AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons011_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944239280
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0884	29	conserved hypothetical integral membrane protein
#1	TP0886	147	polyribonucleotide nucleotidyltransferase (pnp)
#2	TP0891	175	translation initiation factor 2 (infB)

Motif 1
         GGGCTTTGCATGGGGAAGTTT	1	1	1
GGGGAAGTTTCGCAGTGCGTGCCGCCGAGG	1	21	1
GCCGCCGAGGGGTTGTGCATAGGACGGTTG	1	41	1
TGCATAGGACGGTTGTCCGTTCTGCTTTCT	1	56	1
CTTCGCAGGTGGCTGTGCCAGGGCTTGGTG	1	94	1
CTAGTGAGCAGGCTGTGCGTTCACCGGTGA	2	60	1
          **********
MAP Score: 12.5566

Motif 2
      TTACCTAGATGTGGAGAAGAGTGCTTTTT       	0	4	1
       GGGCTTTGCATGGGGAAGTTTCGCAGTGCGTGCCG	1	3	1
CCGCCGAGGGGTTGTGCATAGGACGGTTGTCCGTTCTGCTTT	1	42	1
CTTTCTTTGTCTAGCTTCGCAGGTGGCTGTGCCAGGGCTTGG	1	80	1
GTGGCTGTGCCAGGGCTTGGTGCGGCCTGCGATACATTCTGT	1	102	1
CACTTCCCGTGTTGCTAGTGAGCAGGCTGTGCGTTCACCGGT	2	46	1
GCAGGCTGTGCGTTCACCGGTGACGTCTGGTCAAACTACCTC	2	67	1
ACATCCGCCCGTGTACGAGAGGTAGTTTGACCAGACGTCACC	2	85	0
          ** *    ** *  *  **  *
MAP Score: 7.75646

Motif 3
TGCATGGGGAAGTTTCGCAGTGCGTGCCGCCGAG	1	16	1
CGCCGAGGGGTTGTGCATAGGACGGTTGTCCGTT	1	43	1
TTCTTTGTCTAGCTTCGCAGGTGGCTGTGCCAGG	1	82	1
AAGAACAGAATGTATCGCAGGCCGCACCAAGCCC	1	114	0
CCTGCTCACTAGCAACACGGGAAGTGTCTTTAGG	2	38	0
CCCGTGTTGCTAGTGAGCAGGCTGTGCGTTCACC	2	51	1
AAACTACCTCTCGTACACGGGCGGATGTTGACGT	2	99	1
          * ** ******  *
MAP Score: 5.61801

Motif 4
       GGGCTTTGCATGGGGAAGTTTCGCAGTGCGTGCCGC	1	3	1
GGAAGTTTCGCAGTGCGTGCCGCCGAGGGGTTGTGCATAGGAC	1	23	1
CTTTGTCTAGCTTCGCAGGTGGCTGTGCCAGGGCTTGGTGCGG	1	84	1
GTGGCTGTGCCAGGGCTTGGTGCGGCCTGCGATACATTCTGTT	1	102	1
CGTGTTGCTAGTGAGCAGGCTGTGCGTTCACCGGTGACGTCTG	2	53	1
ACCTCTCGTACACGGGCGGATGTTGACGTAAAGGAGAAAAGAC	2	104	1
          **  ** **  *  *   *   *
MAP Score: 3.10989

Motif 5
        GGGCTTTGCATGGGGAAGTTTCGC	1	2	1
TTCGCAGTGCGTGCCGCCGAGGGGTTGTGCAT	1	29	1
GAGGGGTTGTGCATAGGACGGTTGTCCGTTCT	1	47	1
TCTTTGTCTAGCTTCGCAGGTGGCTGTGCCAG	1	83	1
CCAGGGCTTGGTGCGGCCTGCGATACATTCTG	1	111	1
ACGCCTAAAGACACTTCCCGTGTTGCTAGTGA	2	35	1
ACCGGTGAACGCACAGCCTGCTCACTAGCAAC	2	56	0
TACCTCTCGTACACGGGCGGATGTTGACGTAA	2	103	1
          **** ***** *
MAP Score: 0.349461