AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_operons031_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236175
 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
GCTGTCTATTTCTATCCCGTTCCTGTAAA   	0	7	0
GATAGAAATAGACAGCGCCTGCGGCGGGCACG	0	23	1
GCAAGAAGTACACTGCCCGTGCCCGCCGCAGG	0	40	0
CGTTTCGGGATCCATGCCGTTTTCTTCCAGAG	0	133	0
TGACACGAAAGCCTCTCCGTTTCGGGATCCAT	0	150	0
CGTCGCCTTTTCCGTTCAGTTTAGCCTGACAC	0	176	0
GGTAAATAACCACGTCGCCTTTTCCGTTCAGT	0	188	0
         ACCCACCTCCTGTTATTTTTTTA	0	287	0
ATGGATTTTATACTACCCGTGTATACAATAAT	1	14	1
CCACCTGCGCTACACCCCGTGCCAATTAATAA	2	34	0
ACCTCTGGCCCCCCATGCCAGCGCGCTACCAC	2	62	0
GTCCGGTCACCCCGACCACTTTCCT       	2	105	1
TCGGGAACTTCCCTTCCCCTGTATACTATCGT	3	28	1
CACAAAGCCGTCTATTCCGTGCTCTTTTGCGT	3	69	1
CGTCAATAACCTCGTTCCCTTCTTCGTAAATG	3	113	1
CGTGGGTCGTCCCTTCCAGATCTACAACTAAA	3	179	1
CAACTAAAGCTCCTATCCTTTCCATAAACTTG	3	203	1
CTTGATTATACCCTTTGACTTCAAAAATTTTG	3	231	1
          ***  *******
MAP Score: 19.1276

Motif 2
      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	2	31	1
TGGTAGCGCGCTGGCATGGGGGGCCAGAGG	2	63	1
ATAGTATACAGGGGAAGGGAAGTTCCCGAA	3	27	0
CTTACGCAAAAGAGCACGGAATAGACGGCT	3	74	0
TTTACGAAGAAGGGAACGAGGTTATTGACG	3	113	0
AGTTGTAGATCTGGAAGGGACGACCCACGA	3	178	0
AATCAAGTTTATGGAAAGGATAGGAGCTTT	3	208	0
          **********
MAP Score: 14.0912

Motif 3
AGTTTAGCCTGACACGAAAGCCTCTCCGTT	0	161	0
TAAGGTTACTTACGCAAAAGAGCACGGAAT	3	82	0
GGCTAAACTGAACGGAAAAGGCGACGTGGT	0	182	1
CCCACGAGATAACGGAAAAGTTAAACGAAG	3	155	0
  TTTACAGGAACGGGATAGAAATAGACAG	0	8	1
CATTTACGAAGAAGGGAACGAGGTTATTGA	3	115	0
TGTGATAGTCTACACGATAGTATACAGGGG	3	43	0
CGCAAAAGAGCACGGAATAGACGGCTTTGT	3	70	0
CAAGTTTATGGAAAGGATAGGAGCTTTAGT	3	205	0
TGAATTATCATTCACGAAAGTGTATACTAA	0	260	1
TGCGGAGTTCGAAGAAAAAGACACTCTGGA	0	110	1
AGACACTCTGGAAGAAAACGGCATGGATCC	0	128	1
          **********
MAP Score: 9.01837

Motif 4
CACAAAGCCGTCTATTCCGTGCTCTTTTGCGT	3	69	1
GTTCCGAAAATCTGTACCCTGCGGAGTTCGAA	0	91	1
GCTGTCTATTTCTATCCCGTTCCTGTAAA   	0	7	0
AAGTACACTGCCCGTGCCCGCCGCAGGCGCTG	0	35	0
AACCACGTCGCCTTTTCCGTTCAGTTTAGCCT	0	181	0
CCTCTGGCCCCCCATGCCAGCGCGCTACCACC	2	61	0
AACTAAAGCTCCTATCCTTTCCATAAACTTGA	3	204	1
GTAAATGCCCTCTATAACTTCGTTTAACTTTT	3	138	1
GCGACGTGGTTATTTACCTTCCTTAAGGAATT	0	202	1
CGTTTCGGGATCCATGCCGTTTTCTTCCAGAG	0	133	0
AACCTTAACGTCAATAACCTCGTTCCCTTCTT	3	105	1
CCCGAAATTATAAGTACCTTGCAAGAAGTACA	0	60	0
TCGGGAACTTCCCTTCCCCTGTATACTATCGT	3	28	1
TTCCAGAGTGTCTTTTTCTTCGAACTCCGCAG	0	109	0
          ***** ** ***
MAP Score: 5.34334

Motif 5
ATAGAAATAGACAGCGCCTGCGGCGGGCACG	0	24	1
CAAGAAGTACACTGCCCGTGCCCGCCGCAGG	0	40	0
TTCCGAAAATCTGTACCCTGCGGAGTTCGAA	0	92	1
CGACGTGGTTATTTACCTTCCTTAAGGAATT	0	203	1
        ACCCACCTCCTGTTATTTTTTTA	0	287	0
TGGATTTTATACTACCCGTGTATACAATAAT	1	15	1
CACCTGCGCTACACCCCGTGCCAATTAATAA	2	34	0
TGCCAGCGCGCTACCACCTGCGCTACACCCC	2	48	0
TCGAGTCCGGTCACCCCGACCACTTTCCT  	2	101	1
TTCTTCGGGAACTTCCCTTCCCCTGTATACT	3	24	1
TCAATAACCTCGTTCCCTTCTTCGTAAATGC	3	115	1
ATCTCGTGGGTCGTCCCTTCCAGATCTACAA	3	175	1
         AAGTGCCCCTCCTTTAAGTTAA	3	288	0
          *** *******
MAP Score: 5.02056