AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons016_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242552
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ileS	300	Isoleucyl-tRNA Synthetase
#1	pfrA	187	Peptide Chain Releasing Factor (RF-1)
#2	rl19	25	L19 Ribosomal Protein
#3	rnhB_2	63	Ribonuclease HII
#4	leuS	196	Leucyl tRNA Synthetase
#5	valS	126	Valyl tRNA Synthetase
#6	CT691	160	hypothetical protein
#7	murB	132	UDP-N-Acetylenolpyruvoylglucosamine Reductase

Motif 1
CCTGAATCCCCTCTCTTTCATTTCCCTTTGCC	0	53	0
ATGGAGGAACCACTCTTTTACTCCTAGGCCAA	0	98	0
ATTTATTGTGCTCTCTTCCGCTCGCTCGATAA	0	128	1
GGGTGTTCGCCCCGCTTTTCTCTAGATAACAG	1	25	0
GGGCGAACACCCCGCTTTTTTTGTTTTAATAA	1	45	1
GTTTTAATAAGTCTCTCTTTTTGAATCTGACT	1	67	1
CTTAATGCCGCTCTCTTTTCTTTA        	3	2	0
GTGTATGTTTGACGCTTATTTCTCTCTAAGTG	4	122	1
CTTGGACGGAGTCGCTTCCCTTACTCTGTCAT	7	54	0
TTGGGCTTGTGTCGCTTCCCTTGAACAGTCAA	7	91	1
          * ******* **
MAP Score: 10.2649

Motif 2
TAACTTGTTCATTAAAAGCGGATTGTGGTCGAGGCAAAGG	0	21	1
GGCAAAGGGAAATGAAAGAGAGGGGATTCAGGCGATTATA	0	53	1
TTGGCCTAGGAGTAAAAGAGTGGTTCCTCCATTTATTGTG	0	98	1
TTAATTAACGGTTTAAAAGGCGAATCGATCATAATCCGTT	0	167	1
CTGTTATCTAGAGAAAAGCGGGGCGAACACCCCGCTTTTT	1	25	1
TGACTTTTCAGAGTAAAGTCTAGTGTTCCCCAAAAATTGA	1	94	1
AGAGATACTAGAGTAAAGGCAGAAGAAGTCGTTC      	1	163	1
        TAAAGAAAAGAGAGCGGCATTAAGCCCTTTCT	3	2	1
TGTAAAGATTGGGGAAAGGGAAGTGTATACCAGGATCGCA	4	23	1
AAGATGATGGATTCGCAGACTGGAGAGGACTTGATTTCGA	4	71	1
ATCTCCTACTATTTGAAGGGGACCTCGAGCGTGAAAAATC	6	18	1
ATCACATTAGAATGACAGAGTAAGGGAAGCGACTCCGTCC	7	43	1
          * * **** * *  *    *
MAP Score: 8.78788

Motif 3
AACTTGTTCATTAAAAGCGGATTGTGGTCGA	0	22	1
AATTAACGGTTTAAAAGGCGAATCGATCATA	0	169	1
ACTGCAAACTTTGTAAGCAGATCGATCAAAC	0	240	1
AGTCTCTCTTTTTGAATCTGACTTTTCAGAG	1	76	1
  AAAAAGAATTTTTAGGTGAAATACA    	2	8	1
ATCATCTTTTTTTTAATGCGATCCTGGTATA	4	48	0
TGCAAGGCGGTTGTAAGGAGAGAAAACCTTA	4	152	1
ACGAGGTGACTTTAACGGAGAACATATTGCC	5	44	0
TCTCCTACTATTTGAAGGGGACCTCGAGCGT	6	19	1
TACTCTGTCATTCTAATGTGATAGATGGTAA	7	34	0
          ******** **
MAP Score: 7.95938

