AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_operons016_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944244752
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH478	49	sulfate transport system permease protein
#1	MTH479	136	conserved protein
#2	MTH480	91	unknown
#3	MTH922	67	unknown
#4	MTH923	21	unknown
#5	MTH925	32	conserved protein
#6	MTH927	139	ferredoxin
#7	MTH928	300	cobalamin biosynthesis protein N
#8	MTH1722	264	transcriptional regulator Icc related protein
#9	MTH1723	141	unknown
#10	MTH1727	117	phosphate-binding protein PstS
#11	MTH1728	83	phosphate-binding protein PstS homolog
#12	MTH1734	21	phosphate transport system regulator

Motif 1
GTTAACATACTACTTTATTTTTAAGACCCCGA	0	15	1
AGAGTAGTCCTTCTTTATCTTTCAGGACGATC	1	30	1
CTCTCCCCAATAATGTATTTTTTCACTGAACA	2	47	0
   TTTCAATTTTTTTATTTTTCAGGAAATAC	6	7	1
GATTGATCGATTCAGAATTTTTCTGAAACGTT	7	34	1
ACTCAAGAAATTAAAAATTTTTATAAATATAA	7	87	0
ATTGCATAATTAATGAATATTTTATCTGCATT	7	140	0
GTGATGAATGTATTAAATTTTCATATAATTAT	7	177	1
ATATAATTATTACTTAATTTTTATTAGAGCAA	7	199	1
TTAAGACTTTTTATTAATTTTTTTATTACATA	7	234	0
TAAAAAGTCTTAAATAATCTTCATACCATATC	7	253	1
CTATTTAAAATTTACTATTTTTGTGTACTTAA	10	63	0
          ** * *******
MAP Score: 10.1419

Motif 2
TTCAGAAAAAGTCGGGGTCTTAAAAATAAAGTA	0	25	0
CATTATAACTGCGGGGGTCCTCAGCTGCCATGT	6	50	1
CAATTACCATGCAGGGGTGCCCGAGCGGCCAAA	8	48	1
GCGGCCAAAGGGGGAGGACTTAAGATCCTCTGG	8	72	1
AGATCCTCTGGCGCAGGCCTTCGAGGGTTCGAA	8	94	1
TGCCTTAGTGGCTCAGGTGGTAGAGCGATGCCT	8	175	1
GTAAGGCATAGGTCGGGGGTTCGAATCCCCCCT	8	210	1
       ATACCCGGGGGCTTCATCATCAATAA	9	3	1
ATTCCTCTGCGCACAGGGTTTAGTTCACAAAAT	10	24	1
TAAGGTAAAGGTTGAGGTGATAAA         	10	103	1
          ** **** * ***
MAP Score: 6.27743

Motif 3
GTCCATTAAGAAAGATTTATATATGGACCTGTG	6	105	1
TGAATGTATTAAATTTTCATATAATTATTACTT	7	181	1
TTTTTGATGCAAAGCTTGATATACCAGCAGAAC	9	41	1
TATGTAATAAAAAAATTAATAAAAAGTCTTAAA	7	234	1
AAGAAATTAAAAATTTTTATAAATATAACGGCA	7	82	0
AATGCAGATAAAATATTCATTAATTATGCAATA	7	140	1
TTGCTCTAATAAAAATTAAGTAATAATTATATG	7	198	0
GCTTTGCATCAAAAATGAATTTATTGATGATGA	9	23	0
AAGCCCTTTAAACGTTTCAGAAAAATTCTGAAT	7	43	0
          ***  ** *****
MAP Score: 5.7704

Motif 4
AATGCAGATAAAATATTCATTAATTATGCAATAACGC	7	140	1
ATTTTCATATAATTATTACTTAATTTTTATTAGAGCA	7	193	1
AATTAATAAAAAGTCTTAAATAATCTTCATACCATAT	7	247	1
GTCCATATATAAATCTTTCTTAATGGACCTCATGAAA	6	96	0
AGCAGAACCTAACTGTTCTCTAATAGAGAAAATAAAT	9	66	1
CAAAAATAGTAAATTTTAAATAGTTCTAGGATAAGGT	10	72	1
TATTGATTTCACCTATTGGTTAATAAAGTTCACTTGA	11	49	0
AAGAAATTAAAAATTTTTATAAATATAACGGCAAGGT	7	78	0
CCTGCATGGTAATTGATTAGTAGTAGAAAGTGGTATA	8	26	0
          ** * **   ****  *
MAP Score: 5.1995

Motif 5
CATACTACTTTATTTTTAAGACCCCGACTTTTTCTGA	0	20	1
     GTTCTGGGAATAACTCCCTCAGAGTAGTCCTT	1	5	1
CAAAGGGGGAGGACTTAAGATCCTCTGGCGCAGGCCT	8	77	1
TGCAGGGGAAGGGATTCGAACCCTCGAAGGCCTGCGC	8	104	0
AGCCTTAGGGGGGATTCGAACCCCCGACCTATGCCTT	8	212	0
TGAATTTATTGATGATGAAGCCCCCGGGTAT      	9	4	0
    TTATTGTGAATTAAATTCCTCTGCGCACAGGGT	10	6	1
TCACAAAATAGGTAATTAAGTACACAAAAATAGTAAA	10	48	1
         TGGTTTTCACAACCACAACATTTTTTCT	11	1	1
          **  ** **  ** * *
MAP Score: 5.17514

