AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions023_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246901
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	gap1	300	glyceraldehyde 3-phosphate dehydrogenase
#1	pgk	128	phosphoglycerate kinase
#2	tpi	188	triosephosphate isomerase
#3	gap2	254	glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)

Motif 1
TGTGATATGTCCAGATTCTTTGACCGTTCTTAATT	0	71	0
CTGGACATATCACAACCCACAATCTAGTATTCAAA	0	92	1
ATCTAGTATTCAAAATCCTTCTGCCTGGCCTTATT	0	113	1
CCCATTGTGCCCAAATCCGACCATTGTTGCCAATT	0	160	1
TCCCATTCTCCCTAATCCTGCGGCCAAGGAGCTGG	0	244	1
ATTGCTTAGACAAAACCTTTTCCTCCTAAATGTCA	1	38	0
CTACCCGGACAAAAACCCGTTTCCCTGCGAGGTCT	1	95	0
GAACTAACCCCCAAACTCAACTGCTTGAAGCCGAA	2	76	0
AAGGTCACAACAAAATTTGCCAACCCCCAGTTTAC	2	143	0
ACATCATAGCAAAAACTCTACCCCCAGGCATAGAC	3	69	1
CAGGCATAGACAAAACCCAGAGGCCACGGTAAACA	3	93	1
AGAAAGGGAAAAAGATTCCCACCCCCCCTTTGAAA	3	137	1
          ********     **
MAP Score: 10.4054

Motif 2
AGAGGCGATTTATCGGCGGGTAAGACTATACAG	0	27	1
TTTGAATACTAGATTGTGGGTTGTGATATGTCC	0	94	0
GTTGCCAATTATTCCCCAGGTAACCACGGCGAT	0	185	1
GAAACGGGTTTTTGTCCGGGTAGATTTTAAT  	1	107	1
CAAGCAGTTGAGTTTGGGGGTTAGTTCCTCGTT	2	84	1
CCAGTTTACGTCGTCCGGGGTCGTCACCATTAA	2	119	0
CGGACGACGTAAACTGGGGGTTGGCAAATTTTG	2	135	1
AGGTGCGGTGAACCGGCAGGTGATTGTAGACGT	3	25	0
GTTTTGTCTATGCCTGGGGGTAGAGTTTTTGCT	3	76	0
CCCGAATTTCAAAGGGGGGGTGGGAATCTTTTT	3	145	0
          *  ******** *
MAP Score: 6.44556

Motif 3
GGCGATTTATCGGCGGGTAAGACTATACAGTA	0	30	1
CCAATTATTCCCCAGGTAACCACGGCGATCGC	0	189	1
CAGGTAACCACGGCGATCGCCAAGGAAAGATT	0	201	1
GCTCCTTGGCCGCAGGATTAGGGAGAATGGGA	0	244	0
TTTGACATTTAGGAGGAAAAGGTTTTGTCTAA	1	36	1
GCCAATTTGACGGAGGCAGACCTCGCAGGGAA	1	78	1
AGGCAGACCTCGCAGGGAAACGGGTTTTTGTC	1	91	1
ATGGTGACGACCCCGGACGACGTAAACTGGGG	2	122	1
AAACTCTACCCCCAGGCATAGACAAAACCCAG	3	81	1
AGACAAAACCCAGAGGCCACGGTAAACAGCGA	3	100	1
TAAACAGCGACGGAGAGAAAGGGAAAAAGATT	3	122	1
          ****** * ***
MAP Score: 6.34953

Motif 4
TGGTTACCTGGGGAATAATTGGCAACAATG	0	181	0
TAGGGAGAATGGGAAAAAATACTTAAATCT	0	228	0
ATACAGTATCGGGAAAAAATTAAGAACGGT	0	54	1
CTATGCCTGGGGGTAGAGTTTTTGCTATGA	3	72	0
CGATCGCCAAGGAAAGATTTAAGTATTTTT	0	214	1
GGAGAGAAAGGGAAAAAGATTCCCACCCCC	3	133	1
GTTTTTGTCCGGGTAGATTTTAAT      	1	114	1
ACATTTAGGAGGAAAAGGTTTTGTCTAAGC	1	40	1
   CAGTGCCGGAACTAATTCCAGTTTATC	2	7	1
TCAGGCAATAGGATATGATTGGTGTCATTA	3	188	1
ATTTATCGGCGGGTAAGACTATACAGTATC	0	34	1
          **********
MAP Score: 6.3129