Motif 4
         AGAAATCAATGTAACTTGTTCATTA	0	1	1
GCGAGCGGAAGAGAGCACAATAAATGGAGGAACC	0	119	0
ACCTGTTTAGGAAAGCAGTTAAACTGCAAACTTT	0	218	1
TCAAACTTTCGAAAGCATCAAAACCCATAAGTGA	0	265	1
TTCAAAAAGAGAGACTTATTAAAACAAAAAAAGC	1	58	0
 TAAAGAAAAGAGAGCGGCATTAAGCCCTTTCTG	3	9	1
TCTTGACGTTGAGAACAGCAGAAAGGGCTTAATG	3	27	0
     AAGCAGAGATCTCTGTAAAGATTGGGGAA	4	5	1
CACTATGTCTGAGATCGAAATCAAGTCCTCTCCA	4	91	0
CACTTAGAGAGAAATAAGCGTCAAACATACACTA	4	120	0
GTTGTAAGGAGAGAAAACCTTAAAAATAACAACA	4	161	1
TTAGAGATGCGAGAATAGTCACAACATATGGAAG	5	96	1
AAAAATCTTAGAAAAAAACAAAAAATTTTGGTTC	6	51	1
          **** ** *  ***
MAP Score: 7.09089

Motif 5
TTAACTAACGGATTATGATCGATTCGCCTTT	0	182	0
TTCCTCCATTTATTGTGCTCTCTTCCGCTCG	0	121	1
ATTAAAAGCGGATTGTGGTCGAGGCAAAGGG	0	31	1
TTTTTTCTAAGATTTTTCACGCTCGAGGTCC	6	37	0
GAGAGGACTTGATTTCGATCTCAGACATAGT	4	93	1
CATATGTTGTGACTATTCTCGCATCTCTAAT	5	95	0
     TCTTTGATTATTCACTTATGGGTTTT	0	284	0
   ATACCTATATTTTTATCTTTAGCATTAC	7	7	1
TTTAGAGCTTGATTATGATCAAGCAAGAGGT	5	13	0
GTTTGACGCTTATTTCTCTCTAAGTGCAAGG	4	128	1
TTAATTAAAATATGCTTATCGAGCGAGCGGA	0	144	0
GGGAACACTAGACTTTACTCTGAAAAGTCAG	1	93	0
          **** ******
MAP Score: 4.52784

Motif 6
GAGCGGAAGAGAGCACAATAAATGGAGGAACCA	0	118	0
ACCTGTTTAGGAAAGCAGTTAAACTGCAAACTT	0	218	1
TCAAACTTTCGAAAGCATCAAAACCCATAAGTG	0	265	1
CTTTTCTCTAGATAACAGAAAGTTCTGTTCAAA	1	10	0
AGAGACTTATTAAAACAAAAAAAGCGGGGTGTT	1	50	0
TCTTGACGTTGAGAACAGCAGAAAGGGCTTAAT	3	28	0
TGTATACCAGGATCGCATTAAAAAAAAGATGAT	4	46	1
TGTAAGGAGAGAAAACCTTAAAAATAACAACAG	4	163	1
AAAAATCTTAGAAAAAAACAAAAAATTTTGGTT	6	51	1
CATTACCATCTATCACATTAGAATGACAGAGTA	7	32	1
          ** ****  ****
MAP Score: 4.03311

Motif 7
ACTTTTCAGAGTAAAGTCTAGTGTTCCCCAA	1	96	1
GATTGCCAATGTACACTCTGGTCTTTGTTAG	1	132	1
AGAGATCTCTGTAAAGATTGGGGAAAGGGAA	4	14	1
TTGGTTCTTAGTACATTCTAGATTGCAAATA	6	78	1
TATGAAGGAGGTATATTTTGGGAGCATTTTT	6	113	1
          *** *******
MAP Score: 0.270329

Motif 8
TGTTGTGACTATTCTCGCATCTCTAATTAACCG	5	89	0
TTCAGAGTAAAGTCTAGTGTTCCCCAAAAATTG	1	100	1
CTGAATCCCCTCTCTTTCATTTCCCTTTGCCTC	0	51	0
TTCTGCCTTTACTCTAGTATCTCTCTAACAAAG	1	154	0
TCTCTTTTTGAATCTGACTTTTCAGAGTAAAGT	1	80	1
TGTTTTAATAAGTCTCTCTTTTTGAATCTGACT	1	66	1
CGCTTCCCTTACTCTGTCATTCTAATGTGATAG	7	41	0
GCCAATGTACACTCTGGTCTTTGTTAGAGAGAT	1	136	1
TTTTTAAGGTTTTCTCTCCTTACAACCGCCTTG	4	154	0
TGGAGGAACCACTCTTTTACTCCTAGGCCAACC	0	96	0
TTAATGCCGCTCTCTTTTCTTTA          	3	0	0
TGAACAGAACTTTCTGTTATCTAGAGAAAAGCG	1	12	1
          * *** ** ****
MAP Score: 0.240931