AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID018_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391011
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	pheS	283	phenylalanine tRNA synthetase, alpha-subunit
#1	rplT	52	50S ribosomal subunit protein L20, and regulator
#2	rpmI	96	50S ribosomal subunit protein A
#3	thrS	300	threonine tRNA synthetase

Motif 1
 ATCCAGGAGGCTAGCGCGTGAGAAGAGAAACGGAAAACA	0	9	1
ATCAGGTGTAATTGTCGCAGCCAGACTGGACACGGCCAGC	0	116	1
ACTGGACACGGCCAGCGCGGAGAAACCGGAGCGTATTTAA	0	140	1
TTGTGTCAGTGGTGACACTGGTTCGTTGGACTTAGAGCCT	0	242	0
ACGAACCAGTGTCACCACTGACACAATGAGGAAAACC   	0	256	1
TGTTTCGTTTATTAACAATGCGAAGTGGAAGTTATTAAA 	2	67	1
AACAACTGATAACATCACGGTGCGTCTGAAAGGTT     	3	5	0
GTTGAGCGATGTTAACACTAAAAAAAGGGAGATTGTACCT	3	110	0
TTTCGTGTGGGTCACCACTGCAAATAAGGATATAAA    	3	274	1
          * ** *** *       ***
MAP Score: 6.66632

Motif 2
TCCTCATTGTGTCAGTGGTGACACTGGTTCGT	0	256	0
AAGTAGCACTGTCTGTGGAGCCTTCGGGCTTC	2	17	1
CTGAAAGCCTCCCAGTGGAGGCTTTTTTTGTA	0	53	1
GGCGAACAAAGCCTGTGAAGCCCGAAGGCTCC	2	33	0
AATTGTCGCAGCCAGACTGGACACGGCCAGCG	0	125	1
TATCCTTATTTGCAGTGGTGACCCACACGAAA	3	274	0
AAAATAAAAAGCCTGTCTCATCAGGTGTAATT	0	97	1
TATTTTACTTGCCATTTTGGTCCCGGGCTGTG	0	198	0
AAGTAAAATAGCCTGATGGGATAGGCTCTAAG	0	220	1
AACCAATTTAGCATTTGTTGGCTAGATGGTTT	3	199	1
          ******** * *
MAP Score: 4.64063

Motif 3
CGGAAAACAGCGCCTGAAAGCCTCCCAGTG	0	40	1
CTAAGTCCAACGAACCAGTGTCACCACTGA	0	247	1
TGTTAATAAACGAAACAAAGGCGAACAAAG	2	54	0
CATCACGGTGCGTCTGAAAGGTT       	3	3	0
GTACTCACTACAAACGAATTGCGAATCGAA	3	64	1
AATTGCGAATCGAATCAATGTGAAACGGAA	3	80	1
ATCAGGTACACAAATGAAAGACATTAACCT	3	165	0
TACCTGATTGCGAACCAATTTAGCATTTGT	3	187	1
AGTGGTGACCCACACGAAAGATCACATACA	3	263	0
          **********
MAP Score: 4.47977

Motif 4
    ATCCAGGAGGCTAGCGCGTGAGAAGAGAAACGGAA	0	6	1
AAGAGAAACGGAAAACAGCGCCTGAAAGCCTCCCAGTGG	0	32	1
CGCAGCCAGACTGGACACGGCCAGCGCGGAGAAACCGGA	0	131	1
CAAAATGGCAAGTAAAATAGCCTGATGGGATAGGCTCTA	0	211	1
CGAAACAAAGGCGAACAAAGCCTGTGAAGCCCGAAGGCT	2	35	0
TGTTTCGTTTATTAACAATGCGAAGTGGAAGTTATTAAA	2	67	1
TTTTTTTAGTGTTAACATCGCTCAACCGGGTGGAAGGTG	3	124	1
AACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCA	3	191	0
TTTCGTGTGGGTCACCACTGCAAATAAGGATATAAA   	3	274	1
          *  ****  **  *   **
MAP Score: 4.20599

Motif 5
CGCGTGAGAAGAGAAACGGAAAACAGCGCC	0	24	1
GGCCAGCGCGGAGAAACCGGAGCGTATTTA	0	149	1
TCTAAGTCCAACGAACCAGTGTCACCACTG	0	246	1
CGAAACAAAGGCGAACAAAGCCTGTGAAGC	2	44	0
TTGTTAATAAACGAAACAAAGGCGAACAAA	2	55	0
CAAACGAATTGCGAATCGAATCAATGTGAA	3	74	1
TCGAATCAATGTGAAACGGAAAGGTACAAT	3	89	1
GTACCTGATTGCGAACCAATTTAGCATTTG	3	186	1
ACAGTTCATTGCGAAACCATCTAGCCAACA	3	214	0
          **********
MAP Score: 3.94798

Motif 6
CACCTTCCACCCGGTTGAGCGATGTTAACA	3	133	0
GACAATTACACCTGATGAGACAGGCTTTTT	0	102	0
GCGAACAAAGCCTGTGAAGCCCGAAGGCTC	2	34	0
AGTAAAATAGCCTGATGGGATAGGCTCTAA	0	221	1
AGTAGCACTGTCTGTGGAGCCTTCGGGCTT	2	18	1
TGTGATCTTTCGTGTGGGTCACCACTGCAA	3	267	1
GAGGCTAGCGCGTGAGAAGAGAAACGGAAA	0	16	1
TGAAAGCCTCCCAGTGGAGGCTTTTTTTGT	0	54	1
ATTTTGGTCCCGGGCTGTGCTCGAAATTCT	0	187	0
TCAGACGCACCGTGATGTTATCAGTTGTTC	3	16	1
CCTCATTGTGTCAGTGGTGACACTGGTTCG	0	257	0
          **********
MAP Score: 2.93635