCTTTAACCTA	3	267	0
          **** ****  **
MAP Score: 5.85787

Motif 3
TTAATTTTTCAGGGGATTGCC         	0	1	0
AGCACAAAAAGGGGAATTTTTTCTGTAACT	0	80	0
ACGAATCATTAAGGGATTCCACAAGGGCCA	1	90	1
TCCATAAACTAAGGAATTTTTAGGCTTGAT	1	273	1
TCCTAACCTTAGCGGATTCCGAGGACCCAT	2	42	1
AGATCCTATCTGGGGATTTTTCCTAGTCAA	2	119	0
CGGGGTTGAAAGTGAATTTTTCCCTGGGCA	3	148	0
CCTTTGCAAAGGAGAATTTTCACAAAACTT	3	184	0
CTCCTTTGCAAAGGAATTCCGATAGATTTT	3	200	1
          **********
MAP Score: 4.86816

Motif 4
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 5
      GGCAATCCCCTGAAAAATTAAGCTTAG	0	4	1
TATCTCGCATAGCCTATCACAAAAGTTTAAGCT	0	44	1
AACCCCACTGTGCCATTCGGTAATCCTTCATCT	1	120	0
GCAAGCCGTTTTCCAGGCGGATAGTTTACCTCC	1	180	1
CCTTGACTTTTTCCTCTGGTTGATTAACTCAGT	1	211	1
TTCGGCTCAGTTCCTGTCAAACAAATACGTTCC	2	12	1
TAGGCTATATTGACTAGGAAAAATCCCCAGATA	2	110	1
CCCTCGCTGTTTACCGGGAAATC          	3	0	0
TGGTTGCCACTGCCTTGCATAGCGAAGTTATTT	3	48	0
ACGTCTTATATGCCCATGATATACTCAACCGCC	3	87	1
CTAGACTGACTGCCCAGGGAAAAATTCACTTTC	3	138	1
CAAAACTTCTTGACCGGGGTTGAAAGTGAATTT	3	159	0
AAAAGCGTCGTACCATTGAAAAATCTATCGGAA	3	216	0
          ***** *** * *
MAP Score: 2.85833