AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions015_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246627
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	trx	300	thioredoxin M
#1	ctaC	300	cytochrome c oxidase subunit II
#2	ctaD	88	cytochrome c oxidase subunit I
#3	ctaE	47	cytochrome c oxidase subunit III
#4	trxA	151	thioredoxin
#5	hypothetical	65	hypothetical protein
#6	trxM	40	thioredoxin M
#7	hypothetical	44	hypothetical protein
#8	eukaryotic	33	eukaryotic protein  kinase
#9	hypothetical	110	hypothetical protein

Motif 1
CATTAAGCTAGCCATCCCCCTAAGCACAGAA	3	21	0
CCACTTCACGGCGATCGCCCGTCGTCTGGGC	0	228	1
         AGCAATGCCCTATGCTCCTAGC	8	21	0
AACAAAAATTACAATCCCCTACAGGGTAAAG	1	254	0
GTATCAAGCGGCGATCGCCTGGGGCAATTTC	7	12	1
GTTTTCTGTTGCTAATCCCTCCCTAATCCTG	1	68	0
ACTGAATAGCCCAAACCCCTAAGTAATCAAA	4	111	1
GTAGGTTTGCCCTAACGCCCAAGGTCTTTCC	4	11	0
CTGGTAGCAGACTATTCCCCCAAAGCTCCGT	1	27	0
ATGTCATTGAGCCAACCGCCAATCATTTTTA	0	92	1
TGCAGGGGTAGAAATCCCCTTTATCAGCGAA	1	108	1
ACAGGGTAAAGCAATTCTCCAGAGCGGGGTC	1	234	0
GAGTCGGGTTGGCATTCCCTAGTCCTTCCAT	4	74	1
CCCTAGTCCTTCCATTGCCCAACTGAATAGC	4	90	1
         AGCAAACCTCTATCTCTCGGAA	1	288	0
CTGATCCCAACTGATCCCCTTGGTTTTGCTA	0	259	0
          ** ********
MAP Score: 13.522

Motif 2
GTCCTACGACGATTTTCCCTGGTTTAAAAACGCTC	0	39	1
TCTGGACGTAGATTTGACCTTGGACATCATCAAAC	0	132	1
CATCCTGAACGTTTTCCCCTAGTTTGTACTGAATC	0	166	1
CGATCGCCGTGAAGTGGCCTTTAACAAGCCAGGTA	0	210	0
CCACTTCACGGCGATCGCCCGTCGTCTGGGCTAGC	0	228	1
CTGATCCCAACTGATCCCCTTGGTTTTGCTAGCCC	0	255	0
TGGTAGCAGACTATTCCCCCAAAGCTCCGTGCGAT	1	22	0
TGCAGGGGTAGAAATCCCCTTTATCAGCGAAGACA	1	108	1
GAACTCTGAAGAATTTGGCTGGAGCTTGACCCCGC	1	207	1
ACAGGGTAAAGCAATTCTCCAGAGCGGGGTCAAGC	1	230	0
CATTAAGCTAGCCATCCCCCTAAGCACAGAAAGTT	3	17	0
TCACAAGGTAGGTTTGCCCTAACGCCCAAGGTCTT	4	14	0
GAGTCGGGTTGGCATTCCCTAGTCCTTCCATTGCC	4	74	1
GTATCAAGCGGCGATCGCCTGGGGCAATTTCGGTG	7	12	1
         AGCAATGCCCTATGCTCCTAGCTTGT	8	17	0
TACGGAGCTAGGTTTTAGCTCATCCAAAGTTTCTA	9	26	0
          *  ******* *  *
MAP Score: 12.2163

Motif 3
TTTCTGTGCTTAGGGGGATGGCTAGCTTAAT	3	20	1
GGCTATTCAGTTGGGCAATGGAAGGACTAGG	4	91	0
GCTAGGAGCATAGGGCATTGCT         	8	21	1
CTTTACCCTGTAGGGGATTGTAATTTTTGTT	1	254	1
TTTGATTACTTAGGGGTTTGGGCTATTCAGT	4	111	0
CACGGAGCTTTGGGGGAATAGTCTGCTACCA	1	26	1
TGGAAAGACCTTGGGCGTTAGGGCAAACCTA	4	10	1
ATAAAAATGATTGGCGGTTGGCTCAATGACA	0	93	0
GGCGATCGCCTGGGGCAATTTCGGTGTTGAA	7	21	1
TTCGCTGATAAAGGGGATTTCTACCCCTGCA	1	108	0
CAGTACAAACTAGGGGAAAACGTTCAGGATG	0	166	0
          * *********
MAP Score: 11.2831

Motif 4
GGGAAAATCGTCGTAGGACAAAAATAACTCA	0	27	0
GCGTTTTTAAACCAGGGAAAATCGTCGTAGG	0	41	0
CGTAGATTTGACCTTGGACATCATCAAACAT	0	138	1
TTCAGTACAAACTAGGGGAAAACGTTCAGGA	0	168	0
GCTAGCCCAGACGACGGGCGATCGCCGTGAA	0	232	0
GGCTAGCAAAACCAAGGGGATCAGTTGGGAT	0	256	1
ATCGCACGGAGCTTTGGGGGAATAGTCTGCT	1	22	1
GCTTGACCCCGCTCTGGAGAATTGCTTTACC	1	230	1
AACTTTCTGTGCTTAGGGGGATGGCTAGCTT	3	17	1
   TGGAAAGACCTTGGGCGTTAGGGCAAAC	4	7	1
TCTTTTGATTACTTAGGGGTTTGGGCTATTC	4	114	0
TAATATCTTTGCGAGGGAAAATACC      	6	25	1
AGCGGCGATCGCCTGGGGCAATTTCGGTGTT	7	18	1
AGCTGGACAAGCTAGGAGCATAGGGCATTGC	8	11	1
AAGAATAGAAACTTTGGATGAGCTAAAACCT	9	21	1
          **** ******
MAP Score: 5.40006

