AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_operons010_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944244376
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH1	170	conserved protein
#1	MTH5	22	ribosomal protein L8 (E.coli L2)
#2	MTH9	46	ribosomal protein L35 (E.coli L29)
#3	MTH21	109	ribosomal protein L19
#4	MTH31	30	ribosomal protein L14
#5	MTH34	236	ribosomal protein S18 (E.coli S13)
#6	MTH40	58	DNA-dependent RNA polymerase, subunit N
#7	MTH42	171	DNA-dependent RNA polymerase, subunit K 
#8	MTH43	51	enolase
#9	MTH44	27	ribosomal protein Sa (E.coli S2)
#10	MTH47	21	conserved protein
#11	MTH1380	167	serine hydroxymethyltransferase
#12	MTH1381	151	heterodisulfide reductase, subunit A 
#13	MTH1383	52	DNA repair protein RadA
#14	MTH1385	300	replication factor A related protein

Motif 1
AACTTTAAGTAAGGTTTATATACTATTACACT	12	74	0
TCACCAGCGGAAAGTTTAAATATGGATACCAT	0	12	1
CTTTGATAATAAGATTTAAATATATAGTAATA	14	203	1
ATCTCCCTTAAATCTTTAAATATTCATTAAGC	13	26	0
CGACGGCAGCAATACTTAAATAGATGTCATAA	5	14	1
ACACAGAATAAACATTTATTTAATATACCTGA	12	28	1
TTTTGATAGAAATATTTATTTAGCACTGTGGT	12	105	1
GCATTGTGGAAATATTTATAAATAAATCCGGA	0	135	1
 ATCAATCGATAACTTTATATATTTTTATTTT	6	9	1
CTCCAAGAAAAACATTAAAATAGAGGTTCTTG	7	145	0
GGAGCTCACCAAGTCTTTTATAGACGGGGCGT	14	250	1
ACCTTACTTAAAGTTTTTGATAGAAATATTTA	12	91	1
CGGCCCTATAAATACTTTGATAATAAGATTTA	14	189	1
          **  ********
MAP Score: 10.2671

Motif 2
GGAAAATATGCCCCTTCCAGTCCTCC      	3	4	0
GGGCATATTTTCCAGTCCAGCGAAAAAACTTT	3	23	1
ATATGATACATCCTGTGCCGGGATAGCCTAGC	5	55	1
CCACAAGATTTCCAGTCTTGCGCCTTACCTGG	5	86	0
GGGTTCAAATCCCAGTCCCGGCGTCGGTTAAA	5	133	1
ATTCGCAAACCCCCGTCCCGCGAATTCACTCT	5	198	1
GCTGACCATCCCCGTTCCAGTTGAAAAGTCCG	7	59	0
TCTCCAGCGTTCCGGTGCTGACCATCCCCGTT	7	75	0
ACCACTATTTTTCAGTCTAGAGTTTATTATGA	8	20	1
          *** ****** *
MAP Score: 9.66606

Motif 3
CTGATACGATGTGGTCTGTGGTTTTACTTGC	0	97	1
TGAATACAAGGAGGTTTCTTGA         	3	97	1
AAAAGTTACTGAGGTGATTTA          	4	19	1
TGGAAATCTTGTGGAGCTTTGCTCCTCCTGG	5	104	1
ACTCTTACTGGAGGTTAATGA          	5	225	1
CATTAAAATAGAGGTTCTTGGATTCGATTTG	7	134	0
CTGAAAAATAGTGGTTTATTAGAGT      	8	4	0
AGTTTATTATGAGGTGTTTTA          	8	40	1
AAACTTATTTGAGGTGATAGA          	9	16	1
GTTCCAGCAAGTGGTCCATGGGGCAGTCTGT	14	49	1
          ******* ***
MAP Score: 4.77421

Motif 4
AGATTTCCAGTCTTGCGCCTTACCTGGCTA	5	83	0
AAAGCAACCCTGTTGCACCTACGACTCTTA	5	162	1
          TCATTAACCTCCAGTAAGAG	5	226	0
          TCTATCACCTCAAATAAGTT	9	17	0
AATTAGAGCCTCTTTAACCTTCTGATGTCC	14	83	1
TGGATAACTGTCTTTCGCCTTCATACTGAA	14	125	1
          **********
MAP Score: 3.8187

Motif 5
ATCCCCTTAAAAAGTTTTTTCGCTGGACTGGA	3	33	0
TGAAATTTTTCGGGTTTATCAGCAAATGCTGA	3	68	1
CCTCTATTTTAATGTTTTTCTTGGAGGCAT  	7	151	1
TTTTCAGTCTAGAGTTTATTATGAGGTGTTTT	8	28	1
GCTATCAACACGCGTTTTTTATGTTGACATCG	11	89	1
ATATTAAATAAATGTTTATTCTGTGTGTATTT	12	22	0
CACTTTCCTCAGTTTTTTTCAGGTATATTAAA	12	46	0
AACCTTACTTAAAGTTTTTGATAGAAATATTT	12	90	1
AAAATTCAGACGAGTTTTTCAGTATGAAGGCG	14	140	0
AGGAGCTCACCAAGTCTTTTATAGACGGGGCG	14	249	1
          ** ****** **
MAP Score: 1.20429