AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons020_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252394
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0324	300	conserved hypothetical protein
#1	TM0356	167	threonine dehydratase catabolic
#2	TM0547	162	aspartokinase II
#3	TM0666	163	serine acetyltransferase
#4	TM0882	135	O-acetylhomoserine sulfhydrylase
#5	TM1265	224	conserved hypothetical protein
#6	TM1266	140	hypothetical protein
#7	TM1270	50	cystathionine gamma-synthase
#8	TM1523	300	aspartate-semialdehyde dehydrogenase

Motif 1
TTTTAATCTTACTCCAGGCTTGAACTCGTTTG	1	111	0
  GAGAAACACCTCCCGGTTTTCTGAGCAACC	1	147	0
TTCCTAAAAACCCCCCGTGATTTATTTATTAT	2	46	0
 TGAAATATCCCTCCTCCTGTGTTAATATACT	3	9	1
GAAAGGTGAACCTCTTCACTTTTTTCACAAAA	3	51	0
  AAGTATCACCTCCACATTTGAGATGGTGTA	4	8	1
  TCTCTCCACCTCCCGTGATAAAATTTTCTG	4	115	0
  AAGAGACACCTCCACATCAGGATTTTACCA	5	8	1
  AGTATGCACCTCCTCTGGAACGAATTATAG	5	204	0
AAATCACAAACCTCCTGAGGTGGAGGGGAAAA	6	48	1
CCATCCATCCCCTCCCCCGGTGTCAGGATTTT	6	76	0
ACGAAAACCCCCTCTCCACGTGCCGGGAGAGG	6	117	0
   GAGTAGGCCTCCTGTTGTGATTGTGTACC	7	31	0
GTCCCCGATTCCTCCCCTGATGGGACAGCCTA	8	79	0
GTGCAGAGTTCCTCCCGCTCTGCATGCCTGGG	8	136	1
ATTCCCCATACCCCCAGGCATGCAGAGCGGGA	8	148	0
          ******* * **
MAP Score: 32.2758

Motif 2
TGCTCAGAAAACCGGGAGGTGTTTCTC    	1	150	1
TAATAAATAAATCACGGGGGGTTTTTAGGAA	2	47	1
GAATCAAACGATCTGGAGGTGGTGGATATGG	3	135	1
ACCATCTCAAATGTGGAGGTGATACTT    	4	6	0
AGAAAATTTTATCACGGGAGGTGGAGAGA  	4	116	1
TAAAATCCTGATGTGGAGGTGTCTCTT    	5	6	0
TAATTCGTTCCAGAGGAGGTGCATACT    	5	207	1
AAACCTCCTGAGGTGGAGGGGAAAATCCTGA	6	55	1
AAATCCTGACACCGGGGGAGGGGATGGATGG	6	77	1
CTCCACGTGCCGGGAGAGGGGTATACTTCCA	6	105	0
CTCTCCCGGCACGTGGAGAGGGGGTTTTCGT	6	118	1
GACGGAGGCGCGCCCGAGATGAGTAGGCTGT	8	56	1
AGGCTGTCCCATCAGGGGAGGAATCGGGGAC	8	80	1
CCCGCTCTGCATGCCTGGGGGTATGGGGAAT	8	149	1
          *** *******
MAP Score: 20.1498

