AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions022_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246849
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	hypothetical	163	hypothetical protein
#1	hypothetical	107	hypothetical protein
#2	ycf37	227	ycf37 gene product
#3	hypothetical	124	hypothetical protein

Motif 1
TTACAACCGGCGATCGCCAAAAATCCGGGGCCA	0	29	1
CACTGGCGGGGTTTGGCCCCGGATTTTTGGCGA	0	42	0
CATGGTTTACCCATCCCCGGGGATTATCAACAC	0	72	0
GATGGGTAAACCATGGCCTAGAATAATTGTCAG	0	90	1
TTGTCAGTAAGTGTCGCCCCCGTAATCCGTCAA	0	116	1
TCAACAGTGACCGTCACCCCATTTTAGG     	0	145	1
AGGTGTTGGGCCCTACCCTATTTAACCTAATGA	1	17	1
GAGACTGTAACGTTCCCCCACGACGGCTCAAAA	1	75	1
CTATCCCTCTCGATCGCCGAAGAAACGTTAACA	2	50	1
TAGGAAAATGCTCTGGCCTAGGTTGTTAACGTT	2	73	0
CTGGGGTTAGCGATCGCCAAAGATGTTGGCCGT	2	140	1
GCCGTCGGGGCCGTTGCCTATTTTGTCGCCCGT	2	168	1
CCCGTTAATTCTTTCACCGAAGTATTAAGTTCA	2	196	1
          ** ***** * **
MAP Score: 16.2906

Motif 2
TTACAACCGGCGATCGCCAAAAATCCGGGGC	0	29	1
TGACGGATTACGGGGGCGACACTTACTGACA	0	117	0
CGTTCCCCCACGACGGCTCAAAACATTGATC	1	85	1
CTATCCCTCTCGATCGCCGAAGAAACGTTAA	2	50	1
CTGGGGTTAGCGATCGCCAAAGATGTTGGCC	2	140	1
GCAACGGCCCCGACGGCCAACATCTTTGGCG	2	154	0
          ******** **
MAP Score: 7.0444

Motif 3
CCCCGGATTTTTGGCGATCGCCGGTTGTAATT	0	27	0
CCAAAAATCCGGGGCCAAACCCCGCCAGTGTT	0	45	1
CCCGCCAGTGTTGATAATCCCCGGGGATGGGT	0	65	1
AGGCCATGGTTTACCCATCCCCGGGGATTATC	0	77	0
CGGGGATGGGTAAACCATGGCCTAGAATAATT	0	86	1
TAATTGTCAGTAAGTGTCGCCCCCGTAATCCG	0	113	1
CCGTCAACAGTGACCGTCACCCCATTTTAGG 	0	142	1
AAATAGGGTAGGGCCCAACACCTTGGTGGT  	1	8	0
CTGGGAGACTGTAACGTTCCCCCACGACGGCT	1	71	1
ACAATACATTTCACCGTAGGCTGCTTCTCTAT	2	22	1
AGAAACGTTAACAACCTAGGCCAGAGCATTTT	2	70	1
CGATCGCTAACCCCAGAAGCCCATTGTACGTG	2	124	0
GCTTCTGGGGTTAGCGATCGCCAAAGATGTTG	2	136	1
ATAGGCAACGGCCCCGACGGCCAACATCTTTG	2	157	0
TTGGCCGTCGGGGCCGTTGCCTATTTTGTCGC	2	165	1
TAGCCTGATCTTGCCTATACCCA         	3	111	1
          * ***** ****
MAP Score: 4.58363

Motif 4
GCCAAAAATCCGGGGCCAAACCCCGCCAGTGT	0	44	1
GACAATTATTCTAGGCCATGGTTTACCCATCC	0	89	0
CACCAAGGTGTTGGGCCCTACCCTATTTAACC	1	12	1
CGTTAACAACCTAGGCCAGAGCATTTTCCTAG	2	75	1
TGTTGGCCGTCGGGGCCGTTGCCTATTTTGTC	2	163	1
GGATTGGGAACTGTGCCAAAGATATCAAAGAT	3	33	0
          ********  **
MAP Score: 4.11671

Motif 5
AACCGGCGATCGCCAAAAATCCGGGGCCAAACCCC	0	33	1
CAGTAAGTGTCGCCCCCGTAATCCGTCAACAGTGA	0	120	1
TCCCCCACGACGGCTCAAAACATTGATCG      	1	88	1
  TGGAGGCTCGTCACAATACATTTCACCGTAGGC	2	8	1
CCCTCTCGATCGCCGAAGAAACGTTAACAACCTAG	2	54	1
GGTTAGCGATCGCCAAAGATGTTGGCCGTCGGGGC	2	144	1
TTAATTCTTTCACCGAAGTATTAAGTTCACTGTTC	2	200	1
CTTTGTTTACCGGCTATGTATGTTGCAATACTTTT	3	76	1
          **** *****    *
MAP Score: 0.743324

Motif 6
GTAATTTAGAATCTGCCACTACC         	0	1	0
GCCAAAAATCCGGGGCCAAACCCCGCCAGTGT	0	44	1
GACAATTATTCTAGGCCATGGTTTACCCATCC	0	89	0
ATTAGGTTAAATAGGGTAGGGCCCAACACCTT	1	16	0
CGTTAACAACCTAGGCCAGAGCATTTTCCTAG	2	75	1
TTCCATCTCACTAGGAAAATGCTCTGGCCTAG	2	85	0
GGGCGACAAAATAGGCAACGGCCCCGACGGCC	2	167	0
     TGGGTATAGGCAAGATCAGGCTAAAAA	3	107	0
          ******** * *
MAP Score: 0.489462