AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_fusions004_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944234398
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	mbhS1	300	hydrogenase small subunit
#1	mbhS3	120	hydrogenase small subunit
#2	mbhS2	300	hydrogenase small subunit

Motif 1
      TTTACAGGAACGGGATAGAAATAG	0	4	1
GCGCCTGCGGCGGGCACGGGCAGTGTACTT	0	37	1
TTATAAGTACCTTGCAAGAAGTACACTGCC	0	55	0
CTGGAAGAAAACGGCATGGATCCCGAAACG	0	135	1
GGCATGGATCCCGAAACGGAGAGGCTTTCG	0	147	1
TCAGTTTAGCCTGACACGAAAGCCTCTCCG	0	163	0
GTCAGGCTAAACTGAACGGAAAAGGCGACG	0	178	1
TAATAAGAAACTTGAATGAATTATCATTCA	0	244	1
AATTTATTAATTGGCACGGGGTGTAGCGCA	1	31	1
TGGTAGCGCGCTGGCATGGGGGGCCAGAGG	1	63	1
ATAGTATACAGGGGAAGGGAAGTTCCCGAA	2	27	0
CTTACGCAAAAGAGCACGGAATAGACGGCT	2	74	0
TTTACGAAGAAGGGAACGAGGTTATTGACG	2	113	0
AGTTGTAGATCTGGAAGGGACGACCCACGA	2	178	0
AATCAAGTTTATGGAAAGGATAGGAGCTTT	2	208	0
          **********
MAP Score: 14.7776

Motif 2
GCAAGGTACTTATAATTTCGGGTTCCGAAAA	0	70	1
AAGGAAGGTAAATAACCACGTCGCCTTTTCC	0	195	0
TTTTTTAGTATACACTTTCGTGAATGATAAT	0	263	0
CCAAAAGTTTTATAATTTATTAATTGGCACG	1	18	1
CCTTCCCCTGTATACTATCGTGTAGACTATC	2	39	1
CCTTAACGTCAATAACCTCGTTCCCTTCTTC	2	107	1
AAATGCCCTCTATAACTTCGTTTAACTTTTC	2	140	1
AGTCAAAGGGTATAATCAAGTTTATGGAAAG	2	220	0
TTAAGTTAAAAATAATGACTTGGATCATGTT	2	266	0
          ****** ****
MAP Score: 5.10556

Motif 3
ACCTTGCAAGAAGTACACTGCCCGTGCCCGCCGC	0	43	0
CCGAAATTATAAGTACCTTGCAAGAAGTACACTG	0	57	0
GACACTCTGGAAGAAAACGGCATGGATCCCGAAA	0	129	1
TACCTTCCTTAAGGAATTTTTATGATTTTAATAA	0	216	1
TGATTTTAATAAGAAACTTGAATGAATTATCATT	0	238	1
          AGGAAAGTGGTCGGGGTGACCGGA	1	106	0
TCTTTTGCGTAAGTAACCTTAACGTCAATAACCT	2	91	1
          *** ** *** * *
MAP Score: 4.47812

Motif 4
TTACCTTCCTTAAGGAATTTTTATGATTTTAATA	0	215	1
ATGATTTTAATAAGAAACTTGAATGAATTATCAT	0	237	1
GAATTATCATTCACGAAAGTGTATACTAAAAAAA	0	261	1
   AGCAAATTCCAAAAGTTTTATAATTTATTAA	1	7	1
CTCTTTTGCGTAAGTAACCTTAACGTCAATAACC	2	90	1
TCCTATCCTTTCCATAAACTTGATTATACCCTTT	2	213	1
CCCTTTGACTTCAAAAATTTTGACAAACATGATC	2	241	1
ATGATCCAAGTCATTATTTTTAACTTAAAGGAGG	2	269	1
          ***  ** *** **
MAP Score: 0.030886