Motif 6
CTTCTTTATCTTTCAGGACGATCCCATGTTCTCATTC	1	39	1
TCAGCACACCTTTCAGGAGCGTTTCCAGTGCAGTGAA	3	18	0
TCTGAAAGTAATTCAGCACACCTTTCAGGAGCGTTTC	3	30	0
TTTTTTTATTTTTCAGGAAATACGTGAGGATATCCAT	6	16	1
ACAGTACTGTTTTCATGAGGTCCATTAAGAAAGATTT	6	86	1
TATATAAATCTTTCTTAATGGACCTCATGAAAACAGT	6	91	0
TGATTGATCGATTCAGAATTTTTCTGAAACGTTTAAA	7	33	1
CCTTTAAACGTTTCAGAAAAATTCTGAATCGATCAAT	7	35	0
CAGATAAAATATTCATTAATTATGCAATAACGCGTGA	7	144	1
      TAAAATCCAGGAGGACTTTTA          	12	4	1
          ****** *    * * *
MAP Score: 4.11302

Motif 7
TCTGATGTTCAGTGAAAAAATACATTATTGG	2	42	1
TTTCCTGAAAAATAAAAAAATTGAAA     	6	5	0
TAACTCAAGAAATTAAAAATTTTTATAAATA	7	90	0
ATACATCGGTAATACATAAATGCAGATAAAA	7	122	1
GTTATTGCATAATTAATGAATATTTTATCTG	7	144	0
AAGAATATGTAATAAAAAAATTAATAAAAAG	7	229	1
GGGGCTTCATCATCAATAAATTCATTTTTGA	9	17	1
TCTCTAATAGAGAAAATAAATATGCATAATA	9	82	1
AAGGTGACGGAAAGAAAAAATGTTGTGGTTG	11	19	0
CAATAGGTGAAATCAATAACTGAAG      	11	68	1
          *** *******
MAP Score: 4.02406

Motif 8
ATATATACATATCGGTTCTGTGAAGGAATG	1	71	0
ATGTCGATATAGGTGTTCTGAGTTAATGGA	1	105	1
CAGTGCAGTGAACTGTCCTA          	3	0	0
CGCTCCTGAAAGGTGTGCTGAATTACTTTC	3	34	1
TTATAACTGCGGGGGTCCTCAGCTGCCATG	6	52	1
ATTACCATGCAGGGGTGCCCGAGCGGCCAA	8	50	1
GCAGGCCTTCGAGGGTTCGAATCCCTTCCC	8	106	1
TAAGAATTTTAACGGTTCTGATCATGTTAT	8	142	1
GGCATAGGTCGGGGGTTCGAATCCCCCCTA	8	214	1
ACTGATTTTAAGGTGTTCTA          	8	254	1
AGCAGAACCTAACTGTTCTCTAATAGAGAA	9	66	1
          **********
MAP Score: 3.66984

Motif 9
   GGTCTTTAACCTCCATTAACTCAGAACACCTATA	1	112	0
GTTCAGTGAAAAAATACATTATTGGGGAGAGAGATAT	2	48	1
  ATGCCCGAAATTGCCATTATACTGGTGCTATT   	5	8	1
AATACGTGAGGATATCCATTATAACTGCGGGGGTCCT	6	34	1
CTGTTTTCATGAGGTCCATTAAGAAAGATTTATATAT	6	92	1
TGAAACGTTTAAAGGGCTTTAACCTTGCCGTTATATT	7	57	1
ATGCAGATAAAATATTCATTAATTATGCAATAACGCG	7	141	1
          **  * ******    *
MAP Score: 3.46234

Motif 10
CTTCACAGAACCGATATGTATATATGTCCATGTCGA	1	76	1
CATGGACAAACTGATAAAGATATCCGGAAG      	2	4	0
TACATTATTGGGGAGAGAGATATATGGAATGGTGAT	2	62	1
GGTCCATTAAGAAAGATTTATATATGGACCTGTGGA	6	104	1
CAGAATTTTTCTGAAACGTTTAAAGGGCTTTAACCT	7	46	1
TTACATACATCGGTAATACATAAATGCAGATAAAAT	7	118	1
ATCCACAATTGTAAAAACTATAAAGGAG        	7	282	1
TTCCCCTGCACTAAGAATTTTAACGGTTCTGATCAT	8	131	1
TAACCAATAGGTGAAATCAATAACTGAAG       	11	64	1
          * ** *   ***** *
MAP Score: 3.23553

Motif 11
ATCCATTATAACTGCGGGGGTCCTCAGCTGCC	6	47	1
   ATCGTATATTCCACAGGTCCATATATAAA	6	120	0
CGATCAATCAACTGAAGAGGCCATTTAGTGCC	7	11	0
AATCAATTACCATGCAGGGGTGCCCGAGCGGC	8	45	1
CGAGCGGCCAAAGGGGGAGGACTTAAGATCCT	8	69	1
TTAAGATCCTCTGGCGCAGGCCTTCGAGGGTT	8	91	1
TAAAATTCTTAGTGCAGGGGAAGGGATTCGAA	8	121	0
ATGCCTTGGTAAGGCATAGGTCGGGGGTTCGA	8	202	1
TATGATCTAAAATGCAGATGTCAGAAGAAATG	9	111	1
ATAAAGTTCACTTGAAGGTGACGGAAAGAAAA	11	32	0
          * ******** *
MAP Score: 1.92477

Motif 12
GACGATCCCATGTTCTCATTCCTTCACAGAAC	1	55	1
 TTTAAACCAGGATCTGATACC          	4	9	1
GGCCTTCGAGGGTTCGAATCCCTTCCCCTGCA	8	109	1
ATAGGTCGGGGGTTCGAATCCCCCCTAAGGCT	8	217	1
          ****** ** **
MAP Score: 1.02521