AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions023_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246883
 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
 AAAATTTAGCAGTTTACAGAGGCGATTTATCGGCG	0	9	1
GATTTATCGGCGGGTAAGACTATACAGTATCGGGAA	0	33	1
TATACAGTATCGGGAAAAAATTAAGAACGGTCAAAG	0	53	1
TTGGGCACAATGGGTAAATACGACCAAATAAGGCCA	0	138	0
AATTATTCCCCAGGTAACCACGGCGATCGCCAAGGA	0	191	1
GCCAAGGAGCTGGGTTAACGTTAGGGCAAGTCGGAT	0	266	1
CGCAGGGAAACGGGTTTTTGTCCGGGTAGATTTTAA	1	101	1
GAACTAATTCCAGTTTATCTTCTCGATTGGACTAGA	2	18	1
CGGCTTCAAGCAGTTGAGTTTGGGGGTTAGTTCCTC	2	78	1
AGTTCCTCGTTGGTTAATGGTGACGACCCCGGACGA	2	106	1
TGCCAACCCCCAGTTTACGTCGTCCGGGGTCGTCAC	2	125	0
GGTGAACCGGCAGGTGATTGTAGACGTTAACATTTA	3	16	0
AATCACCTGCCGGTTCACCGCACCTGTAATTGAGCG	3	33	1
CCAGAGGCCACGGTAAACAGCGACGGAGAGAAAGGG	3	109	1
          ***** *   *  ***
MAP Score: 7.6751

Motif 2
AAATAAGGCCAGGCAGAAGGATTTTGAATA	0	119	0
TCGGATTTGGGCACAATGGGTAAATACGAC	0	150	0
GCAGGATTAGGGAGAATGGGAAAAAATACT	0	235	0
CCCTAATCCTGCGGCCAAGGAGCTGGGTTA	0	253	1
TGACATTTAGGAGGAAAAGGTTTTGTCTAA	1	38	1
CAGACCTCGCAGGGAAACGGGTTTTTGTCC	1	94	1
GACTAGATTGAAAGCCAGGGCGGCATTAAT	2	47	1
ACAAAACCCAGAGGCCACGGTAAACAGCGA	3	102	1
GCCACGGTAAACAGCGACGGAGAGAAAGGG	3	115	1
ACAGCGACGGAGAGAAAGGGAAAAAGATTC	3	125	1
AATTTCAAAGGGGGGGTGGGAATCTTTTTC	3	144	0
CTAAGTGTTCAGGCAATAGGATATGATTGG	3	180	1
CTGAGCTAAAACAGAGAGGGCAAGACGAAC	3	234	1
          **********
MAP Score: 7.02485

Motif 3
AGAGGCGATTTATCGGCGGGTAAGACTATACAGT	0	27	1
ATTCTCCCTAATCCTGCGGCCAAGGAGCTGGGTT	0	248	1
GAGCTGGGTTAACGTTAGGGCAAGTCGGATGTCC	0	272	1
CAAGCAGTTGAGTTTGGGGGTTAGTTCCTCGTTG	2	84	1
CGGACGACGTAAACTGGGGGTTGGCAAATTTTGT	2	135	1
GGTTTTGTCTATGCCTGGGGGTAGAGTTTTTGCT	3	76	0
CATAGACAAAACCCAGAGGCCACGGTAAACAGCG	3	97	1
AGGCCACGGTAAACAGCGACGGAGAGAAAGGGAA	3	113	1
CCCGAATTTCAAAGGGGGGGTGGGAATCTTTTTC	3	144	0
CTGAGCTAAAACAGAGAGGGCAAGACGAAC    	3	234	1
          *  * ****** **
MAP Score: 6.11374

Motif 4
TCCAGATTCTTTGACCGTTCTTAATTTTTTC	0	66	0
TTGGTCGTATTTACCCATTGTGCCCAAATCC	0	147	1
CCGACCATTGTTGCCAATTATTCCCCAGGTA	0	176	1
TTAAGTATTTTTTCCCATTCTCCCTAATCCT	0	232	1
ATTGTAGACGTTAACATTTATGGCTT     	3	5	0
TGGGAATCTTTTTCCCTTTCTCTCCGTCGCT	3	127	0
   GTTCGTCTTGCCCTCTCTGTTTTAGCTC	3	236	0
          ****** ****
MAP Score: 5.09423

Motif 5
ACCCATTGTGCCCAAATCCGACCATTGTTGCCAATTATTCCC	0	159	1
CAATTATTCCCCAGGTAACCACGGCGATCGCCAAGGAAAGAT	0	190	1
TTCCCATTCTCCCTAATCCTGCGGCCAAGGAGCTGGGTTAAC	0	243	1
AAACCCGTTTCCCTGCGAGGTCTGCCTCCGTCAAATTGGCGA	1	76	0
GGAACTAACCCCCAAACTCAACTGCTTGAAGCCGAATTAATG	2	70	0
TTGCCAACCCCCAGTTTACGTCGTCCGGGGTCGTCACCATTA	2	120	0
      GATTCCAATCTTTAACGATGAAGGTCACAACAAAAT	2	162	0
ATAGACAAAACCCAGAGGCCACGGTAAACAGCGACGGAGAGA	3	98	1
          ***     *  ****    * *
MAP Score: 4.09873

