AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions012_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246521
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	hypothetical	140	hypothetical protein
#1	hypothetical	41	hypothetical protein
#2	hypothetical	167	hypothetical protein
#3	hypothetical	216	hypothetical protein
#4	hypothetical	197	hypothetical protein
#5	hypothetical	300	hypothetical protein

Motif 1
AACCTTAACAGAGTCTCTTTCCAAGACTGACCA	0	31	0
TCTCTTCAGTTGGCCGCCAGCCCGACGTTTTTT	2	103	1
TGGTGTACGGTTGCCATTTTCCCTGGTCGTGTT	2	141	1
CCATTTTCCCTGGTCGTGTTCCC          	2	154	1
TCCAGTTGGTTGGACACTTTCAAGATACCGTCC	3	82	1
TGCATCCAGTTGATCCCATTCCCAACTCCAGAT	3	186	1
GGCTAAACGGGGAACTTTTGCCCCCGTAACTAG	4	74	0
AGTTCCCCGTTTAGCCCTAGCCCAAGGGTAAGG	4	91	1
CCAAGCAAAATAGTCCCTTACCCTTGGGCTAGG	4	106	0
GATGATTGACTGACCTTTTGCCAATTTTGCCTG	4	173	1
TTATAGTTTTTGCTCACTTCCCCTAGCTGATCT	5	19	1
GAGTAATTTTTGACCTTTATCCCCTCAAATTAA	5	215	1
          *** * *** ***
MAP Score: 13.3821

Motif 2
TTAAATGGGGTCGTCATTTGGTCAGTCTTGGAA	0	13	1
TTTTTTTGAGGACACGTTTCGCCTAAGTAAATT	0	67	1
TGGGGCGATCGCCGGATTTATCCATCTTCCTTG	2	26	0
GGCCGCCAGCCCGACGTTTTTTCCCACTGGTGT	2	114	1
TGGTGTACGGTTGCCATTTTCCCTGGTCGTGTT	2	141	1
CCATTTTCCCTGGTCGTGTTCCC          	2	154	1
GGGCAAAAGTTCCCCGTTTAGCCCTAGCCCAAG	4	84	1
CCAAGCAAAATAGTCCCTTACCCTTGGGCTAGG	4	106	0
GGATGATTGACTGACCTTTTGCCAATTTTGCCT	4	172	1
TTATAGTTTTTGCTCACTTCCCCTAGCTGATCT	5	19	1
GGGCAGCGCATGGTGGTTTCTCCAGGCAAAAGT	5	64	0
GGTCAAAAATTACTCCATTGTCCGCACTTAAAT	5	197	0
GGAGTAATTTTTGACCTTTATCCCCTCAAATTA	5	214	1
          * * ***** ***
MAP Score: 10.0669

Motif 3
AATTTACTTAGGCGAAACGTGTCCTCAAAA	0	70	0
AATTAAACATGGCGGTAAGTCTCTTCAGTT	2	84	1
CAGAAGACCTGGAAATAATTAAACCGTCCA	3	56	1
AGATTACCGCGGAGAAAATTTACAATGAGT	3	156	1
TAGTTACGGGGGCAAAAGTTCCCCGTTTAG	4	75	1
CTTGGGCTAGGGCTAAACGGGGAACTTTTG	4	87	0
AGGCAAAATTGGCAAAAGGTCAGTCAATCA	4	175	0
GGTTTCTCCAGGCAAAAGTCAGAATTAGTC	5	53	0
ACCTGTTCTTGGCTATAGGCAGGGCAGGAA	5	126	0
TAATTTGAGGGGATAAAGGTCAAAAATTAC	5	217	0
          **********
MAP Score: 5.83829

Motif 4
GAAAGAGACTCTGTTAAGGTTAAGTTTTTTTGAGGACA	0	43	1
GAAGCATGATATTAGAATATATGATTTTACTCGTAATA	0	101	1
TCCGCAGATAATGCAAATATTCTTTTTTAAATTGACAG	3	21	1
TCGTTAATTGCTAGTAAGTTTAGTCTTTGTGAGTTGAA	4	21	1
CCCTAGCCCAAGGGTAAGGGACTATTTTGCTTGGAAAC	4	105	1
        AGCTAATAATTATAGTTTTTGCTCACTTCC	5	2	1
TAGCTGATCTCGACTAATTCTGACTTTTGCCTGGAGAA	5	42	1
CTGCCCTTGGCTATTAATTCTTAGTTTTTTTTTCTTTC	5	91	1
GATTTAAGTGCGGACAATGGAGTAATTTTTGACCTTTA	5	196	1
CTTAATTTACCTAGAAAGCCAAGATTTTGATCCTTATT	5	264	1
          **   ***  *   ****
MAP Score: 5.52706

Motif 5
TTTGAGGACACGTTTCGCCTAAGTAAATTT	0	71	1
TAAGTCTCTTCAGTTGGCCGCCAGCCCGAC	2	99	1
GTACGGTTGCCATTTTCCCTGGTCGTGTTC	2	145	1
        ATAATTTCGCCTCCGCAGATAA	3	2	1
GTCGGAAGTCAAGTTCACCGGGGCGCAATA	3	120	1
ACGGGGGCAAAAGTTCCCCGTTTAGCCCTA	4	80	1
ACCTTTTGCCAATTTTGCCTGA        	4	185	1
AGTTTTTGCTCACTTCCCCTAGCTGATCTC	5	23	1
          **********
MAP Score: 5.22976

Motif 6
TCTTGGAAAGAGACTCTGTTAAGGTTAAGT	0	38	1
GTTAAGGTTAAGTTTTTTTGAGGACACGTT	0	55	1
TAATGCAAATATTCTTTTTTAAATTGACAG	3	29	1
TCCCAACTCCAGATTTTTTTA         	3	205	1
TAGTAAGTTTAGTCTTTGTGAGTTGAATTT	4	32	1
TAATAATTATAGTTTTTGCTCACTTCCCCT	5	13	1
ATTAATTCTTAGTTTTTTTTTCTTTCCTGC	5	103	1
TAGAAAGCCAAGATTTTGATCCTTATTTAA	5	275	1
          **********
MAP Score: 1.64706

Motif 7
GTACACCAGTGGGAAAAAACGTCGGGCTGG	2	119	0
CTAGTTACGGGGGCAAAAGTTCCCCGTTTA	4	74	1
CCTTACCCTTGGGCTAGGGCTAAACGGGGA	4	94	0
AGGCAAAATTGGCAAAAGGTCAGTCAATCA	4	175	0
        TCAGGCAAAATTGGCAAAAGGT	4	185	0
AGGGGAAGTGAGCAAAAACTATAATTATTA	5	13	0
GGTTTCTCCAGGCAAAAGTCAGAATTAGTC	5	53	0
AAGAATTAATAGCCAAGGGCAGCGCATGGT	5	83	0
CCCTGCCTATAGCCAAGAACAGGTAGAAAT	5	132	1
TTACCTAGAAAGCCAAGATTTTGATCCTTA	5	270	1
          **********
MAP Score: 0.886835