AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons022_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944239720
 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
CAGATTTACGCTACGCTGGCGTCTCGCCGCGCGTT	2	43	1
GCCGCGCGTTCTGCGCACGCTACTCCTCCTTGTCG	2	68	1
GTAGTTTCCGCTACGCTCCTGCCAGCTTGGATTCC	3	128	1
AGTAAACTCGCTCCTTCCGAGCCTGTGCTACGCAC	3	72	1
AACAGGTAGTCTCGGCCCGTGCGCCTTCTGTTCGA	3	258	1
CGAGCCTGTGCTACGCACGAGTATACCTTGACCAT	3	89	1
ACTTTTATTCCTGCGTAGGAGGGGACAAAACGT  	0	82	1
CAAGAAGAAGCTTCGCAAGAATCGGCACAAGAACA	3	227	1
TGAGGAGTTTCTACGTGCCCTGCGGAAAGAAAAGA	3	163	1
GCTACTCCTCCTTGTCGGGTGAGTCTAGTGCAGCC	2	86	1
TGCGAAGCTTCTTCTTGCGCTTGTGGGTTGCTATC	3	209	0
CACGTAGAAACTCCTCAGGAATCCAAGCTGGCAGG	3	145	0
GACGGCTCACCTTATCAGGCTGCACTAGACTCACC	2	103	0
          ** *** ** * * *
MAP Score: 14.8729

Motif 2
TTCATTATGCATGCTCCTTGTGGGGAAAGAGA	1	11	0
AAAAGTATGACCGAACCTGGCGTTCGCCTGGA	1	44	1
ATTCCTTTCTGAGGTCCAGGCGAACGCCAGGT	1	58	0
ACAGATTTACGCTACGCTGGCGTCTCGCCGCG	2	42	1
TACGCTGGCGTCTCGCCGCGCGTTCTGCGCAC	2	54	1
CGACAAGGAGGAGTAGCGTGCGCAGAACGCGC	2	71	0
CGCTACTCCTCCTTGTCGGGTGAGTCTAGTGC	2	85	1
CTACCTAAATCAGGTCCGTGGGTAAAGCGTCA	3	23	1
TTCAGTAAACTCGCTCCTTCCGAGCCTGTGCT	3	69	1
ATGGTCAAGGTATACTCGTGCGTAGCACAGGC	3	92	0
AGGAGTTTCTACGTGCCCTGCGGAAAGAAAAG	3	165	1
GAAGCTTCTTCTTGCGCTTGTGGGTTGCTATC	3	209	0
TGTTCTTGTGCCGATTCTTGCGAAGCTTCTTC	3	230	0
GCCGAGACTACCTGTTCTTGTGCCGATTCTTG	3	242	0
ACAGGTAGTCTCGGCCCGTGCGCCTTCTGTTC	3	259	1
          ***  *******
MAP Score: 13.5775

Motif 3
      AGAGGCGCTGATTCTACCTAAATCAGGTCC	3	4	1
TGGCGTCTCGCCGCGCGTTCTGCGCACGCTACTCCT	2	59	1
CGCTCCTTCCGAGCCTGTGCTACGCACGAGTATACC	3	80	1
TGCCTATGCACAGCAACTTCTACTGAACTAGGAAAA	0	30	0
ACCTGTTCTTGTGCCGATTCTTGCGAAGCTTCTTCT	3	229	0
GGAATTGGGCGTGCTAATTTTTCCACTTCTAGGAGC	1	85	1
TTGGATTCCTGAGGAGTTTCTACGTGCCCTGCGGAA	3	154	1
CTGGTATACAGCGGTTGTTTTTCCTAGTTCAGTAGA	0	12	1
CAGGTAGTCTCGGCCCGTGCGCCTTCTGTTCGACAT	3	260	1
CATAGGCAGAGTGGCTCTGCGTGGACTTTTATTCCT	0	58	1
          * **   **** ** *
MAP Score: 7.48737

Motif 4
GTTTTTCCTAGTTCAGTAGAAGTTGCTGTGCATAGGCAGAG	0	28	1
GAATAAAAGTCCACGCAGAGCCACTCTGCCTATGCACAGCA	0	51	0
ACTTGATGCGGCACACAGATTTACGCTACGCTGGCGTCTCG	2	28	1
CGTCTCGCCGCGCGTTCTGCGCACGCTACTCCTCCTTGTCG	2	62	1
CCTATGGACGGCTCACCTTATCAGGCTGCACTAGACTCACC	2	103	0
ACCTAAATCAGGTCCGTGGGTAAAGCGTCACCCACCTGTAC	3	25	1
CAAGCTGGCAGGAGCGTAGCGGAAACTACCCAAATGGTCAA	3	116	0
TTTCTTTCCGCAGGGCACGTAGAAACTCCTCAGGAATCCAA	3	154	0
AGCAACCCACAAGCGCAAGAAGAAGCTTCGCAAGAATCGGC	3	212	1
CGAACAGAAGGCGCACGGGCCGAGACTACCTGTTCTTGTGC	3	251	0
          *  * *  *   * *** * *
MAP Score: 4.46399