Motif 6
TTAGCAGTTTACAGAGGCGATTTATCGGCGGGTAAGACTATACAG	0	15	1
AGATTCTTTGACCGTTCTTAATTTTTTCCCGATACTGTATAGTCT	0	49	0
AAATCCGACCATTGTTGCCAATTATTCCCCAGGTAACCACGGCGA	0	172	1
CAGACCTCGCAGGGAAACGGGTTTTTGTCCGGGTAGATTTTAAT 	1	94	1
TATCTTCTCGATTGGACTAGATTGAAAGCCAGGGCGGCATTAATT	2	33	1
GTCGTCCGGGGTCGTCACCATTAACCAACGAGGAACTAACCCCCA	2	98	0
CATAAATGTTAACGTCTACAATCACCTGCCGGTTCACCGCACCTG	3	14	1
GAGCGACATCATAGCAAAAACTCTACCCCCAGGCATAGACAAAAC	3	64	1
GACAAAACCCAGAGGCCACGGTAAACAGCGACGGAGAGAAAGGGA	3	101	1
          *  *     * *      ***** *
MAP Score: 4.06359

Motif 7
CCACAATCTAGTATTCAAAATCCTTCTGCCTGGCCTTATTTGGTC	0	108	1
TTGCCAATTATTCCCCAGGTAACCACGGCGATCGCCAAGGAAAGA	0	186	1
TTAAGTATTTTTTCCCATTCTCCCTAATCCTGCGGCCAAGGAGCT	0	232	1
CGATCGCCAATTTGACGGAGGCAGACCTCGCAGGGAAACGGGTTT	1	73	1
TCAACTGCTTGAAGCCGAATTAATGCCGCCCTGGCTTTCAATCTA	2	50	0
TACGTCGTCCGGGGTCGTCACCATTAACCAACGAGGAACTAACCC	2	101	0
TAATGGTGACGACCCCGGACGACGTAAACTGGGGGTTGGCAAATT	2	120	1
AGCCATAAATGTTAACGTCTACAATCACCTGCCGGTTCACCGCAC	3	11	1
GTAATTGAGCGACATCATAGCAAAAACTCTACCCCCAGGCATAGA	3	58	1
AACTCTACCCCCAGGCATAGACAAAACCCAGAGGCCACGGTAAAC	3	82	1
AAAACCCAGAGGCCACGGTAAACAGCGACGGAGAGAAAGGGAAAA	3	104	1
          *    **    **  *  *   ***
MAP Score: 3.27664

Motif 8
GGCGATTTATCGGCGGGTAAGACTATACAGT	0	30	1
GATTTGGGCACAATGGGTAAATACGACCAAA	0	146	0
GTAACCACGGCGATCGCCAAGGAAAGATTTA	0	204	1
GGATTAGGGAGAATGGGAAAAAATACTTAAA	0	231	0
CTCCCTAATCCTGCGGCCAAGGAGCTGGGTT	0	251	1
CTGGGTTAACGTTAGGGCAAGTCGGATGTCC	0	275	1
CGTAAACTGGGGGTTGGCAAATTTTGTTGTG	2	142	1
CAGGTGCGGTGAACCGGCAGGTGATTGTAGA	3	28	0
AGACAAAACCCAGAGGCCACGGTAAACAGCG	3	100	1
GCGACGGAGAGAAAGGGAAAAAGATTCCCAC	3	128	1
AGCTAAAACAGAGAGGGCAAGACGAAC    	3	237	1
          *** *******
MAP Score: 3.13281

Motif 9
CATTCTCCCTAATCCTGCGGCCAAGGAGCTGGGTTAACGTTA	0	247	1
TTTATTTGACATTTAGGAGGAAAAGGTTTTGTCTAAGCAATC	1	32	1
ACGGAGGCAGACCTCGCAGGGAAACGGGTTTTTGTCCGGGTA	1	87	1
CTAGATTGAAAGCCAGGGCGGCATTAATTCGGCTTCAAGCAG	2	49	1
CAAGCAGTTGAGTTTGGGGGTTAGTTCCTCGTTGGTTAATGG	2	84	1
AATGGTGACGACCCCGGACGACGTAAACTGGGGGTTGGCAAA	2	121	1
CCGGCAGGTGATTGTAGACGTTAACATTTATGGCTT      	3	4	0
TCGCTCAATTACAGGTGCGGTGAACCGGCAGGTGATTGTAGA	3	28	0
GGTTTTGTCTATGCCTGGGGGTAGAGTTTTTGCTATGATGTC	3	68	0
CCCGAATTTCAAAGGGGGGGTGGGAATCTTTTTCCCTTTCTC	3	136	0
TCGGGATCTAAGTGTTCAGGCAATAGGATATGATTGGTGTCA	3	173	1
          *  * ** **  *     * **
MAP Score: 2.08163

Motif 10
ACCGTTCTTAATTTTTTCCCGATACTGTATA	0	53	0
TTATTTGGTCGTATTTACCCATTGTGCCCAA	0	143	1
ATTGTTGCCAATTATTCCCCAGGTAACCACG	0	182	1
AGATTTAAGTATTTTTTCCCATTCTCCCTAA	0	228	1
AGGGAAACGGGTTTTTGTCCGGGTAGATTTT	1	104	1
TGCCCTCTCTGTTTTAGCTCAGTACATTTAA	3	225	0
          ****** ****
MAP Score: 1.78088