AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions026_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246974
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	aroK	191	shikimate kinase
#1	aroB	300	3-dehydroquinate synthase
#2	aroA	187	3-phosphoshikimate 1-carboxyvinyltransferase
#3	aroE	279	shikimate 5-dehydrogenase

Motif 1
TCACCATTACCATTGGAGGGAAAGACGTTGAACTTGTTTAATCG	0	15	0
CAAGATAATTTAAGCTAGGGAACGCCGATGCGTTGCCGAACCCT	0	87	1
AGGGGGCAAATTGGCTTCGGACTGACATCCAATTACTGTTCACT	0	131	1
GTGCCAAATTCCGGCAATGGTTTGAAGCAGAATTCGGTCAGCCC	1	30	1
TGAGAACTGGTCTGGGTTGGGTTGCCAGGCTTTTCCCCAGGGCT	1	69	0
GTCTGCTTTACGGTCTGCGGTTTGTCAAGCTGATCTAACCCATC	1	124	0
     TGGTTTGGCCTCTGGTCTGGCAATGGTTGCTAGGCGATC	2	5	1
ATCGTTACCATGGTCAGTGGAAGGGCGACAGTTTGTTAATTTCA	2	55	0
CCCCGCCAAATTTTCCTCGGTTAGTCAAGGAAGTAAAAAACATC	2	96	0
CGAGGAAAATTTGGCGGGGGGCAGAAATGCCAATACAATTTAGC	2	121	1
GGGGACAAATTAGGGGCAGGGAAGACCAAGCTAAATTGTATTGG	2	150	0
AGAGGATTTGCGGCCAACGGCGGGAATTTGTGATCATCTCCCAC	3	70	0
          * ***   **   * *   *   *
MAP Score: 16.3673

Motif 2
CCGAACCCTAGGGGGCAAATTGGCTTCGGACT	0	122	1
TTCAAACCATTGCCGGAATTTGGCACCTTAAC	1	24	0
CTACACCAGCGGCCATAATTTTGTTCCTCGCT	1	213	1
GTCAGTGGAAGGGCGACAGTTTGTTAATTTCA	2	55	0
TTGACTAACCGAGGAAAATTTGGCGGGGGGCA	2	112	1
ATTTGGCGGGGGGCAGAAATGCCAATACAATT	2	129	1
       GGAGGGGACAAATTAGGGGCAGGGA	2	172	0
ATCTCCCACAGGGCGGCATTGTACAGCTACGA	3	47	0
TGCGGCCAACGGCGGGAATTTGTGATCATCTC	3	74	0
TCCCGCCGTTGGCCGCAAATCCTCTGGACGAA	3	89	1
CAAATCCTCTGGACGAAATTTTTCCTTTAACC	3	104	1
AGGGATTTTCGGGGAACAAGTTTATGGACGTA	3	140	1
ACAAGTTTATGGACGTAACTGGATTCGAACCA	3	155	1
TTGACATCGATGGGGTCACTGGTTCGAATCCA	3	174	0
          GGGGAGCAATTGTTAATTTAAA	3	267	0
          ***** ** ***
MAP Score: 15.5951

Motif 3
ATTACCATTGGAGGGAAAGACGTTGAACTT	0	24	0
GCCGAACCCTAGGGGGCAAATTGGCTTCGG	0	121	1
CGGTCAGCCCTGGGGAAAAGCCTGGCAACC	1	64	1
TTATCAAAGCGAGGAACAAAATTATGGCCG	1	222	0
GTCAGTGGAAGGGCGACAGTTTGTTAATTT	2	57	0
AAAATTTGGCGGGGGGCAGAAATGCCAATA	2	126	1
GGGGACAAATTAGGGGCAGGGAAGACCAAG	2	164	0
        GGAGGGGACAAATTAGGGGCAG	2	175	0
TTTCCAAGGAGTGGGGCAAAA         	3	1	0
ATCTCCCACAGGGCGGCATTGTACAGCTAC	3	49	0
AGGGATTTTCGGGGAACAAGTTTATGGACG	3	140	1
          GGGGAGCAATTGTTAATTTA	3	269	0
          **********
MAP Score: 12.7955