Motif 5
TTCAAAATCCTTCTGCCTGGCCTTATTTGGT	0	121	1
CGATCGCCGTGGTTACCTGGGGAATAATTGG	0	189	0
AGGGCAAGTCGGATGTCCTGGT         	0	288	1
CCTGCGAGGTCTGCCTCCGTCAAATTGGCGA	1	76	0
GACAAAAACCCGTTTCCCTGCGAGGTCTGCC	1	92	0
GGAAACGGGTTTTTGTCCGGGTAGATTTTAA	1	106	1
GCCGAATTAATGCCGCCCTGGCTTTCAATCT	2	51	0
CCCCAGTTTACGTCGTCCGGGGTCGTCACCA	2	123	0
TGGGTTTTGTCTATGCCTGGGGGTAGAGTTT	3	81	0
CTGTTTACCGTGGCCTCTGGGTTTTGTCTAT	3	98	0
CTTTTTCCCTTTCTCTCCGTCGCTGTTTACC	3	120	0
          GTTCGTCTTGCCCTCTCTGTT	3	243	0
          ** ********
MAP Score: 3.82184

Motif 6
AGAGGCGATTTATCGGCGGGTAAGACTATACAGT	0	27	1
AGTATTCAAAATCCTTCTGCCTGGCCTTATTTGG	0	117	1
ATTCTCCCTAATCCTGCGGCCAAGGAGCTGGGTT	0	248	1
GAGCTGGGTTAACGTTAGGGCAAGTCGGATGTCC	0	272	1
CAAGCAGTTGAGTTTGGGGGTTAGTTCCTCGTTG	2	84	1
CGGACGACGTAAACTGGGGGTTGGCAAATTTTGT	2	135	1
GTTTTGTCTATGCCTGGGGGTAGAGTTTTTGCTA	3	75	0
CATAGACAAAACCCAGAGGCCACGGTAAACAGCG	3	97	1
CCCGAATTTCAAAGGGGGGGTGGGAATCTTTTTC	3	144	0
CTGAGCTAAAACAGAGAGGGCAAGACGAAC    	3	234	1
          *  * ****** **
MAP Score: 3.68962

Motif 7
 AAAATTTAGCAGTTTACAGAGGCGATTTATCGGCGG	0	9	1
GCGGGTAAGACTATACAGTATCGGGAAAAAATTAAGA	0	42	1
AATTATTCCCCAGGTAACCACGGCGATCGCCAAGGAA	0	191	1
CCTAATCCTGCGGCCAAGGAGCTGGGTTAACGTTAGG	0	254	1
GGACAAAAACCCGTTTCCCTGCGAGGTCTGCCTCCGT	1	87	0
GAACTAATTCCAGTTTATCTTCTCGATTGGACTAGAT	2	18	1
CGGCTTCAAGCAGTTGAGTTTGGGGGTTAGTTCCTCG	2	78	1
GGGGTCGTCACCATTAACCAACGAGGAACTAACCCCC	2	99	0
CGACCCCGGACGACGTAAACTGGGGGTTGGCAAATTT	2	129	1
CCAGAGGCCACGGTAAACAGCGACGGAGAGAAAGGGA	3	109	1
TCCCACCCCCCCTTTGAAATTCGGGATCTAAGTGTTC	3	153	1
          * **  *    ******
MAP Score: 2.59046

Motif 8
TATTCAAAATCCTTCTGCCTGGCCTTATTTGGT	0	119	1
TTGTTGCCAATTATTCCCCAGGTAACCACGGCG	0	183	1
CTTTCCTTGGCGATCGCCGTGGTTACCTGGGGA	0	197	0
TAACGTTAACCCAGCTCCTTGGCCGCAGGATTA	0	256	0
TAGGGCAAGTCGGATGTCCTGGT          	0	287	1
AAAAACCCGTTTCCCTGCGAGGTCTGCCTCCGT	1	87	0
GGGAAACGGGTTTTTGTCCGGGTAGATTTTAAT	1	105	1
AGCCGAATTAATGCCGCCCTGGCTTTCAATCTA	2	50	0
CCCCCAGTTTACGTCGTCCGGGGTCGTCACCAT	2	122	0
ACAAAATTTGCCAACCCCCAGTTTACGTCGTCC	2	136	0
ACGTCTACAATCACCTGCCGGTTCACCGCACCT	3	25	1
TAGCAAAAACTCTACCCCCAGGCATAGACAAAA	3	75	1
CTTTTTCCCTTTCTCTCCGTCGCTGTTTACCGT	3	118	0
GAAAAAGATTCCCACCCCCCCTTTGAAATTCGG	3	144	1
          **  ***** ***
MAP Score: 2.39552