AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_profile014_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944234407
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0071	219	oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
#1	TM0072	76	oligopeptide ABC transporter, permease protein
#2	TM0168	91	leucyl-tRNA synthetase
#3	TM0271	64	hypothetical protein
#4	TM0272	74	pyruvate,orthophosphate dikinase
#5	TM0481	300	conserved hypothetical protein
#6	TM1066	61	oligopeptide ABC transporter, permease protein
#7	TM1067	243	oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
#8	TM1068	24	alpha-glucosidase, putative
#9	TM1069	107	transcriptional regulator, DeoR family
#10	TM1501	50	ribosomal protein S10
#11	TM1505	115	ribosomal protein S12
#12	TM1506	46	conserved hypothetical protein

Motif 1
GGGGGTTGTCCCCCCGGCCCCCTGTTTGAAAAT	1	21	0
CTTCTGACTCCCTCCTTTTCCTTTCGTATCCAA	4	51	0
 AACATGAAACCTCCTTCTCTATGATTTAACGA	0	9	1
TAGGGGAGGGCCTCCCTCCCTTTTATTTACACC	6	14	1
   ATCAACACCTCCTTTCCTTTCGAAAAATTT	9	87	0
 GGTATCTGCCCTCCTTTTCTCTTTAAAGGACC	1	54	0
   CGTGCTACCTCCTTTCCTGTGTTATCATAA	3	7	1
GGGGGGACAACCCCCGGTCCTTTAAAGAGAAAA	1	39	1
GGAGGGAGGCCCTCCCCTATCGT          	6	0	0
  GTTCAGAACCTCCTTCTTTTTTCTTCACCAA	3	43	0
  GGGGGACGCTTCCCCCTCCTTTTTGAGAGAA	10	8	1
         CCTTCCAGCTCCTTTCCGAAAAAT	2	1	1
TGAGCTACACCCGCCTGCTCTATCTTGGTGCGA	5	153	0
      ACCACCCCCTGCGTTATAGAATGATCA	7	226	0
          CCTCCCTTCCGTTTTACTCCAAG	11	102	0
TTCTAAGCACCCTCCCTCTTCTCTCAAAAAGGA	10	26	0
GTGCAGATAACCTCCATTATCCCAAAAAAACGC	0	114	1
GGGGAAATTTCCCCTTCTTCTTTTTCTTTATGT	5	259	1
TCAAGTCCCACCTCTCGCACCAAGATAGAGCAG	5	139	1
TCTGCCAGTTCCGCCACTCTCGCACCGCTGGTG	5	64	0
GGGGAAATTTCCCCTTCTTTTTTGTCTGGAGCG	5	240	0
GAACCCGCGACCCCCAGCTTGGCAAGCTGGTGC	5	194	0
      GGCTCTTCTACCTCCACGACATAAAGA	5	283	0
TGTCGTTTTTCTTCTTTTTTCTCTTTTTTCCTT	0	57	0
          ***** ** ** *
MAP Score: 47.2613

Motif 2
ATAACATACAATCAAGGGAGGTGAGTTTTC   	0	199	1
AAATATTTTCAAACAGGGGGCCGGGGGGACAAC	1	17	1
TCTCTTTAAAGGACCGGGGGTTGTCCCCCCGGC	1	36	0
TCCTTTAAAGAGAAAAGGAGGGCAGATACC   	1	56	1
AGAATTTTTCGGAAAGGAGCTGGAAGG      	2	4	0
TGAGAAGGAAATATCAGGAGGTGTAGAC     	2	73	1
TGATAACACAGGAAAGGAGGTAGCACG      	3	4	0
TTTGGTGAAGAAAAAAGAAGGAGGTTCTGAAC 	3	42	1
GGATACGAAAGGAAAAGGAGGGAGTCAGAAG  	4	53	1
CCTGACTTTTAATCAGGGGGTCGTGGGTTCGAA	5	19	1
CCAGCTTGCCAAGCTGGGGGTCGCGGGTTCGAA	5	197	1
CGCTCCAGACAAAAAAGAAGGGGAAATTTCCCC	5	240	1
ACATAAAGAAAAAGAAGAAGGGGAAATTTCCCC	5	259	0
          ACGATAGGGGAGGGCCTCCCTCC	6	0	1
AGGTGTAAATAAAAGGGAGGGAGGCCCTCCCCT	6	15	0
TACACCTTAGATAGAACGAGGTGGTAAATC   	6	41	1
ATCATTCTATAACGCAGGGGGTGGT        	7	228	1
    TTAATTCAACAGGGAGGTGCACAC     	8	6	1
ATTTTTCGAAAGGAAAGGAGGTGTTGAT     	9	89	1
TTCTCTCAAAAAGGAGGGGGAAGCGTCCCCC  	10	8	0
CTCCTTTTTGAGAGAAGAGGGAGGGTGCTTAGA	10	25	1
GGCTTGGAGTAAAACGGAAGGGAGG        	11	100	1
TAAGGAAATTATACTACAGGGAGCGTGAAGCC 	12	24	1
          * * ******* *
MAP Score: 20.8486

