AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID077_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391674
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	hyaA	300	hydrogenase-1 small subunit
#1	b2997	188	putative hydrogenase subunit

Motif 1
TTACTCGTTTAGCAACCGGCTAAACATCCC	0	24	1
AAACATCCCCACCGCCCGGCCAAAAGAAAA	0	45	1
AATACTTTCTGGCGACGTGCGCCAGTGCAG	0	156	1
ATGGTCGGCAAGCGACGTCCCTGTAGCAAG	0	233	0
GCCGACCATAAGCGCCCGGTGTCCTGCCGG	0	254	1
CGCAAGGAGGAGAGACGTGCGAT       	0	287	1
CCTTCGTTTTAGCGCCCCGCCGCAGTATCA	1	59	1
          **********
MAP Score: 11.8519

Motif 2
AATTCCTTCTCTTTTACTCGTTTAGCAACCGGCTAAACATC	0	11	1
ATTAACAATACTTTCTGGCGACGTGCGCCAGTGCAGAAGGA	0	150	1
TCACGTGAAGCGATGGTTTGCCTTGCTACAGGGACGTCGCT	0	212	1
ACACCGGGCGCTTATGGTCGGCAAGCGACGTCCCTGTAGCA	0	235	0
    ATCGCACGTCTCTCCTCCTTGCGACACCGGCAGGACA	0	273	0
TTCTTCCCTTCGTTTTAGCGCCCCGCCGCAGTATCATGATA	1	53	1
          ***     ** *  **  * *
MAP Score: 7.16226

Motif 3
ACCATAAGCGCCCGGTGTCCTGCCGGTGTC	0	258	1
GCTAAACATCCCCACCGCCCGGCCAAAAGA	0	42	1
GTTTTAGCGCCCCGCCGCAGTATCATGATA	1	64	1
CCGGTGTCCTGCCGGTGTCGCAAGGAGGAG	0	269	1
GGCGACGTGCGCCAGTGCAGAAGGATGAGC	0	166	1
CTTATGGTCGGCAAGCGACGTCCCTGTAGC	0	236	0
          **********
MAP Score: 3.58204