Motif 5
AAAAATGATTGGCGGTTGGCTCAATGACAT	0	92	0
GCCACTTCACGGCGATCGCCCGTCGTCTGG	0	227	1
GCAAAACCAAGGGGATCAGTTGGGATCAGT	0	261	1
ATTATCGCACGGAGCTTTGGGGGAATAGTC	1	19	1
AGGATTAGGGAGGGATTAGCAACAGAAAAC	1	69	1
CGCTGATAAAGGGGATTTCTACCCCTGCAG	1	107	0
GAATTTGGCTGGAGCTTGACCCCGCTCTGG	1	217	1
ACCCCGCTCTGGAGAATTGCTTTACCCTGT	1	235	1
TCCGAGAGATAGAGGTTTGCT         	1	289	1
TCTGTGCTTAGGGGGATGGCTAGCTTAATG	3	22	1
     TGGAAAGACCTTGGGCGTTAGGGCA	4	5	1
TGGAAGGACTAGGGAATGCCAACCCGACTC	4	74	0
TGATTACTTAGGGGTTTGGGCTATTCAGTT	4	110	0
GGTATCAAGCGGCGATCGCCTGGGGCAATT	7	11	1
CTAGGAGCATAGGGCATTGCT         	8	22	1
AAATAAATACGGAGCTAGGTTTTAGCTCAT	9	38	0
         GGGGCCTCTCCTCGGCTTAAT	9	99	0
          **********
MAP Score: 5.00018

Motif 6
TTTGTCCTACGACGATTTTCCCTGGTTTAAAAAC	0	36	1
CTCTGGTAAAACATATTTTCAATGTCATTGAGCC	0	71	1
GCCAACCGCCAATCATTTTTATTGGCCCGATCTG	0	102	1
ATTAGCAACAGAAAACATTCGTTGCTGCAGGGGT	1	83	1
AAAGAACTCTGAAGAATTTGGCTGGAGCTTGACC	1	204	1
TGTAGGGGATTGTAATTTTTGTTGTTTTCCGAGA	1	262	1
GAGTCGTACTGGTCAGTTTTGCTTTAAAACCCTG	2	32	1
TGTAAATTTTGACAAATTTGGTAGAAAACTTTTT	2	64	1
CCTTGTGATGGGTTAATTTCGTGGGATGATAGAG	4	41	1
TTAATACTCTGCTTATTTTCAGTGTAACGGATGG	5	19	0
CGATCGCCTGGGGCAATTTCGGTGTTGAACC   	7	23	1
TACTAAGAATAGAAACTTTGGATGAGCTAAAACC	9	17	1
          **  * ***** **
MAP Score: 4.70969

Motif 7
CCTACGACGATTTTCCCTGGTTTAAAAACGCTCTGGTAAAACA	0	41	1
GTAAAACATATTTTCAATGTCATTGAGCCAACCGCCAATCATT	0	76	1
TCCTGAACGTTTTCCCCTAGTTTGTACTGAATCTTAATTAATT	0	168	1
TGAAGTGGCCTTTAACAAGCCAGGTAATTAATTAAGATTCAGT	0	193	0
TGGCTGGAGCTTGACCCCGCTCTGGAGAATTGCTTTACCCTGT	1	222	1
GGAGAATTGCTTTACCCTGTAGGGGATTGTAATTTTTGTTGTT	1	245	1
ATTTTTGTTGTTTTCCGAGAGATAGAGGTTTGCT         	1	276	1
TTTGTCAAAATTTACAGGGTTTTAAAGCAAAACTGACCAGTAC	2	37	0
CCCTGTAAATTTTGACAAATTTGGTAGAAAACTTTTT      	2	61	1
ACTCTGCTTATTTTCAGTGTAACGGATGGGAGTGTTGG     	5	5	0
     GGTATTTTCCCTCGCAAAGATATTAATCCAGTTCTAAC	6	12	0
          *** **  *    * *    * *
MAP Score: 2.97428

Motif 8
GATCGCCCGTCGTCTGGGCTAGCAAAACCAA	0	240	1
GATCAGTCCTCCCTTTGGGGTCGAAA     	0	284	1
ATCGCACGGAGCTTTGGGGGAATAGTCTGCT	1	22	1
ACATTCGTTGCTGCAGGGGTAGAAATCCCCT	1	97	1
GCTTGACCCCGCTCTGGAGAATTGCTTTACC	1	230	1
ATTGCTTTACCCTGTAGGGGATTGTAATTTT	1	250	1
AACTTTCTGTGCTTAGGGGGATGGCTAGCTT	3	17	1
AAGACCTTGGGCGTTAGGGCAAACCTACCTT	4	14	1
ATTACTTAGGGGTTTGGGCTATTCAGTTGGG	4	107	0
AAGCGGCGATCGCCTGGGGCAATTTCGGTGT	7	17	1
          ********* *
MAP Score: 0.711194