Motif 3
AAAGAAGGATTTCCTCATTTTGCATGTGAGAA	1	79	0
TGAATGATTATACCAGACCTGGAATAATAAAT	2	23	1
   TGAAATATCCCTCCTCCTGTGTTAATATA	3	7	1
ATACCATATCCACCACCTCCAGATCGTTTGAT	3	137	0
       TCTCTCCACCTCCCGTGATAAAATT	4	120	0
 AAGAGACACCTCCACATCAGGATTTTACCAC	5	9	1
ATCAGGATTTTACCACTTCTTAGTTTCCAGGT	5	25	1
    AGTATGCACCTCCTCTGGAACGAATTAT	5	206	0
GTTCATATTATACCACCTTCTGAGAG      	6	4	0
GGATTTTCCCCTCCACCTCAGGAGGTTTGTGA	6	51	0
AGGGGAAAATCCTGACACCGGGGGAGGGGATG	6	71	1
TGGAAGTATACCCCTCTCCCGGCACGTGGAGA	6	105	1
 AACGAAAACCCCCTCTCCACGTGCCGGGAGA	6	119	0
CCGTCCCCGATTCCTCCCCTGATGGGACAGCC	8	81	0
CTTTTTCTGATTCCAGACCCGATCGGCTCTCC	8	211	0
CAGAAAAAGATTTCAGACCTGATTTGGCGTCT	8	234	1
CCTGATTTGGCGTCTCTTCGGGGAGCGAAGAG	8	251	1
          * ******* **
MAP Score: 13.6244

Motif 4
ATTCTGAGTTCTTTCGGAGAATTTCTTCAC	0	62	0
TCAGTACAGTTGTTCTGAAGAGCAGAATCG	0	235	0
CTATACTCTTCTTTGTGAAAAAAGTGTGAA	1	48	1
CACCTCCCGGTTTTCTGAGCAACCACAGTT	1	141	0
TTGAATCGAATTTTTTGTTAGAAGTAGCAT	2	110	1
TCACAAAAGCCTTTGTGTAGTATATTAACA	3	29	0
ACACAAAGGCTTTTGTGAAAAAAGTGAAGA	3	41	1
AGAGGTTCACCTTTCTGTGATGAAAAGGTT	3	68	1
CGTGATAAAATTTTCTGATGTCCTCTTTTA	4	102	0
TCCAGGTTTTCTTTGTGTGATTTCACATGG	5	50	1
GCCGACTCTTCGTTCTGAAAGAGAACGATT	5	98	1
AAGAGAACGATTTTGTGAGACTATCGTTCT	5	116	1
TTCTATTTTCCGTTCTGTTATAGAACGATA	5	137	0
AAAAATCGTTCTTTTTGAGAACGTTTTGTG	5	174	1
TTTTTGAGAACGTTTTGTGCTATAATTCGT	5	185	1
TATTATACCACCTTCTGAGAG         	6	1	0
ATTTTTCTCACTTTCTGTTCATATTATACC	6	22	0
          **********
MAP Score: 12.9781

Motif 5
ATCAAACGATCTGGAGGTGGTGGATATGGTAT	3	137	1
GAAAATTTTATCACGGGAGGTGGAGAGA    	4	117	1
AGAGACACCTCCACATCAGGATTTTACCACTT	5	11	1
ATAATTCGTTCCAGAGGAGGTGCATACT    	5	206	1
         CTCTCAGAAGGTGGTATAATATG	6	1	1
AAATCACAAACCTCCTGAGGTGGAGGGGAAAA	6	48	1
AATCCTGACACCGGGGGAGGGGATGGATGGAA	6	78	1
TATACCCCTCTCCCGGCACGTGGAGAGGGGGT	6	111	1
CGGTACACAATCACAACAGGAGGCCTACTC  	7	30	1
AGTCATTGACCCGACGGAGGCGCGCCCGAGAT	8	44	1
GAGTAGGCTGTCCCATCAGGGGAGGAATCGGG	8	76	1
AGATTTCAGACCTGATTTGGCGTCTCTTCGGG	8	241	1
          ** ******* *
MAP Score: 6.75202