Motif 5
AAAGGAATTGGGCGTGCTAATTTTTCCACTTCTAGGA	1	82	1
ACAGATTTACGCTACGCTGGCGTCTCGCCGCGCGTTC	2	42	1
ACCTTATCAGGCTGCACTAGACTCACCCGACAAGGAG	2	93	0
         AGAGGCGCTGATTCTACCTAAATCAGGT	3	1	1
GTACAGGTGGGTGACGCTTTACCCACGGACCTGATTT	3	29	0
ACTCGCTCCTTCCGAGCCTGTGCTACGCACGAGTATA	3	77	1
GGTAGTTTCCGCTACGCTCCTGCCAGCTTGGATTCCT	3	127	1
TTGCGCTTGTGGGTTGCTATCTTTTGCTTTTTTCTTT	3	193	0
GCCGATTCTTGCGAAGCTTCTTCTTGCGCTTGTGGGT	3	216	0
ACAGAAGGCGCACGGGCCGAGACTACCTGTTCTTGTG	3	252	0
          *  * ***    *****
MAP Score: 4.1599

Motif 6
AGAGCCACTCTGCCTATGCACAGCAACTTCTACTGAACTA	0	36	0
CTTTTATTCCTGCGTAGGAGGGGACAAAACGT        	0	83	1
CCAATTCCTTTCTGAGGTCCAGGCGAACGCCAGGTTCGGT	1	53	0
CGCGCGGCGAGACGCCAGCGTAGCGTAAATCTGTGTGCCG	2	36	0
CTGGCGTCTCGCCGCGCGTTCTGCGCACGCTACTCCTCCT	2	58	1
GTCTAGTGCAGCCTGATAAGGTGAGCCGTCCATAGGAGTT	2	108	1
CTAAATCAGGTCCGTGGGTAAAGCGTCACCCACCTGTACG	3	27	1
CTTCCGAGCCTGTGCTACGCACGAGTATACCTTGACCATT	3	85	1
AATCCAAGCTGGCAGGAGCGTAGCGGAAACTACCCAAATG	3	121	0
CTGAGGAGTTTCTACGTGCCCTGCGGAAAGAAAAGAAAAA	3	162	1
CTGTTCTTGTGCCGATTCTTGCGAAGCTTCTTCTTGCGCT	3	223	0
TCGAACAGAAGGCGCACGGGCCGAGACTACCTGTTCTTGT	3	253	0
CCGTGCGCCTTCTGTTCGACATGAGGCGTTTTCGTC    	3	274	1
          ****   *    *** *  *
MAP Score: 3.1408

Motif 7
TACAGCGGTTGTTTTTCCTAGTTCAGTAGAA	0	18	1
AGGCAGAGTGGCTCTGCGTGGACTTTTATTC	0	61	1
TGGACTTTTATTCCTGCGTAGGAGGGGACAA	0	79	1
       GTCTCTTTCCCCACAAGGAGCATG	1	3	1
CGCTACGCTGGCGTCTCGCCGCGCGTTCTGC	2	51	1
CTCGCCGCGCGTTCTGCGCACGCTACTCCTC	2	65	1
GGTGGGTGACGCTTTACCCACGGACCTGATT	3	30	0
TTCCGAGCCTGTGCTACGCACGAGTATACCT	3	86	1
TTTCCGCTACGCTCCTGCCAGCTTGGATTCC	3	132	1
TCCTGAGGAGTTTCTACGTGCCCTGCGGAAA	3	160	1
TTTTTTCTTTTCTTTCCGCAGGGCACGTAGA	3	172	0
          ***** *****
MAP Score: 3.05564

Motif 8
AGTTGCTGTGCATAGGCAGAGTGGCTCTGCGTGGACTTTTAT	0	48	1
GACTTTTATTCCTGCGTAGGAGGGGACAAAACGT        	0	81	1
ATGACCGAACCTGGCGTTCGCCTGGACCTCAGAAAGGAATTG	1	50	1
AAGACTTGATGCGGCACACAGATTTACGCTACGCTGGCGTCT	2	25	1
GGAGGAGTAGCGTGCGCAGAACGCGCGGCGAGACGCCAGCGT	2	55	0
AAATCAGGTCCGTGGGTAAAGCGTCACCCACCTGTACGCATT	3	29	1
CTGTGCTACGCACGAGTATACCTTGACCATTTGGGTAGTTTC	3	94	1
TTTTCTTTCCGCAGGGCACGTAGAAACTCCTCAGGAATCCAA	3	154	0
TAGCAACCCACAAGCGCAAGAAGAAGCTTCGCAAGAATCGGC	3	211	1
AGAATCGGCACAAGAACAGGTAGTCTCGGCCCGTGCGCCTTC	3	244	1
          *  ***** *  *   *    *
MAP Score: 0.730392