AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions026_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246993
 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
ATCACCATTACCATTGGAGGGAAAGACGTTGAACT	0	25	0
CAAATTCCCGCCGTTGGCCGCAAATCCTCTGGACG	3	84	1
CGTTGCCGAACCCTAGGGGGCAAATTGGCTTCGGA	0	117	1
CCAGGCTTTTCCCCAGGGCTGACCGAATTCTGCTT	1	54	0
GGCCGCAAATCCTCTGGACGAAATTTTTCCTTTAA	3	99	1
GTAAAGCAGACCAAGGGTGACCCCGGTAAAAACAG	1	157	1
GCTTGACAAACCGCAGACCGTAAAGCAGACCAAGG	1	138	1
TGATCATCTCCCACAGGGCGGCATTGTACAGCTAC	3	49	0
AATGCCTACACCAGCGGCCATAATTTTGTTCCTCG	1	208	1
GGAAAATTTGGCGGGGGGCAGAAATGCCAATACAA	2	124	1
GGGCAAATTGGCTTCGGACTGACATCCAATTACTG	0	134	1
ACCAGTGACCCCATCGATGTCAACGATGTACTCTA	3	183	1
CATTGCCAGACCAGAGGCCAAACCA          	2	0	0
GTTCGGCAACGCATCGGCGTTCCCTAGCTTAAATT	0	93	0
CCCGAAAATCCCTTTGTGGTTAAAGGAAAAATTTC	3	118	0
CAAATTAGGGGCAGGGAAGACCAAGCTAAATTGTA	2	154	0
AAGCGAGCCTTCTTTGGACATCAAGATAATTTAAG	0	66	1
          **   ** ** ****
MAP Score: 17.6089

Motif 2
ATTAAACAAGTTCAACGTCTTTCCCTCCAATGGTAATGGTGA	0	17	1
GGTTCGGCAACGCATCGGCGTTCCCTAGCTTAAATTATCTTG	0	87	0
GGAACGCCGATGCGTTGCCGAACCCTAGGGGGCAAATTGGCT	0	105	1
TGAACAGTAATTGGATGTCAGTCCGAAGCCAATTTGCCCCCT	0	131	0
GCTGACCGAATTCTGCTTCAAACCATTGCCGGAATTTGGCAC	1	30	0
TTTGAAGCAGAATTCGGTCAGCCCTGGGGAAAAGCCTGGCAA	1	50	1
CCCTGGGGAAAAGCCTGGCAACCCAACCCAGACCAGTTCTCA	1	71	1
TGGGTTAGATCAGCTTGACAAACCGCAGACCGTAAAGCAGAC	1	126	1
TAATTGTTTGCTATTGTACGATCCAGCGCCACCGATTGAACC	1	260	1
TCGCCTAGCAACCATTGCCAGACCAGAGGCCAAACCA     	2	5	0
AAATTAACAAACTGTCGCCCTTCCACTGACCATGGTAACGAT	2	57	1
TGTTTTTTACTTCCTTGACTAACCGAGGAAAATTTGGCGGGG	2	98	1
TAAATTGTATTGGCATTTCTGCCCCCCGCCAAATTTTCCTCG	2	121	0
AATACAATTTAGCTTGGTCTTCCCTGCCCCTAATTTGTCCCC	2	152	1
          TTTTGCCCCACTCCTTGGAAAAATTACCAGCT	3	0	1
ATCGTAGCTGTACAATGCCGCCCTGTGGGAGATGATCACAAA	3	46	1
GGGAGATGATCACAAATTCCCGCCGTTGGCCGCAAATCCTCT	3	72	1
TATGGACGTAACTGGATTCGAACCAGTGACCCCATCGATGTC	3	162	1
          * *   * *   **   *** *
MAP Score: 14.9392

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
TTTCGGGAATCACCATTACCATTGGAGGGA	0	38	0
TTGGCACCTTAACCAGTTCTTGGGGGC   	1	7	0
TTCTGCTTCAAACCATTGCCGGAATTTGGC	1	32	0
ACCCAACCCAGACCAGTTCTCAGTTAACCT	1	91	1
AAAATGCCTACACCAGCGGCCATAATTTTG	1	206	1
CTATTGTACGATCCAGCGCCACCGATTGAA	1	270	1
CCACCGATTGAACCAGCAACTT        	1	288	1
ACCATTGCCAGACCAGAGGCCAAACCA   	2	7	0
ATCGCCTAGCAACCATTGCCAGACCAGAGG	2	18	0
ACTGGTTCGAATCCAGTTACGTCCATAAAC	3	159	0
ACTGGATTCGAACCAGTGACCCCATCGATG	3	172	1
          **********
MAP Score: 12.1131

Motif 5
ACAAGTTCAACGTCTTTCCCTCCAATGGTAATGGTGATT	0	22	1
CAGTCCGAAGCCAATTTGCCCCCTAGGGTTCGGCAACGC	0	116	0
       GCCCCCAAGAACTGGTTAAGGTGCCAAATTCC	1	3	1
TGGTTAAGGTGCCAAATTCCGGCAATGGTTTGAAGCAGA	1	22	1
CTTCAGGTTAACTGAGAACTGGTCTGGGTTGGGTTGCCA	1	86	0
AAACCGCAGACCGTAAAGCAGACCAAGGGTGACCCCGGT	1	145	1
  TGGTTTGGCCTCTGGTCTGGCAATGGTTGCTAGGCGA	2	8	1
CAAACTGTCGCCCTTCCACTGACCATGGTAACGATGTTT	2	64	1
GGAGATGATCACAAATTCCCGCCGTTGGCCGCAAATCCT	3	73	1
AACTTGTTCCCCGAAAATCCCTTTGTGGTTAAAGGAAAA	3	123	0
TGGATTCGAACCAGTGACCCCATCGATGTCAACGATGTA	3	174	1
          **  *   *** *   ***
MAP Score: 11.4384

