AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons024_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242917
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ribC	300	Riboflavin Synthase
#1	zntA	23	Metal Transport P-type ATPase
#2	CT728	36	hypothetical protein
#3	serS_ribD	41	serS: Seryl tRNA Synthetase, ribD: Riboflavin Deaminase
#4	ribA/ribB	109	GTP Cyclohydratase and DHBP Synthase

Motif 1
CTGCAGGACGCTCAAGATACCACGGTTTTTATTTTAATG	0	66	1
TGAAAAGAACCTCTTCTTAGAAAGGTTTTCTCTACGGGC	0	127	1
TACGGGCGGTCTCGGAGTATAATTATTTTTTGATTATAA	0	159	1
GAGAGGGCTTTTTCGTGTATCTAGTTTTTCAAGATTGCT	0	227	1
CCTTGCATCTCTCTCGCTATCTGATTTTTCAGGTTGAGT	3	12	0
CAAAGAACGTTTCCCACTGGCTAAGTTTTCCTCAAAAAC	4	66	1
         TCTCAATCTACCCCGTTTTTGAGGAAAACT	4	89	0
          ***    ** *    ****
MAP Score: 11.473

Motif 2
CAGGACGCTCAAGATACCACGGTTTTTATTTTAAT	0	69	1
CTTGTGTTGAAAAGAACCTCTTCTTAGAAAGGTTT	0	120	1
TTTTGATTATAAGTAACCGCTGTTTGCCTTGATCA	0	186	1
CAGAGTATAACACAAACCTCTACTTTCTGCGACC 	4	9	0
      TCTCAATCTACCCCGTTTTTGAGGAAAAC	4	90	0
          **   *** ** ***
MAP Score: 6.04626

Motif 3
TGCCTTGATCAGATCCGGAGAGGGCTTTTTC	0	210	1
GCAATCTTGAAAAACTAGATACACGAAAAAG	0	234	0
      CCTTATAGTGAGATAGAAAGCTAGA	2	4	1
AGTGAGATAGAAAGCTAGAGGAGCGGCACG 	2	16	1
GAAAAATCAGATAGCGAGAGAGATGCAAGG 	3	21	1
TACTCTGCGCACAGCGAGGGGATTATAGACA	4	37	1
GTTTTCCTCAAAAACGGGGTAGATTGAGA  	4	90	1
          * *********
MAP Score: 2.41764