AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons025_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242925
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	rl31	75	L31 Ribosomal Protein
#1	pfrA	187	Peptide Chain Releasing Factor (RF-1)
#2	yebC	184	YebC family
#3	Peptide	300	Peptide Chain Release Factor 2

Motif 1
AATCTCACATAACAGAAGGGAGAGCATACCCGAA	0	16	0
TGTTATCTAGAGAAAAGCGGGGCGAACACCCCGC	1	26	1
TATTAAAACAAAAAAAGCGGGGTGTTCGCCCCGC	1	42	0
GACTTTTCAGAGTAAAGTCTAGTGTTCCCCAAAA	1	95	1
GTATCTCTCTAACAAAGACCAGAGTGTACATTGG	1	137	0
GAGATACTAGAGTAAAGGCAGAAGAAGTCGTTC 	1	164	1
CAGGATCCCCAAAAAAGGGCGGAATTTTTTAAAA	2	72	0
 AAGATGATAAGAAAAGTTTAGGGCTCTTCCTTC	3	9	1
CTTCAGCAAGAAGAGAGGTAAAAGCGAATTAGAA	3	99	1
TCTTTGAAAAAGAAGAGTTTAAAGTTGGATATTT	3	256	1
          ** **** * ** *
MAP Score: 11.4083

Motif 2
GGTATGCTCTCCCTTCTGTTATGTGAGATT	0	20	1
TTTGAACAGAACTTTCTGTTATCTAGAGAA	1	10	1
GGGGTGTTCGCCCCGCTTTTCTCTAGATAA	1	28	0
GGGGCGAACACCCCGCTTTTTTTGTTTTAA	1	44	1
TTTTAATAAGTCTCTCTTTTTGAATCTGAC	1	68	1
TAGAGCTGAAACTTGCTTTTGTGTAAGATG	2	20	1
GTTATTGAGGACTTTGTTTTTAAAAAATTC	2	55	1
TTAAAAAATTCCGCCCTTTTTTGGGGATCC	2	74	1
TTCGCTTTTACCTCTCTTCTTGCTGAAGAC	3	97	0
TCGTTTTCTAATTCGCTTTTACCTCTCTTC	3	108	0
CAACTTTAAACTCTTCTTTTTCAAAGAGCT	3	253	0
          **********
MAP Score: 11.2415

Motif 3
TCACATAACAGAAGGGAGAGCATACCCGAA	0	16	0
TTATCTAGAGAAAAGCGGGGCGAACACCCC	1	28	1
TTAAAACAAAAAAAGCGGGGTGTTCGCCCC	1	44	0
AGTCAGATTCAAAAAGAGAGACTTATTAAA	1	69	0
TTTACTCTGAAAAGTCAGATTCAAAAAGAG	1	81	0
CTCTCTAACAAAGACCAGAGTGTACATTGG	1	137	0
ATACTAGAGTAAAGGCAGAAGAAGTCGTTC	1	167	1
CATCTTACACAAAAGCAAGTTTCAGCTCTA	2	20	0
GGAATTTTTTAAAAACAAAGTCCTCAATAA	2	56	0
ATCCCCAAAAAAGGGCGGAATTTTTTAAAA	2	72	0
AAAGAGTTGCGAAGGAAGAGCCCTAAACTT	3	23	0
CGTCAAAATAAAAAACATAGCCAAGTCTTC	3	73	1
AGTCTTCAGCAAGAAGAGAGGTAAAAGCGA	3	96	1
GAAGAGAGGTAAAAGCGAATTAGAAAACGA	3	108	1
ATTGATCCCTAAGAGAAGATCATGTTACCA	3	165	1
AGCTCTTTGAAAAAGAAGAGTTTAAAGTTG	3	253	1
          **********
MAP Score: 10.5031

Motif 4
AAAATCTCACATAACAGAAGGGAGAGCATACC	0	20	0
TGTTATCTAGAGAAAAGCGGGGCGAACACCCC	1	26	1
TATTAAAACAAAAAAAGCGGGGTGTTCGCCCC	1	44	0
TAGTTAAGGCATAAAAGAGTTGCGAAGGAAGA	3	34	0
GTCTTCAGCAAGAAGAGAGGTAAAAGCGAATT	3	97	1
          * ** *******
MAP Score: 2.54684