Motif 4
GAGGGAAAGACGTTGAACTTGTTTAATCGCCAT	0	11	0
      GCCCCCAAGAACTGGTTAAGGTGCCAA	1	4	1
GGTGCCAAATTCCGGCAATGGTTTGAAGCAGAA	1	29	1
TTGATAAAAACGTTGTAATTGTTTGCTATTGTA	1	245	1
TGGCCTCTGGTCTGGCAATGGTTGCTAGGCGAT	2	15	1
GGTCTTCCCTGCCCCTAATTTGTCCCCTCC   	2	167	1
ACGATAATTAGCTGGTAATTTTTCCAAGGAGTG	3	18	0
TGCGGCCAACGGCGGGAATTTGTGATCATCTCC	3	73	0
CAAATCCTCTGGACGAAATTTTTCCTTTAACCA	3	104	1
         GGGGAGCAATTGTTAATTTAAATG	3	265	0
          **  * *******
MAP Score: 7.31565

Motif 5
ACCATTACCATTGGAGGGAAAGACGTTGAACTTGT	0	22	0
CCTAGGGTTCGGCAACGCATCGGCGTTCCCTAGCT	0	99	0
GTAATTGGATGTCAGTCCGAAGCCAATTTGCCCCC	0	132	0
CGAATTCTGCTTCAAACCATTGCCGGAATTTGGCA	1	31	0
GCCAGGCTTTTCCCCAGGGCTGACCGAATTCTGCT	1	55	0
AGAACTGGTCTGGGTTGGGTTGCCAGGCTTTTCCC	1	76	0
AGATCAGCTTGACAAACCGCAGACCGTAAAGCAGA	1	132	1
CCGTAAAGCAGACCAAGGGTGACCCCGGTAAAAAC	1	155	1
AAGTTGCTGGTTCAATCGGTGGCGCTGGATCGTAC	1	275	0
AGCAACCATTGCCAGACCAGAGGCCAAACCA    	2	6	0
CGTTACCATGGTCAGTGGAAGGGCGACAGTTTGTT	2	62	0
AGGAAAATTTGGCGGGGGGCAGAAATGCCAATACA	2	123	1
GGACAAATTAGGGGCAGGGAAGACCAAGCTAAATT	2	157	0
CTGGTAATTTTTCCAAGGAGTGGGGCAAAA     	3	5	0
TGTGATCATCTCCCACAGGGCGGCATTGTACAGCT	3	51	0
TGATCACAAATTCCCGCCGTTGGCCGCAAATCCTC	3	78	1
CGTAACTGGATTCGAACCAGTGACCCCATCGATGT	3	168	1
          * **  ***  ****
MAP Score: 6.4973

Motif 6
CCCCTAGGGTTCGGCAACGCATCGGCGTTCCCTAGCT	0	99	0
GTGCCAAATTCCGGCAATGGTTTGAAGCAGAATTCGG	1	30	1
GGGGAAAAGCCTGGCAACCCAACCCAGACCAGTTCTC	1	75	1
AAACCGCAGACCGTAAAGCAGACCAAGGGTGACCCCG	1	145	1
AAGGGTGACCCCGGTAAAAACAGCAATATAACCAATA	1	169	1
GGCCTCTGGTCTGGCAATGGTTGCTAGGCGATCGCCT	2	16	1
TTTCTGCCCCCCGCCAAATTTTCCTCGGTTAGTCAAG	2	111	0
CGATAATTAGCTGGTAATTTTTCCAAGGAGTGGGGCA	3	13	0
          **** **     ** **
MAP Score: 5.3528

Motif 7
TTCAACGTCTTTCCCTCCAATGGTAATGGTGATTC	0	27	1
GTTCACTATTTTTCAACCTCTGTAACTTTTGCC  	0	168	1
AGCAGAATTCGGTCAGCCCTGGGGAAAAGCCTGGC	1	55	1
CATAATTTTGTTCCTCGCTTTGATAAAAACGTTGT	1	226	1
TACGATCCAGCGCCACCGATTGAACCAGCAACTT 	1	276	1
        TGGTTTGGCCTCTGGTCTGGCAATGGT	2	2	1
ACAAACTGTCGCCCTTCCACTGACCATGGTAACGA	2	63	1
AGCTGTACAATGCCGCCCTGTGGGAGATGATCACA	3	51	1
TGATCACAAATTCCCGCCGTTGGCCGCAAATCCTC	3	78	1
CGTAACTGGATTCGAACCAGTGACCCCATCGATGT	3	168	1
          ****  **  *** *
MAP Score: 0.325838