AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_operons031_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236162
 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
TCTATTTCTATCCCGTTCCTGTAAA       	0	3	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
CCACCTGCGCTACACCCCGTGCCAATTAATAA	1	34	0
ACCTCTGGCCCCCCATGCCAGCGCGCTACCAC	1	62	0
GCCAGAGGTCGCCGGTTCGAGTCCGGTCACCC	1	85	1
GTCCGGTCACCCCGACCACTTTCCT       	1	105	1
TCGGGAACTTCCCTTCCCCTGTATACTATCGT	2	28	1
CACAAAGCCGTCTATTCCGTGCTCTTTTGCGT	2	69	1
CGTCAATAACCTCGTTCCCTTCTTCGTAAATG	2	113	1
CGTGGGTCGTCCCTTCCAGATCTACAACTAAA	2	179	1
CAACTAAAGCTCCTATCCTTTCCATAAACTTG	2	203	1
CTTGATTATACCCTTTGACTTCAAAAATTTTG	2	231	1
          ***  *******
MAP Score: 15.7714

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	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 3
AACCACGTCGCCTTTTCCGTTCAGTTTAGCC	0	182	0
TTGATTATACCCTTTGACTTCAAAAATTTTG	2	232	1
GTCAATAACCTCGTTCCCTTCTTCGTAAATG	2	114	1
TTCCAGAGTGTCTTTTTCTTCGAACTCCGCA	0	110	0
        AACCTTTATCCTCATTCTTCGGG	2	2	1
GGGATCCATGCCGTTTTCTTCCAGAGTGTCT	0	128	0
CACAAAGCCGTCTATTCCGTGCTCTTTTGCG	2	69	1
GCTGTCTATTTCTATCCCGTTCCTGTAAA  	0	8	0
GTAAATGCCCTCTATAACTTCGTTTAACTTT	2	138	1
ACTTCGTTTAACTTTTCCGTTATCTCGTGGG	2	154	1
TCGGGAACTTCCCTTCCCCTGTATACTATCG	2	28	1
GCGACGTGGTTATTTACCTTCCTTAAGGAAT	0	202	1
AACTAAAGCTCCTATCCTTTCCATAAACTTG	2	204	1
TGCGTAAGTAACCTTAACGTCAATAACCTCG	2	96	1
GTTCCGAAAATCTGTACCCTGCGGAGTTCGA	0	91	1
          ***** *****
MAP Score: 11.7332

Motif 4
  TTTACAGGAACGGGATAGAAATAGACAGCG	0	8	1
TCTGGAAGAAAACGGCATGGATCCCGAAACGG	0	134	1
TGTCAGGCTAAACTGAACGGAAAAGGCGACGT	0	177	1
TTTAATAAGAAACTTGAATGAATTATCATTCA	0	242	1
GATAGTATACAGGGGAAGGGAAGTTCCCGAAG	2	26	0
ACTTACGCAAAAGAGCACGGAATAGACGGCTT	2	73	0
GATAACGGAAAAGTTAAACGAAGTTATAGAGG	2	146	0
GACGACCCACGAGATAACGGAAAAGTTAAACG	2	158	0
GGGTATAATCAAGTTTATGGAAAGGATAGGAG	2	212	0
CATTATTTTTAACTTAAAGGAGGGGCACTT  	2	280	1
          ***** * ****
MAP Score: 7.526

Motif 5
GCGCTGTCTATTTCTATCCCGTTCCTGTAA	0	11	0
GATCCATGCCGTTTTCTTCCAGAGTGTCTT	0	127	0
GACGTGGTTATTTACCTTCCTTAAGGAATT	0	204	1
TCTTCGGGAACTTCCCTTCCCCTGTATACT	2	25	1
ATCACAAAGCCGTCTATTCCGTGCTCTTTT	2	67	1
CAATAACCTCGTTCCCTTCTTCGTAAATGC	2	116	1
TCTCGTGGGTCGTCCCTTCCAGATCTACAA	2	176	1
CTAAAGCTCCTATCCTTTCCATAAACTTGA	2	206	1
          **********
MAP Score: 4.48714

Motif 6
GGGATCCATGCCGTTTTCTTCCAGAGTGTCTTTTTCTTCGAA	0	117	0
AACCACGTCGCCTTTTCCGTTCAGTTTAGCCTGACACGAAAG	0	171	0
         ACCCACCTCCTGTTATTTTTTTAGTATACACTT	0	277	0
        AACCTTTATCCTCATTCTTCGGGAACTTCCCTTC	2	2	1
TCGGGAACTTCCCTTCCCCTGTATACTATCGTGTAGACTATC	2	28	1
CACAAAGCCGTCTATTCCGTGCTCTTTTGCGTAAGTAACCTT	2	69	1
TGCGTAAGTAACCTTAACGTCAATAACCTCGTTCCCTTCTTC	2	96	1
AACCTCGTTCCCTTCTTCGTAAATGCCCTCTATAACTTCGTT	2	120	1
ACTTCGTTTAACTTTTCCGTTATCTCGTGGGTCGTCCCTTCC	2	154	1
AAAGCTCCTATCCTTTCCATAAACTTGATTATACCCTTTGAC	2	208	1
TTGATTATACCCTTTGACTTCAAAAATTTTGACAAACATGAT	2	232	1
          ** **  * *  *     ** *
MAP Score: 3.39283

Motif 7
GAAGTACACTGCCCGTGCCCGCCGCAGGCGCTGTC	0	33	0
AGGTAAATAACCACGTCGCCTTTTCCGTTCAGTTT	0	186	0
AGTCCGGTCACCCCGACCACTTTCCT         	1	104	1
TATCCTCATTCTTCGGGAACTTCCCTTCCCCTGTA	2	16	1
GCTCTTTTGCGTAAGTAACCTTAACGTCAATAACC	2	89	1
ACGTCAATAACCTCGTTCCCTTCTTCGTAAATGCC	2	112	1
TCGTAAATGCCCTCTATAACTTCGTTTAACTTTTC	2	136	1
TACAACTAAAGCTCCTATCCTTTCCATAAACTTGA	2	201	1
          ** **   ***** *
MAP Score: 0.303544