AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons022_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944239735
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0060	105	ribosomal protein L9 (rplI)
#1	TP0061	116	ribosomal protein S18 (rpsR)
#2	TP0063	141	ribosomal protein S6 (rpsF)
#3	TP0824	300	transketolase B (tktB)

Motif 1
ATGAATAAAAGTATGACCGAACCTGGCGTTCGCCTGGA	1	38	1
CGCCCAATTCCTTTCTGAGGTCCAGGCGAACGCCAGGT	1	58	0
TTACGCTACGCTGGCGTCTCGCCGCGCGTTCTGCGCAC	2	48	1
CCTTATCAGGCTGCACTAGACTCACCCGACAAGGAGGA	2	91	0
CTGATTCTACCTAAATCAGGTCCGTGGGTAAAGCGTCA	3	17	1
TACGCATTCAGTAAACTCGCTCCTTCCGAGCCTGTGCT	3	63	1
TTCCTGAGGAGTTTCTACGTGCCCTGCGGAAAGAAAAG	3	159	1
ACTACCTGTTCTTGTGCCGATTCTTGCGAAGCTTCTTC	3	230	0
ACAAGAACAGGTAGTCTCGGCCCGTGCGCCTTCTGTTC	3	253	1
          **     **  ** ****
MAP Score: 19.093

Motif 2
ACTTTTATTCCTGCGTAGGAGGGGACAAAACGT  	0	82	1
CAGATTTACGCTACGCTGGCGTCTCGCCGCGCGTT	2	43	1
GCCGCGCGTTCTGCGCACGCTACTCCTCCTTGTCG	2	68	1
GCTACTCCTCCTTGTCGGGTGAGTCTAGTGCAGCC	2	86	1
GACGGCTCACCTTATCAGGCTGCACTAGACTCACC	2	103	0
AGTAAACTCGCTCCTTCCGAGCCTGTGCTACGCAC	3	72	1
CGAGCCTGTGCTACGCACGAGTATACCTTGACCAT	3	89	1
GTAGTTTCCGCTACGCTCCTGCCAGCTTGGATTCC	3	128	1
CACGTAGAAACTCCTCAGGAATCCAAGCTGGCAGG	3	145	0
TGAGGAGTTTCTACGTGCCCTGCGGAAAGAAAAGA	3	163	1
TGCGAAGCTTCTTCTTGCGCTTGTGGGTTGCTATC	3	209	0
CAAGAAGAAGCTTCGCAAGAATCGGCACAAGAACA	3	227	1
AACAGGTAGTCTCGGCCCGTGCGCCTTCTGTTCGA	3	258	1
          ** *** ** * * *
MAP Score: 14.8729

Motif 3
  ACGTTTTGTCCCCTCCTACGCAGGAATA	0	87	0
CATTATGCATGCTCCTTGTGGGGAAAGAGA	1	11	0
GAAAGGAATTGGGCGTGCTAATTTTTCCAC	1	81	1
CGCTACGCTGGCGTCTCGCCGCGCGTTCTG	2	51	1
GCGTCTCGCCGCGCGTTCTGCGCACGCTAC	2	61	1
TTCTGCGCACGCTACTCCTCCTTGTCGGGT	2	76	1
CTGATAAGGTGAGCCGTCCATAGGAGTTAT	2	120	1
CAGTAAACTCGCTCCTTCCGAGCCTGTGCT	3	71	1
TTTCCGCTACGCTCCTGCCAGCTTGGATTC	3	132	1
CTGAGGAGTTTCTACGTGCCCTGCGGAAAG	3	162	1
TTGCGAAGCTTCTTCTTGCGCTTGTGGGTT	3	215	0
TTCTTGTGCCGATTCTTGCGAAGCTTCTTC	3	230	0
GAACAGGTAGTCTCGGCCCGTGCGCCTTCT	3	257	1
CTCGGCCCGTGCGCCTTCTGTTCGACATGA	3	268	1
          **********
MAP Score: 2.43666