Motif 3
 AACATGAAACCTCCTTCTCTATGATTTAA	0	9	1
TTTTCTCTTTTTTCCTTTCTGGTATTATAT	0	44	0
TTTTCTTCTTTTTTCTCTTTTTTCCTTTCT	0	54	0
ATATTGTCGTTTTTCTTCTTTTTTCTCTTT	0	64	0
TGTTATATTTTTTCCTTTCGGGAAATATTT	0	175	0
    GAAAACTCACCTCCCTTGATTGTATG	0	203	0
GACCGGGGGTTGTCCCCCCGGCCCCCTGTT	1	28	0
 GGTATCTGCCCTCCTTTTCTCTTTAAAGG	1	57	0
      CCTTCCAGCTCCTTTCCGAAAAAT	2	4	1
CCTCCTGATATTTCCTTCTCAAAGTTAATA	2	64	0
      GTCTACACCTCCTGATATTTCCTT	2	77	0
      CGTGCTACCTCCTTTCCTGTGTTA	3	4	1
CCTCCTTCTTTTTTCTTCACCAAAACTTAT	3	36	0
  GTTCAGAACCTCCTTCTTTTTTCTTCAC	3	46	0
ACTCCCTCCTTTTCCTTTCGTATCCAAGAA	4	48	0
    CTTCTGACTCCCTCCTTTTCCTTTCG	4	58	0
TTCGAACCCACGACCCCCTGATTAAAAGTC	5	22	0
GGTTCAAGTCCCACCTCTCGCACCAAGATA	5	136	1
GAAGGGGAAATTTCCCCTTCTTTTTTGTCT	5	246	0
GAAGGGGAAATTTCCCCTTCTTCTTTTTCT	5	256	1
CCCTTCTTCTTTTTCTTTATGTCGTGGAGG	5	270	1
   GGCTCTTCTACCTCCACGACATAAAGA	5	283	0
GGAGGGAGGCCCTCCCCTATCGT       	6	3	0
TAGGGGAGGGCCTCCCTCCCTTTTATTTAC	6	14	1
TTATATTAGTTTTCCTTTTGCTTACAACCC	7	65	0
         ACCACCCCCTGCGTTATAGAA	7	232	0
   GTGTGCACCTCCCTGTTGAATTAA   	8	7	0
TCAACACCTCCTTTCCTTTCGAAAAATTTT	9	86	0
  GGGGGACGCTTCCCCCTCCTTTTTGAGA	10	8	1
TTCTAAGCACCCTCCCTCTTCTCTCAAAAA	10	29	0
          CCTCCCTTCCGTTTTACTCC	11	105	0
CTGTAGTATAATTTCCTTAGAAAGTATACC	12	13	0
          **********
MAP Score: 19.312

Motif 4
TTGTAAAAGATTATTTCAAAATATTGTCGT	0	84	0
ATAACCTCCATTATCCCAAAAAAACGCACC	0	120	1
CCGAAAAATTCTATCACAAATGGCTGAAAA	2	25	1
CTTTCCTGTGTTATCATAAGTTTTGGTGAA	3	21	1
ATCCAAGAATTTATTATAAAATCAAAACCG	4	27	0
GGCGCTACGGTTTTTACAAATCGATTTT  	7	8	0
CGTTATAGAATGATCATAAAAATGAACCAT	7	212	0
ATACATAAAGTTATCATAAATTAATCACAA	9	36	1
TATCATAAATTAATCACAAAAGTCAACGAT	9	47	1
TCGAAAAATTTTATCACAAATATCGTTGAC	9	68	0
ACCCTCCCTCTTCTCTCAAAAAGGAGGGGG	10	21	0
TCTGATCAATTTATCATAAGTAGTTTAAAA	11	16	0
          **********
MAP Score: 11.3442