AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions017_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246674
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	narB	300	nitrate reductase
#1	hoxU	26	hydrogenase subunit
#2	hypothetical	40	hypothetical protein
#3	hoxF	76	hydrogenase subunit
#4	potential	300	potential NAD-reducing hydrogenase subunit

Motif 1
TGACAGTGATAATCAGCTTTGCTACTATCGCAATAGTG	0	52	1
TGCCATCAATAATTATCTGCTGTAATTTATTGCCACTA	0	85	0
CGCCAGGAAAAATCAGTTTTTCCTTATTCCAGGTGCCA	0	118	0
CCTCAGGACAAATTAACTATTAAAGTTTTTCACTGCGA	0	179	1
TATTAACTGTATTCATCTTTTGGTCAATTAGTGGTCAA	0	235	1
AATTCGCTTCAATTAACTGCCAATATTTTA        	0	280	1
AAGATCAAGCAATCACCTGATACTTAATATCCG     	3	5	0
TTGTTGCTTAAAACAACTTTTTCGTTGTCTAAATTATC	4	31	1
TTCATTGTTACATCAACTTTTAAAAAGTGAGCAAATCT	4	101	0
TCGCAATCAAATTTACCTGGTTTAGGCTCTCCCAATCA	4	232	1
AGGCTCTCCCAATCATCTTTTATCTGCTGTATTGCTCC	4	255	1
          ***** *** *      *
MAP Score: 12.1376

Motif 2
GTAGCAAAGCTGATTATCACTGTCATGGATCGAG	0	43	0
TTACAGCAGATAATTATTGATGGCACCTGGAATA	0	98	1
AATCAGTTTTTCCTTATTCCAGGTGCCATCAATA	0	112	0
AAGGAAAAACTGATTTTTCCTGGCGAACAGTTAT	0	131	1
TGGCGAACAGTTATTATTTTGGGCTAGCCCTCAG	0	151	1
         TTCATTTTCAAAGGAGTTTTTGGCC	1	1	1
GAGATTCCATTCGTTATTGTGGGCAAGATTGTGG	4	151	1
          * ******   ***
MAP Score: 4.58708

Motif 3
AGCTTTGCTACTATCGCAATAGTGGCAATA	0	66	1
GTCCTGAGGGCTAGCCCAAAATAATAACTG	0	158	0
GTTGTCTAAATTATCCCGATTAAGTAATCG	4	54	1
CCTCCACAATCTTGCCCACAATAACGAATG	4	158	0
CACACAAATTCTTTCCCGACTAAGGGTGAA	4	188	1
ATCAGGCTAACTTTCGCAATCAAATTTACC	4	219	1
CTGGTTTAGGCTCTCCCAATCATCTTTTAT	4	248	1
          **********
MAP Score: 3.88507

Motif 4
GCCATCAATAATTATCTGCTGTAATTTATTGCC	0	89	0
AAAAACTGATTTTTCCTGGCGAACAGTTATTAT	0	135	1
CGAACAGTTATTATTTTGGGCTAGCCCTCAGGA	0	154	1
     TGCAATTTATTTGAACTATTTTTGTTGC	4	5	1
ATTTGAACTATTTTTGTTGCTTAAAACAACTTT	4	18	1
TAAAACAACTTTTTCGTTGTCTAAATTATCCCG	4	39	1
ATTCCATTCGTTATTGTGGGCAAGATTGTGGAG	4	154	1
CGCAATCAAATTTACCTGGTTTAGGCTCTCCCA	4	233	1
CCAATCATCTTTTATCTGCTGTATTGCTCCTTT	4	263	1
          ***** ***  **
MAP Score: 2.64041