AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID018_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391059
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	pheS	283	phenylalanine tRNA synthetase, alpha-subunit
#1	pheM	122	phenylalanyl-tRNA synthetase (pheST) operon leader peptide
#2	rplT	52	50S ribosomal subunit protein L20, and regulator
#3	rpmI	96	50S ribosomal subunit protein A
#4	thrS	300	threonine tRNA synthetase

Motif 1
TCAGGCGCTGTTTTCCGTTTCTCTTCTCACG	0	26	0
TGAGACAGGCTTTTTATTTTTCAAAACGCGC	0	86	0
TTTCTCCGCGCTGGCCGTGTCCAGTCTGGCT	0	134	0
GGCTATTTTACTTGCCATTTTGGTCCCGGGC	0	202	0
TTTCCTCATTGTGTCAGTGGTGACACTGGTT	0	259	0
TAGTCTCCCTCTTTTCGTTTCAACGCCATCA	1	29	1
TTTTATCGCCGTAGCCTTTTCAATAAAGGTC	1	70	1
ACAGGCTTTGTTCGCCTTTGTTTCGTTTATT	3	49	1
TAACTTCCACTTCGCATTGTTAATAAACGAA	3	70	0
CACCGTGATGTTATCAGTTGTTCTTTAAGCG	4	23	1
GAGATTGTACCTTTCCGTTTCACATTGATTC	4	91	0
AATCTCCCTTTTTTTAGTGTTAACATCGCTC	4	116	1
AGGTTAATGTCTTTCATTTGTGTACCTGATT	4	165	1
GCGAACCAATTTAGCATTTGTTGGCTAGATG	4	196	1
AATAAACAAATTTTTCTTTGTATGTGATCTT	4	245	1
TATATCCTTATTTGCAGTGGTGACCCACACG	4	277	0
          ** ********
MAP Score: 12.1725

Motif 2
CTTCACAGGCTTTGTTCGCCTTTGTTTCGTTT	3	45	1
TTAATAACTTCCACTTCGCATTGTTAATAAAC	3	73	0
TCACATTGATTCGATTCGCAATTCGTTTGTAG	4	71	0
TTGTACCTTTCCGTTTCACATTGATTCGATTC	4	86	0
AAATGCTAAATTGGTTCGCAATCAGGTACACA	4	183	0
GATTGCGAACCAATTTAGCATTTGTTGGCTAG	4	192	1
GTTGGCTAGATGGTTTCGCAATGAACTGTTAA	4	215	1
          * * ********
MAP Score: 5.39431

Motif 3
GGACACGGCCAGCGCGGAGAAACCGGAGCGTATTTAA	0	143	1
GAGCGATGTTAACACTAAAAAAAGGGAGATTGTACCT	4	110	0
CCAGGAGGCTAGCGCGTGAGAAGAGAAACGGAAAACA	0	12	1
ATTGTTAATAAACGAAACAAAGGCGAACAAAGCCTGT	3	49	0
TGCGAATCGAATCAATGTGAAACGGAAAGGTACAATC	4	83	1
CACACGAAAGATCACATACAAAGAAAAATTTGTTTAT	4	246	0
TTCGTTTATTAACAATGCGAAGTGGAAGTTATTAAA 	3	70	1
TATTTTTCAAAACGCGCATACAAAAAAAGCCTCCACT	0	66	0
AACCAGTGTCACCACTGACACAATGAGGAAAACC   	0	259	1
CGTGTGGGTCACCACTGCAAATAAGGATATAAA    	4	277	1
ACATCGCTCAACCGGGTGGAAGGTGAGAGGTTAATGT	4	138	1
CAATGTTTTGATGGCGTTGAAACGAAAAGAGGGAGAC	1	31	0
TGAAAAGGCTACGGCGATAAAAGTCAATGTTTTGATG	1	55	0
          * ***    ***  ***
MAP Score: 4.88624

Motif 4
AAAATAAAAAGCCTGTCTCATCAGGTGTAATTGTC	0	97	1
          GCCAGTTGAAAGAGGGAGCTAGTCT	1	0	1
GGCGAACAAAGCCTGTGAAGCCCGAAGGCTCCACA	3	30	0
AAGTAAAATAGCCTGATGGGATAGGCTCTAAGTCC	0	220	1
GACACGGCCAGCGCGGAGAAACCGGAGCGTATTTA	0	144	1
TACAAAAAAAGCCTCCACTGGGAGGCTTTCAGGCG	0	50	0
AATTGTCGCAGCCAGACTGGACACGGCCAGCGCGG	0	125	1
CAGGAGGCTAGCGCGTGAGAAGAGAAACGGAAAAC	0	13	1
CGTGAGAATTTCGAGCACAGCCCGGGACCAAAATG	0	183	1
TCGCTCAACCGGGTGGAAGGTGAGAGGTTAATGTC	4	141	1
GAAGCCCGAAGGCTCCACAGACAGTGCTACTTGAA	3	14	0
          *****    * ****
MAP Score: 3.9896

