AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_operons016_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944244737
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH478	49	sulfate transport system permease protein
#1	MTH479	136	conserved protein
#2	MTH922	67	unknown
#3	MTH923	21	unknown
#4	MTH925	32	conserved protein
#5	MTH927	139	ferredoxin
#6	MTH1723	141	unknown
#7	MTH1727	117	phosphate-binding protein PstS
#8	MTH1728	83	phosphate-binding protein PstS homolog
#9	MTH1734	21	phosphate transport system regulator

Motif 1
TATTTTTAAGACCCCGACTTTTTCTGAAG    	0	30	1
GCAGCTGAGGACCCCCGCAGTTATAATGGATAT	5	45	0
ATTTCTTCTGACATCTGCATTTTAGATCATATT	6	109	0
          CCCTCAGCCATTTCTTCTGACAT	6	128	0
    TTTATCACCTCAACCTTTACCTTATCCTA	7	98	0
GGTTTTCACAACCACAACATTTTTTCTTTCCGT	8	11	1
          *** * ** ****
MAP Score: 5.36174

Motif 2
    TAGGACAGTTCACTGCACTGGAAACGCTCCTGAA	2	6	1
AGAACCTAACTGTTCTCTAATAGAGAAAATAAATATGC	6	69	1
CACAGGGTTTAGTTCACAAAATAGGTAATTAAGTACAC	7	35	1
TAGGTAATTAAGTACACAAAAATAGTAAATTTTAAATA	7	56	1
AATTTTAAATAGTTCTAGGATAAGGTAAAGGTTGAGGT	7	83	1
TGGTTAATAAAGTTCACTTGAAGGTGACGGAAAGAAAA	8	32	0
TCAGTTATTGATTTCACCTATTGGTTAATAAAGTTCAC	8	53	0
          ***** *      ** **
MAP Score: 4.98759

Motif 3
GGGGTCTTAAAAATAAAGTAGTATGTTAACTGTT	0	11	0
TCGTCCTGAAAGATAAAGAAGGACTACTCTGAGG	1	26	0
CAGAACACCTATATCGACATGGACATATATACAT	1	91	0
GGTAATCTGAAAGTAATTCAGCACACCTTTCAGG	2	38	0
ATTTTTCAGGAAATACGTGAGGATATCCATTATA	5	23	1
CTCAGCTGCCATGTAAAACAGTACTGTTTTCATG	5	69	1
ATTAAGAAAGATTTATATATGGACCTGTGGAATA	5	109	1
CTAATAGAGAAAATAAATATGCATAATATGATCT	6	85	1
TTCACAAAATAGGTAATTAAGTACACAAAAATAG	7	47	1
        TAAAATCCAGGAGGACTTTTA     	9	2	1
          * *** *  *****
MAP Score: 4.57106

Motif 4
AACATACTACTTTATTTTTAAGACCCCGACTT	0	18	1
GTAGTCCTTCTTTATCTTTCAGGACGATCCCA	1	33	1
TTTCAATTTTTTTATTTTTCAGGAAATACGTG	5	10	1
GCATATTTATTTTCTCTATTAGAGAACAGTTA	6	75	0
ACCACAACATTTTTTCTTTCCGTCACCTTCAA	8	21	1
          *** ***** **
MAP Score: 4.54109

Motif 5
TAAGACCCCGACTTTTTCTGAAG         	0	36	1
TCTGGGAATAACTCCCTCAGAGTAGTCCTTCT	1	12	1
CCCTCAGAGTAGTCCTTCTTTATCTTTCAGGA	1	25	1
AGTCCTTCTTTATCTTTCAGGACGATCCCATG	1	35	1
CCATGTTCTCATTCCTTCACAGAACCGATATG	1	62	1
TCAATTTTTTTATTTTTCAGGAAATACGTGAG	5	12	1
TCCATATATAAATCTTTCTTAATGGACCTCAT	5	100	0
 CCCTCAGCCATTTCTTCTGACATCTGCATTT	6	120	0
TTGTGAATTAAATTCCTCTGCGCACAGGGTTT	7	13	1
CAACCACAACATTTTTTCTTTCCGTCACCTTC	8	19	1
      TAAAAGTCCTCCTGGATTTTA     	9	5	0
          * ******** *
MAP Score: 4.16204