AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_fusions004_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944234409
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	mbhS1	300	hydrogenase small subunit
#1	aq_796	41	putative protein
#2	mbhS3	120	hydrogenase small subunit
#3	mbhS2	300	hydrogenase small subunit

Motif 1
CTGTCTATTTCTATCCCGTTCCTGTAAA   	0	7	0
ACCACGTCGCCTTTTCCGTTCAGTTTAGCCT	0	181	0
ACAAAGCCGTCTATTCCGTGCTCTTTTGCGT	3	70	1
TTCCGAAAATCTGTACCCTGCGGAGTTCGAA	0	92	1
GTTTCGGGATCCATGCCGTTTTCTTCCAGAG	0	133	0
GTCAATAACCTCGTTCCCTTCTTCGTAAATG	3	114	1
CGGGAACTTCCCTTCCCCTGTATACTATCGT	3	29	1
GACACGAAAGCCTCTCCGTTTCGGGATCCAT	0	150	0
AGTACACTGCCCGTGCCCGCCGCAGGCGCTG	0	35	0
CTTCGTTTAACTTTTCCGTTATCTCGTGGGT	3	155	1
AACTAAAGCTCCTATCCTTTCCATAAACTTG	3	204	1
ATCTCGTGGGTCGTCCCTTCCAGATCTACAA	3	175	1
CACCTGCGCTACACCCCGTGCCAATTAATAA	2	34	0
ATAAACTTGATTATACCCTTTGACTTCAAAA	3	226	1
CGACGTGGTTATTTACCTTCCTTAAGGAATT	0	203	1
TGGATTTTATACTACCCGTGTATACAATAAT	1	15	1
          **** ******
MAP Score: 12.4552

Motif 2
GCGACCTCTGGCCCCCCATGCCAGCGCGCTAC	2	65	0
TATCTCGTGGGTCGTCCCTTCCAGATCTACAA	3	174	1
AACTAAAGCTCCTATCCTTTCCATAAACTTGA	3	204	1
CAAGAAGTACACTGCCCGTGCCCGCCGCAGGC	0	39	0
CTATCACAAAGCCGTCTATTCCGTGCTCTTTT	3	65	1
CACCTGCGCTACACCCCGTGCCAATTAATAAA	2	33	0
CTGTCTATTTCTATCCCGTTCCTGTAAA    	0	6	0
AAATAACCACGTCGCCTTTTCCGTTCAGTTTA	0	185	0
ATTCTTCGGGAACTTCCCTTCCCCTGTATACT	3	23	1
GACACGAAAGCCTCTCCGTTTCGGGATCCATG	0	149	0
TCTCCGTTTCGGGATCCATGCCGTTTTCTTCC	0	137	0
          *** *** ****
MAP Score: 12.2028

Motif 3
GTACACTGCCCGTGCCCGCCGCAGGCGCTG	0	35	0
CTTGCAAGAAGTACACTGCCCGTGCCCGCC	0	45	0
CCGAAAATCTGTACCCTGCGGAGTTCGAAG	0	94	1
ACCACCTGCGCTACACCCCGTGCCAATTAA	2	37	0
CCGGCGACCTCTGGCCCCCCATGCCAGCGC	2	70	0
GTTCGAGTCCGGTCACCCCGACCACTTTCC	2	99	1
TCTTCGGGAACTTCCCTTCCCCTGTATACT	3	25	1
CAATAACCTCGTTCCCTTCTTCGTAAATGC	3	116	1
TCTCGTGGGTCGTCCCTTCCAGATCTACAA	3	176	1
        AAGTGCCCCTCCTTTAAGTTAA	3	288	0
          **********
MAP Score: 7.97279

Motif 4
TTTTCCGTTCAGTTTAGCCTGACACGAAAG	0	171	0
CATTCACGAAAGTGTATACTAAAAAAATAA	0	268	1
  TTTTATGGATTTTATACTACCCGTGTAT	1	8	1
TTATACTACCCGTGTATACAATAATTTCTT	1	21	1
        AACCTTTATCCTCATTCTTCGG	3	2	1
CTTCCCTTCCCCTGTATACTATCGTGTAGA	3	35	1
TGTATACTATCGTGTAGACTATCACAAAGC	3	47	1
          **********
MAP Score: 5.57601

Motif 5
CCTTTTCCGTTCAGTTTAGCCTGACACGAAAGCC	0	169	0
          AACCTTTATCCTCATTCTTCGGGA	3	0	1
TTCGGGAACTTCCCTTCCCCTGTATACTATCGTG	3	27	1
TCTATTCCGTGCTCTTTTGCGTAAGTAACCTTAA	3	79	1
TTTGCGTAAGTAACCTTAACGTCAATAACCTCGT	3	94	1
ATAACCTCGTTCCCTTCTTCGTAAATGCCCTCTA	3	118	1
TAACTTCGTTTAACTTTTCCGTTATCTCGTGGGT	3	152	1
CTAAAGCTCCTATCCTTTCCATAAACTTGATTAT	3	206	1
ACTTGATTATACCCTTTGACTTCAAAAATTTTGA	3	230	1
TCCAAGTCATTATTTTTAACTTAAAGGAGGGGCA	3	273	1
          *******  * * *
MAP Score: 4.01

Motif 6
TTGCAAGGTACTTATAATTTCGGGTTCCGA	0	68	1
TTAAGGAATTTTTATGATTTTAATAAGAAA	0	224	1
TTCCAAAAGTTTTATAATTTATTAATTGGC	2	16	1
GTAAATGCCCTCTATAACTTCGTTTAACTT	3	138	1
TCTATAACTTCGTTTAACTTTTCCGTTATC	3	148	1
TTGATTATACCCTTTGACTTCAAAAATTTT	3	232	1
CAAGTCATTATTTTTAACTTAAAGGAGGGG	3	275	1
          **********
MAP Score: 3.1566

Motif 7
TCTTCGGGAACTTCCCTTCCCCTGTATACT	3	25	1
CAATAACCTCGTTCCCTTCTTCGTAAATGC	3	116	1
TCTCGTGGGTCGTCCCTTCCAGATCTACAA	3	176	1
TACAACTAAAGCTCCTATCCTTTCCATAAA	3	201	1
          **********
MAP Score: 0.440125

Motif 8
    TTTACAGGAACGGGATAGAAATAGAC	0	6	1
GCCCGCCGCAGGCGCTGTCTATTTCTATCC	0	22	0
GCCTGCGGCGGGCACGGGCAGTGTACTTCT	0	39	1
AAAAATAACAGGAGGTGGGT          	0	290	1
TTTATTAATTGGCACGGGGTGTAGCGCAGG	2	33	1
CGGGGTGTAGCGCAGGTGGTAGCGCGCTGG	2	47	1
CAGGTGGTAGCGCGCTGGCATGGGGGGCCA	2	59	1
 AGGAAAGTGGTCGGGGTGACCGGACTCGA	2	101	0
TAGTATACAGGGGAAGGGAAGTTCCCGAAG	3	26	0
TACGCAAAAGAGCACGGAATAGACGGCTTT	3	72	0
TACGAAGAAGGGAACGAGGTTATTGACGTT	3	111	0
TTTAACTTAAAGGAGGGGCACTT       	3	287	1
          **********
MAP Score: 0.179969