AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_sum_all080_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944244893
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0951	213	ribosomal protein L28 (rpL28)
#1	HI0952_HI0953	124	HI0952: DNA repair protein (radC), HI0953: DNA/pantothenate metabolism flavoprotein (dfp)
#2	HI0954	47	deoxyuridinetriphosphatase (dut)

Motif 1
TATAATATTGACCATTTTTTTACCGATTACAT	0	15	1
ATAATTTGCGACCTTTAATATAGTAAGCGGGT	0	92	1
CGTAAGCTCGAGCTTATATTTAATTATTGGAG	0	185	1
TCGTTATTTTACTTTAATTTTATTGAATGCCC	1	42	1
TGAATGCCCAACGCTATTTTTACGATATGCAT	1	65	1
     TTCCAACCGTACTTTTACCTAAAAATG	2	5	1
          *** ** *****
MAP Score: 4.93701

Motif 2
CTGAATGTAATCGGTAAAAAAATGGTCAAT	0	21	0
AGTAAGCGGGTCGGATTAGCGCGACCTGAC	0	113	1
GGTAGCAAGCTAGGTTTAACCAGCTTTAAA	0	145	1
GCTCGAGCTTACGGTTCGGATTGTTTAAAG	0	168	0
AGTACTAACAAAGGTTAAAAC         	1	1	0
      TTTTTAGGTTTGACGAGCAAGTGA	1	110	0
AGGTAAAAGTACGGTTGGAA          	2	0	0
AATTCATTTTTAGGTAAAAGTACGGTTGGA	2	11	0
   TTAATACTCCGTTTGAAATTCATTTTT	2	30	0
          **********
MAP Score: 1.51533