AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons024_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242910
 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
AGGACGCTCAAGATACCACGGTTTTTATTTTAAT	0	70	1
TTGTGTTGAAAAGAACCTCTTCTTAGAAAGGTTT	0	121	1
TTTGATTATAAGTAACCGCTGTTTGCCTTGATCA	0	187	1
  AGACAATTAAATACCTTTGCTAGGTCGTGACA	0	278	0
AGAGTATAACACAAACCTCTACTTTCTGCGACC 	4	9	0
     TCTCAATCTACCCCGTTTTTGAGGAAAAC	4	90	0
          *  **** ** ***
MAP Score: 6.18029

Motif 2
TGCCTTGATCAGATCCGGAGAGGGCTTTTTC	0	210	1
GCAATCTTGAAAAACTAGATACACGAAAAAG	0	234	0
      CCTTATAGTGAGATAGAAAGCTAGA	2	4	1
AGTGAGATAGAAAGCTAGAGGAGCGGCACG 	2	16	1
GAAAAATCAGATAGCGAGAGAGATGCAAGG 	3	21	1
TACTCTGCGCACAGCGAGGGGATTATAGACA	4	37	1
TGAGGAAAACTTAGCCAGTGGGAAACGTTCT	4	69	0
GTTTTCCTCAAAAACGGGGTAGATTGAGA  	4	90	1
          * *********
MAP Score: 1.34049

Motif 3
ATCTAGTTTTTCAAGATTGCTAAAAAGTATTGT	0	245	1
TATTGTTGTCACGACCTAGCAAAGGTATTTAAT	0	272	1
CCTCTAGCTTTCTATCTCACTATAAGG      	2	4	0
      ATACTCAACCTGAAAAATCAGATAGCG	3	4	1
   CCTTGCATCTCTCTCGCTATCTGATTTTTC	3	21	0
AAAGAACGTTTCCCACTGGCTAAGTTTTCCTCA	4	67	1
          ** * ** *****
MAP Score: 1.04325