AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions013_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246565
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	hypothetical	167	hypothetical protein
#1	mannose-1-phosphate	165	mannose-1-phosphate guanyltransferase
#2	hypothetical	171	hypothetical protein
#3	rfbA	157	glucose-1-phosphate thymidylyltransferase

Motif 1
          ATTTCGCCGGAATCAGAATTT	0	0	1
ACGCCCCACTGGATTGCCTCAGGGGTTGAAC	0	81	0
AGTGGGGCGTGATTTACCTGAAATTTCCCGG	0	102	1
ATTTACCTGAAATTTCCCGGAGCAGTTATCC	0	113	1
TTCCCGGAGCAGTTATCCTGAGAGGAAGAAT	0	126	1
     CTGAAAATTTTCCTCACACAATTCTT	0	151	0
AGTCTATCAAGATTCTTCTCACTACTCCAAT	1	94	0
      CAACAATTTTCCTCAAACTCAATCA	1	150	0
TTACGCTGTTGTTTTGTCTGAAGTTCGGTGA	2	17	1
TGGTTTGGCTATTTTGCTTCAATTTCCCTAG	2	131	1
GCCCCATCTCAACTTGCCTGATATGTTTATT	3	57	0
ATCTGCCCGTAAATTGACTGATTTCGTGTCA	3	105	0
          ***** *****
MAP Score: 10.1015

Motif 2
ATTTCGCCGGAATCAGAATTTAAAAATTGGG	0	10	1
TTATCCTGAGAGGAAGAATTGTGTGAGGAAA	0	138	1
AGAATTGTGTGAGGAAAATTTTCAG      	0	152	1
GCTGGCGGGAAAGCAGAATCTATCTCCATCA	1	18	0
TGAAAGCTTGGAGGAGTAACTAACCCCATGG	1	54	0
TTGGAGTAGTGAGAAGAATCTTGATAGACTG	1	95	1
GATTGAGTTTGAGGAAAATTGTTG       	1	151	1
TCGGTGAATGGGTCAGAAATTGTTGGGGAGT	2	41	1
AGAAATTGTTGGGGAGTATTTTACAAACCTA	2	55	1
AGAGTTGAAAAAGTAGAAACTAGGGAAATTG	2	150	0
    AGGGCAAGGGAGCAATGGGTCGGTTAG	3	6	1
          *** *******
MAP Score: 8.85458

Motif 3
GGTTGAACGTCCGCTACCCTTAGAACTGTG	0	59	0
TTTCCCGGAGCAGTTATCCTGAGAGGAAGA	0	125	1
      CTGAAAATTTTCCTCACACAATTC	0	153	0
CTATCTCCATCATCTTTGCC          	1	0	0
GAGATAGATTCTGCTTTCCCGCCAGCGGTC	1	23	1
TCCAAGCTTTCAGCTATGCTTATTGGAGTA	1	73	1
       CAACAATTTTCCTCAAACTCAAT	1	152	0
      TTTTCCTTTACGCTGTTGTTTTGT	2	4	1
TCTGGTTTGGCTATTTTGCTTCAATTTCCC	2	129	1
TATTTTGCTTCAATTTCCCTAGTTTCTACT	2	140	1
TGCCCCATCTCAACTTGCCTGATATGTTTA	3	59	0
          **********
MAP Score: 8.08043

Motif 4
AGAATTTAAAAATTGGGCGGATTTTTACAAATCGT	0	24	1
GAGGCAATCCAGTGGGGCGTGATTTACCTGAAATT	0	92	1
GAGGAAGAATTGTGTGAGGAAAATTTTCAG     	0	147	1
TTATTGGAGTAGTGAGAAGAATCTTGATAGACTGG	1	92	1
ATCTTGATAGACTGGCGGGTGAGTTATGCCAACTT	1	112	1
TGTGTGATTGAGTTTGAGGAAAATTGTTG      	1	146	1
TTACGCTGTTGTTTTGTCTGAAGTTCGGTGAATGG	2	17	1
AAGTTCGGTGAATGGGTCAGAAATTGTTGGGGAGT	2	37	1
GTCAGAAATTGTTGGGGAGTATTTTACAAACCTAG	2	52	1
TTACAAACCTAGTTTGGATAAAATTGTTGAGCTTA	2	75	1
TGGTTTGGCTATTTTGCTTCAATTTCCCTAGTTTC	2	131	1
CTGATATGTTTATTGGTGGTGGCTTTTGCCTTCCC	3	36	0
          * ****  * ** **
MAP Score: 6.28478

Motif 5
GCCGGAATCAGAATTTAAAAATTGGGCGGATTTTTACAAATCG	0	15	1
CAACCCCTGAGGCAATCCAGTGGGGCGTGATTTACCTGAAATT	0	84	1
TATCCTGAGAGGAAGAATTGTGTGAGGAAAATTTTCAG     	0	139	1
          GGCAAAGATGATGGAGATAGATTCTGCTTTCCC	1	0	1
CAAGCTTTCAGCTATGCTTATTGGAGTAGTGAGAAGAATCTTG	1	75	1
GAAGAATCTTGATAGACTGGCGGGTGAGTTATGCCAACTTGTG	1	107	1
GCCAACTTGTGTGATTGAGTTTGAGGAAAATTGTTG       	1	139	1
CGGTGAATGGGTCAGAAATTGTTGGGGAGTATTTTACAAACCT	2	42	1
ACCTAGTTTGGATAAAATTGTTGAGCTTATAAGGAATTGAATA	2	81	1
GAATTGAATAGACAATCTGGTTTGGCTATTTTGCTTCAATTTC	2	114	1
CAACTTGCCTGATATGTTTATTGGTGGTGGCTTTTGCCTTCCC	3	36	0
AACATATCAGGCAAGTTGAGATGGGGCATAGAGATTTTTGATG	3	61	1
          *  *     * *****     **
MAP Score: 4.93044