AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_operons010_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944244363
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH34	236	ribosomal protein S18 (E.coli S13)
#1	MTH40	58	DNA-dependent RNA polymerase, subunit N
#2	MTH42	171	DNA-dependent RNA polymerase, subunit K 
#3	MTH43	51	enolase
#4	MTH44	27	ribosomal protein Sa (E.coli S2)
#5	MTH47	21	conserved protein
#6	MTH1380	167	serine hydroxymethyltransferase

Motif 1
TGGCTAGGCTATCCCGGCACAGGATGTATCATA	0	56	0
CTGGGTTCAAATCCCAGTCCCGGCGTCGGTTAA	0	131	1
AATTCGCAAACCCCCGTCCCGCGAATTCACTCT	0	197	1
   TCATTAACCTCCAGTAAGAGTGAATTCGCG	0	216	0
TTGGTCCATCCTCCCAGCCATTGAAGAAGTTTC	2	26	1
GGTGCTGACCATCCCCGTTCCAGTTGAAAAGTC	2	61	0
AACGCTGGAGACCCGAGTTCAAATCTCGGCGGT	2	96	1
  ATGGGTTAACCCCATCAAATCCTTTATCCTT	6	8	1
TTACATAATACTCCGAGCAATCGGATTCGGAAT	6	49	1
ATTCGGAATCCCCCCAGCTATCAACACGCGTTT	6	73	1
TTGGTGTTAACTTCCATTACCAGTTGCGATGTC	6	114	0
          ******** *  *
MAP Score: 10.0197

Motif 2
GGGTTCAAATCCCAGTCCCGGCGTCGGTTA	0	133	1
GTTAAAGCAACCCTGTTGCACCTACGACTC	0	159	1
ATTCGCAAACCCCCGTCCCGCGAATTCACT	0	198	1
TGCTGACCATCCCCGTTCCAGTTGAAAAGT	2	62	0
CTCGGGTCTCCAGCGTTCCGGTGCTGACCA	2	83	0
CGCTGGAGACCCGAGTTCAAATCTCGGCGG	2	98	1
AACTTCCATTACCAGTTGCGATGTCAACAT	6	109	0
          **********
MAP Score: 8.77708

Motif 3
TGGCTAGGCTATCCCGGCACAGGATGTATCATATAA	0	53	0
GTGCCGGGATAGCCTAGCCAGGTAAGGCGCAAGACT	0	69	1
CTTTAACCGACGCCGGGACTGGGATTTGAACCCAGG	0	130	0
AATTCGCAAACCCCCGTCCCGCGAATTCACTCTTAC	0	197	1
TTGGTCCATCCTCCCAGCCATTGAAGAAGTTTCCGG	2	26	1
CCGGACTTTTCAACTGGAACGGGGATGGTCAGCACC	2	58	1
GGATGGTCAGCACCGGAACGCTGGAGACCCGAGTTC	2	80	1
      ATGCCTCCAAGAAAAACATTAAAATAGAGG	2	151	0
TTACATAATACTCCGAGCAATCGGATTCGGAATCCC	6	49	1
GTTGACATCGCAACTGGTAATGGAAGTTAACACCAA	6	111	1
          * ** ** *   ****
MAP Score: 5.09869

Motif 4
CCTGGGTTCAAATCCCAGTCCCGGCGTCGGTTAA	0	130	1
AAGAATTCGCAAACCCCCGTCCCGCGAATTCACT	0	194	1
GTTATATGATACATCCTGTGCCGGGATAGCCTAG	0	52	1
ATTGGTGTTAACTTCCATTACCAGTTGCGATGTC	6	114	0
CGGTGCTGACCATCCCCGTTCCAGTTGAAAAGTC	2	61	0
CGGTCCCATCAAATCGAATCCAAGAACCTCTATT	2	125	1
GGGGATTCCGAATCCGATTGCTCGGAGTATTATG	6	52	0
          AAACCGACGGCAGCAATACTTAAA	0	0	1
          ******  * ** *
MAP Score: 3.62681

Motif 5
GTCCCGGCGTCGGTTAAAGCAACCCTGTTGCAC	0	147	1
TTCATAAGAGTCGTAGGTGCAACAGGGTTGCTT	0	163	0
GCTGGGAGGATGGACCAAGCTACCCTACGGTCC	2	11	0
AAGAAGTTTCCGGACTTTTCAACTGGAACGGGG	2	49	1
CAAATCTCGGCGGTCCCATCAAATCGAATCCAA	2	115	1
GTTTTTTATGTTGACATCGCAACTGGTAATGGA	6	102	1
CAATTTTATATTGTCATTGCAACTATTTTCCTA	6	144	1
          *****   *****
MAP Score: 2.28551

Motif 6
   TCATTAACCTCCAGTAAGAGTGAATTC	0	219	0
CTTGGTCCATCCTCCCAGCCATTGAAGAAG	2	25	1
CATCAAATCGAATCCAAGAACCTCTATTTT	2	131	1
       ATGCCTCCAAGAAAAACATTAAA	2	158	0
          ACTCTAATAAACCACTATTT	3	0	1
   TCTATCACCTCAAATAAGTTTCAATAT	4	10	0
CTTACATAATACTCCGAGCAATCGGATTCG	6	48	1
          **********
MAP Score: 1.76426