AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_operons029_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944245333
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH783	83	hydrogenase expression/formation protein HypA
#1	MTH1072	67	hydrogenase expression/formation protein HypD
#2	MTH1287	177	transcriptional regulator HypF homolog
#3	MTH1649	110	hydrogenase expression/formation protein HypC
#4	MTH1864	109	phosphoribosylformylglycinamidine synthase II related protein

Motif 1
GTAATTAACAATTTTTATATAGATAACTCTA	0	26	1
TCTGACAAAATTTTATAATTAGAATTAATAG	0	54	0
TATCACGATCATATATATATGGAGGAGGCCA	1	17	0
TGATAAATAGATCTTTAAGTGTAATGGTGGT	1	43	1
    TACCTAATTTATAAGTACATCAATATA	2	6	1
GGCACGGTACATTTCTATCTACCTTGAGTTT	2	61	0
TTTCCCACAAATCTTTATATGTGACGGATCT	3	31	1
TATGTGACGGATCTTTATCTAAACATTAGTG	3	48	1
          ******** **
MAP Score: 5.16375

Motif 2
ATTAACAATTTTTATATAGATAACTCTATT	0	29	1
GACAAAATTTTATAATTAGAATTAATAGAG	0	52	0
CACGATCATATATATATGGAGGAGGCCAAA	1	15	0
TAAATAGATCTTTAAGTGTAATGGTGGTCT	1	46	1
   TACCTAATTTATAAGTACATCAATATA	2	7	1
AATATAATCTTAGCATAGGAGAACTCATGC	2	31	1
TCAAGGTAGATAGAAATGTACCGTGCCCAT	2	65	1
GTCTACAGACTTGCAAAGGAACTCAGCCTC	2	140	1
CACTAATGTTTAGATAAAGATCCGTCACAT	3	49	0
TTTAATCCTATTAATTTGGAGAGGGTTATT	3	88	1
     CACAATTGAAGTGGAGGACTTGGAA	4	5	1
TTGGAAACTTTTAAAAAGGATCTGCTACAG	4	29	1
          **********
MAP Score: 4.31825

Motif 3
   AATCCTTTGGCCTCCTCCATATATATATGATCGTGA	1	7	1
GTCCAGGGCGTTGGCTTCAGGCCAGCGGTCTACAGACTT	2	113	1
GCAAAGGAACTCAGCCTCACGGGATACGTGAGAAC    	2	152	1
      TCAATAACCCTCTCCAAATTAATAGGATTAAAG	3	87	0
AAAGTTTCCAAGTCCTCCACTTCAATTGTG         	4	1	0
TTAAAAAGGATCTGCTACAGATTATAGATAATACAGGTG	4	39	1
GAATACACTGTGAGATACACCTAAACGATACAAAGAGGT	4	80	1
          *  *** ***   *   **
MAP Score: 1.04803