AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons020_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944239671
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0015	190	phenylalanyl-tRNA synthetase beta subunit (pheT)
#1	TP0848	32	ribosomal protein L20 (rplT)
#2	TP0849	52	ribosomal protein L35 (rpmI)
#3	TP0850	162	translation initiation factor 3 (infC)
#4	TP0973	87	phenylalanyl-tRNA synthetase alpha subunit (pheS)

Motif 1
TGACCGTATACTGAGCACGGTCGGAGGGCTC          	0	169	1
GATGCCACTACACGGCACACGTGCTCTACACTTTAGTCATA	0	82	0
 CTATTTCTCCACACTACGGCAGATGTACCCTGATGCAGAA	4	9	1
CCTTTGTGCGCACGGTACTTATGCCGTGCGCATATGAGCGC	0	17	1
CCACGCTCCTCCGTCCTCTCACGCTTGCCAC          	1	0	0
TCAAAAAAAGGACACCACAAGGGCCAGCCACCACACCGTCT	0	131	0
AATTGAGAAACAGCCTACATCTAAACGGCGCGAAAATACGT	4	55	1
CATATGAGCGCTCAGTTTAAGAGTGTTACGCGTATTATGAC	0	47	1
AGCCACCACACCGTCTTTGCAGAGGATGCCACTACACGGCA	0	106	0
TAAAAATTCACCACCTATAGTGGGCATCCAAAAGGGAGA  	3	8	0
TCCAACAACACGAACTGCAGTTACCCGACACTCCA      	2	4	0
          * * ****    *   * * *
MAP Score: 9.52981

Motif 2
GAGTGTTACGCGTATTATGACTAAAGTGTA	0	67	1
GCACGTGTGCCGTGTAGTGGCATCCTCTGC	0	99	1
CTGCAAAGACGGTGTGGTGGCTGGCCCTTG	0	125	1
GTGGCTGGCCCTTGTGGTGTCCTTTTTTTG	0	141	1
TTTTTTTGACCGTATACTGAGCACGGTCGG	0	163	1
AACTGCAGTTCGTGTTGTTGGATAAAGGGG	2	23	1
AAATTCACCACCTATAGTGGGCATCCAAAA	3	16	0
ATAAGGAATTGGGGTTGTGATGGGGATGGT	3	56	1
GGTTGTGATGGGGATGGTGATTTCCTGCAT	3	68	1
GTACATCTGCCGTAGTGTGGAGAAATAG  	4	8	0
          **********
MAP Score: 8.58223

Motif 3
GCGCACGGTACTTATGCCGTGCGCATATGAG	0	24	1
GTGTAGAGCACGTGTGCCGTGTAGTGGCATC	0	92	1
CTGCAAAGACGGTGTGGTGGCTGGCCCTTGT	0	125	1
GTGGCTGGCCCTTGTGGTGTCCTTTTTTTGA	0	141	1
TACTGAGCACGGTCGGAGGGCTC        	0	177	1
  GTGGCAAGCGTGAGAGGACGGAGGAGCGT	1	8	1
GTGAGAGGACGGAGGAGCGTGGT        	1	19	1
         TGGAGTGTCGGGTAACTGCAGT	2	1	1
AGGAATTGGGGTTGTGATGGGGATGGTGATT	3	59	1
TACATCTGCCGTAGTGTGGAGAAATAG    	4	6	0
          ****** ****
MAP Score: 4.06306

Motif 4
CGCGTATTATGACTAAAGTGTAGAGCACGTGTGCCGTGTAGTGGC	0	75	1
CCGTGTAGTGGCATCCTCTGCAAAGACGGTGTGGTGGCTGGCCCT	0	108	1
TTTTTTGACCGTATACTGAGCACGGTCGGAGGGCTC         	0	164	1
        GTGGCAAGCGTGAGAGGACGGAGGAGCGTGGT     	1	2	1
    TGGAGTGTCGGGTAACTGCAGTTCGTGTTGTTGGATAAAGG	2	6	1
TCTCCCTTTTGGATGCCCACTATAGGTGGTGAATTTTTACATGTA	3	10	1
ATTTTTACATGTAAATAAGGAATTGGGGTTGTGATGGGGATGGTG	3	42	1
          * *      * *  *  ****   *
MAP Score: 3.93091

Motif 5
TAAGTACCGTGCGCACAAAGGCATGAGC       	0	3	0
GCGCTCATATGCGCACGGCATAAGTACCGTGCGCA	0	23	0
CTAAAGTGTAGAGCACGTGTGCCGTGTAGTGGCAT	0	87	1
ACCGTATACTGAGCACGGTCGGAGGGCTC      	0	171	1
GCAAGCGTGAGAGGACGGAGGAGCGTGGT      	1	13	1
CCTTTTGGATGCCCACTATAGGTGGTGAATTTTTA	3	14	1
CTAGATTGGGGCCCAGTCTTGTTTTTTAGCGTGCA	3	127	1
          *******   *  **
MAP Score: 1.97083

Motif 6
CACGTGTGCCGTGTAGTGGCATCCTCTGCA	0	100	1
TGCAAAGACGGTGTGGTGGCTGGCCCTTGT	0	126	1
TGGCTGGCCCTTGTGGTGTCCTTTTTTTGA	0	142	1
    TCTCCCTTTTGGATGCCCACTATAGG	3	6	1
          **********
MAP Score: 1.75485

Motif 7
AGCGCTCATATGCGCACGGCATAAGTACCGTGCGCACAAAGG	0	17	0
TTATGACTAAAGTGTAGAGCACGTGTGCCGTGTAGTGGCATC	0	81	1
TGGCATCCTCTGCAAAGACGGTGTGGTGGCTGGCCCTTGTGG	0	116	1
GTCCTTTTTTTGACCGTATACTGAGCACGGTCGGAGGGCTC 	0	159	1
  GTGGCAAGCGTGAGAGGACGGAGGAGCGTGGT        	1	8	1
     TGGAGTGTCGGGTAACTGCAGTTCGTGTTGTTGGATA	2	5	1
 TCTCCCTTTTGGATGCCCACTATAGGTGGTGAATTTTTACA	3	9	1
AATAAGGAATTGGGGTTGTGATGGGGATGGTGATTTCCTGCA	3	55	1
          **         ** **  ****
MAP Score: 1.74623

Motif 8
    GCTCATGCCTTTGTGCGCACGGTACTTATGCCGTGC	0	6	1
CGGTACTTATGCCGTGCGCATATGAGCGCTCAGTTTAAGA	0	29	1
GAGCACGTGTGCCGTGTAGTGGCATCCTCTGCAAAGACGG	0	97	1
GTGGTGGCTGGCCCTTGTGGTGTCCTTTTTTTGACCGTAT	0	138	1
       TCTCCCTTTTGGATGCCCACTATAGGTGGTGAA	3	3	1
GTATTTTCGCGCCGTTTAGATGTAGGCTGTTTCTCAATTT	4	54	0
          *** **  * **    *  *
MAP Score: 1.04162

Motif 9
AGCGCTCAGTTTAAGAGTGTTACGCGTATT	0	53	1
GTATTATGACTAAAGTGTAGAGCACGTGTG	0	78	1
TACATGTAAATAAGGAATTGGGGTTGTGAT	3	47	1
ACATGACATATTAGGAATGGCTAGATTGGG	3	107	1
TTAGCGTGCATTAGAAGTGG          	3	152	1
TTCGCGCCGTTTAGATGTAGGCTGTTTCTC	4	59	0
          **********
MAP Score: 0.0634156