Motif 6
GAAGCCAATTTGCCCCCTAGGGTTCGGCAACG	0	117	0
TCAACGTCTTTCCCTCCAATGGTAATGGTGAT	0	28	1
GATCACAAATTCCCGCCGTTGGCCGCAAATCC	3	79	1
AGCTGTACAATGCCGCCCTGTGGGAGATGATC	3	51	1
TACGATCCAGCGCCACCGATTGAACCAGCAAC	1	276	1
AGGTGCCAAATTCCGGCAATGGTTTGAAGCAG	1	28	1
CCCGAAAGCGAGCCTTCTTTGGACATCAAGAT	0	61	1
AGTACATCGTTGACATCGATGGGGTCACTGGT	3	183	0
TTTTTACCGGGGTCACCCTTGGTCTGCTTTAC	1	157	0
          **** ** ****
MAP Score: 7.00123

Motif 7
CAACGTCTTTCCCTCCAATGGTAATGGTGATTCC	0	29	1
CCGAAAGCGAGCCTTCTTTGGACATCAAGATAAT	0	62	1
GGACTGACATCCAATTACTGTTCACTATTTTTCA	0	149	1
CAGGCTTTTCCCCAGGGCTGACCGAATTCTGCTT	1	54	0
AGCCTGGCAACCCAACCCAGACCAGTTCTCAGTT	1	82	1
TAATTTTGTTCCTCGCTTTGATAAAAACGTTGTA	1	228	1
CGCCTAGCAACCATTGCCAGACCAGAGGCCAAAC	2	12	0
AAACTGTCGCCCTTCCACTGACCATGGTAACGAT	2	65	1
GCCAAATTTTCCTCGGTTAGTCAAGGAAGTAAAA	2	102	0
   TTTTGCCCCACTCCTTGGAAAAATTACCAGC	3	7	1
ATCACAAATTCCCGCCGTTGGCCGCAAATCCTCT	3	80	1
AACCAGTGACCCCATCGATGTCAACGATGTACTC	3	182	1
          ***  * *** ***
MAP Score: 6.58111

Motif 8
GCTAGGGAACGCCGATGCGTTGCCGAACCCTAGG	0	100	1
GGGGCAAATTGGCTTCGGACTGACATCCAATTAC	0	133	1
GCCAAATTCCGGCAATGGTTTGAAGCAGAATTCG	1	32	1
GTTTGAAGCAGAATTCGGTCAGCCCTGGGGAAAA	1	49	1
GTCAGCCCTGGGGAAAAGCCTGGCAACCCAACCC	1	66	1
AGATCAGCTTGACAAACCGCAGACCGTAAAGCAG	1	132	1
   TGGTTTGGCCTCTGGTCTGGCAATGGTTGCT	2	7	1
AATTTCAACAGGCGATCGCCTAGCAACCATTGCC	2	28	0
ACAAACTGTCGCCCTTCCACTGACCATGGTAACG	2	63	1
AGGAAAATTTGGCGGGGGGCAGAAATGCCAATAC	2	123	1
GAGGATTTGCGGCCAACGGCGGGAATTTGTGATC	3	79	0
GCCGTTGGCCGCAAATCCTCTGGACGAAATTTTT	3	93	1
          ***   ** *****
MAP Score: 4.1852

Motif 9
ACGCCGATGCGTTGCCGAACCCTAGGGGGCA	0	108	1
GGCTTTTCCCCAGGGCTGACCGAATTCTGCT	1	55	0
TCTGGGTTGGGTTGCCAGGCTTTTCCCCAGG	1	72	0
GTTTGTCAAGCTGATCTAACCCATCTTCAGG	1	118	0
GTTAGATCAGCTTGACAAACCGCAGACCGTA	1	129	1
TGCCAGACCAGAGGCCAAACCA         	2	1	0
CCTAGCAACCATTGCCAGACCAGAGGCCAAA	2	13	0
GCCTGTTGAAATTAACAAACTGTCGCCCTTC	2	49	1
TTTTTACTTCCTTGACTAACCGAGGAAAATT	2	101	1
TTAGCTTGGTCTTCCCTGCCCCTAATTTGTC	2	160	1
          **** ******
MAP Score: 1.01888

Motif 10
AGCGAGCCTTCTTTGGACATCAAGATAATTTAAGCTAGGGAACG	0	67	1
GGCAAATTGGCTTCGGACTGACATCCAATTACTGTTCACTATTT	0	135	1
GGTCTGGGTTGGGTTGCCAGGCTTTTCCCCAGGGCTGACCGAAT	1	61	0
CCGGGGTCACCCTTGGTCTGCTTTACGGTCTGCGGTTTGTCAAG	1	139	0
ATGCCTACACCAGCGGCCATAATTTTGTTCCTCGCTTTGATAAA	1	209	1
        TGGTTTGGCCTCTGGTCTGGCAATGGTTGCTAGGCG	2	2	1
ATACAATTTAGCTTGGTCTTCCCTGCCCCTAATTTGTCCCCTCC	2	153	1
AAATTCCCGCCGTTGGCCGCAAATCCTCTGGACGAAATTTTTCC	3	85	1
          * **** *     * *  *    *
MAP Score: 0.434911