Motif 5
CGCGTGAGAAGAGAAACGGAAAACAGCGCCTGAAAG	0	24	1
TTTTCAAAACGCGCATACAAAAAAAGCCTCCACTGG	0	64	0
TAGGCTCTAAGTCCAACGAACCAGTGTCACCACTGA	0	241	1
TTTTGATGGCGTTGAAACGAAAAGAGGGAGACTAGC	1	27	0
TCGCATTGTTAATAAACGAAACAAAGGCGAACAAAG	3	54	0
CCAGCAAAACGCTTAAAGAACAACTGATAACATCAC	4	27	0
CAAACGAATTGCGAATCGAATCAATGTGAAACGGAA	4	74	1
TTGCGAAACCATCTAGCCAACAAATGCTAAATTGGT	4	200	0
          *   * **** ** **
MAP Score: 3.63983

Motif 6
CTTCACAGGCTTTGTTCGCCTTTGTTTCGTTTATTAACAATGC	3	45	1
AAACATTGACTTTTATCGCCGTAGCCTTTTCAATAAAGGTCTT	1	60	1
TACGCTCCGGTTTCTCCGCGCTGGCCGTGTCCAGTCTGGCTGC	0	132	0
TCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGAT         	0	1	0
CCTCTTTTCGTTTCAACGCCATCAAAACATTGACTTTTATCGC	1	36	1
  TTTATATCCTTATTTGCAGTGGTGACCCACACGAAAGATCA	4	269	0
CAATCTCCCTTTTTTTAGTGTTAACATCGCTCAACCGGGTGGA	4	115	1
CAGTGGAGGCTTTTTTTGTATGCGCGTTTTGAAAAATAAAAAG	0	65	1
GTAGCACTGTCTGTGGAGCCTTCGGGCTTCACAGGCTTTGTTC	3	19	1
CAATTTAGCATTTGTTGGCTAGATGGTTTCGCAATGAACTGTT	4	202	1
          ***    **  * *   * *  *
MAP Score: 2.74143

Motif 7
GCGTGAGAAGAGAAACGGAAAACAGCGCCTGA	0	25	1
GCCAGCGCGGAGAAACCGGAGCGTATTTAAGT	0	150	1
CGTTGAAACGAAAAGAGGGAGACTAGCTCCCT	1	22	0
TTGAAGAGTACCAAAAGGTAACGCAAGCA   	1	103	1
TTAAAAAGTTAAAAACGTTAACGGC       	2	3	0
TAGAATATAGATACAGGAGAGCACAT      	2	36	1
AATAAACGAAACAAAGGCGAACAAAGCCTGTG	3	48	0
CGCTTAAAGAACAACTGATAACATCACGGTGC	4	22	0
TGTAGTGAGTACACCAGCAAAACGCTTAAAGA	4	44	0
GTTAACACTAAAAAAAGGGAGATTGTACCTTT	4	108	0
AATCAGGTACACAAATGAAAGACATTAACCTC	4	164	0
CATCTAGCCAACAAATGCTAAATTGGTTCGCA	4	195	0
CAGTGGTGACCCACACGAAAGATCACATACAA	4	262	0
          ***** * ****
MAP Score: 2.58621

Motif 8
TTTTTATTTTTCAAAACGCGCATACAAAAA	0	77	0
CTCACGTACTTAAATACGCTCCGGTTTCTC	0	159	0
TTCAACGCCATCAAAACATTGACTTTTATC	1	47	1
ATTAAAAAGTTAAAAACGTTAACGGC    	2	6	0
TTTCGTTTATTAACAATGCGAAGTGGAAGT	3	69	1
GAACAACTGATAACATCACGGTGCGTCTGA	4	16	0
GAGTACACCAGCAAAACGCTTAAAGAACAA	4	40	0
TTTTTAGTGTTAACATCGCTCAACCGGGTG	4	126	1
          **********
MAP Score: 1.64242