Motif 6
AAGGCAAGAATGATAAGGTAATTCACTATTCTGA	0	85	0
TTAGTGTTCCTGTTGGTGCGATTCTGCTCTTCAG	0	217	1
GTACTGAAGCTGATAGGAGAATTCAGAGGCAACA	0	258	1
TTCAATTGTTTGACGATAAAATTCTATACTCTTC	1	25	1
TTAACAATTAGGTTGATATAATTCCATTGAATCA	3	107	1
CCATCTCAAATGTGGAGGTGATACTT        	4	2	0
ATAACAGAACGGAAAATAGAATTCTACGAAAAAT	5	146	1
TCTCACTTTCTGTTCATATTATACCACCTTCTGA	6	13	0
CTCCTGAGGTGGAGGGGAAAATCCTGACACCGGG	6	59	1
CCACGTGCCGGGAGAGGGGTATACTTCCATCCAT	6	100	0
CATGCCTGGGGGTATGGGGAATACCCATACCACT	8	158	1
          ***  *** *** *
MAP Score: 5.88955

Motif 7
   GTCATCTTTCCTCCTTCTTGTTGCCTCT	0	282	0
      ACGAATACCTCCTTTTTCAATTGTT	1	4	1
AAATGAGGAAATCCTTCTTTCAAACGAGTTC	1	91	1
    TGAAATATCCCTCCTCCTGTGTTAATA	3	6	1
     AAGAGACACCTCCACATCAGGATTTT	5	5	1
CATCAGGATTTTACCACTTCTTAGTTTCCAG	5	24	1
TGTTCATATTATACCACCTTCTGAGAG    	6	6	0
GTCAGGATTTTCCCCTCCACCTCAGGAGGTT	6	56	0
CTTCCATCCATCCCCTCCCCCGGTGTCAGGA	6	80	0
GGAGAGGGGTATACTTCCATCCATCCCCTCC	6	93	0
ATGGAAGTATACCCCTCTCCCGGCACGTGGA	6	104	1
     AACGAAAACCCCCTCTCCACGTGCCG	6	124	0
GCCGTCCCCGATTCCTCCCCTGATGGGACAG	8	83	0
GGGAATACCCATACCACTGTCACGGAGGTCT	8	174	1
          ******** **
MAP Score: 5.82261

Motif 8
GAATTACCTTATCATTCTTGCCTTCATTGTT	0	95	1
TGGGGCTTTTATCTTTCCTATAAAACAAGAT	0	138	1
       GTCATCTTTCCTCCTTCTTGTTGC	0	286	0
      ACGAATACCTCCTTTTTCAATTGTT	1	4	1
AAATGAGGAAATCCTTCTTTCAAACGAGTTC	1	91	1
    TGAAATATCCCTCCTCCTGTGTTAATA	3	6	1
ATGGTGTAAAATATTTCTTACACACCTCTGA	4	32	1
TCTACGAAAAATCGTTCTTTTTGAGAACGTT	5	168	1
TGTTCATATTATACCACCTTCTGAGAG    	6	6	0
GGAGAGGGGTATACTTCCATCCATCCCCTCC	6	93	0
          ********* *
MAP Score: 4.56605

Motif 9
AGCAGAATCGCACCAACAGGAACACTAAGT	0	215	0
AATTCAGAGGCAACAAGAAGGAGGAAAGAT	0	277	1
ATCATTCAATCTCCGAGAGGA         	2	1	0
AATACTAAATCTAAAAGAGGACATCAGAAA	4	91	1
AGAGACACCTCCACATCAGGATTTTACCAC	5	11	1
ATTTTCCCCTCCACCTCAGGAGGTTTGTGA	6	51	0
CGGTACACAATCACAACAGGAGGCCTACTC	7	30	1
GAGTAGGCTGTCCCATCAGGGGAGGAATCG	8	76	1
CGAAGAGACGCCAAATCAGGTCTGAAATCT	8	241	0
          **********
MAP Score: 3.02139

Motif 10
AGCAGAATCGCACCAACAGGAACACTAAGT	0	215	0
CAAACAATTGAAAAAGGAGGTATTCGT   	1	7	0
ACACTTTTTTCACAAAGAAGAGTATAGAAT	1	45	0
TTCTCACATGCAAAATGAGGAAATCCTTCT	1	79	1
TTGCTCAGAAAACCGGGAGGTGTTTCTC  	1	149	1
ATCATTCAATCTCCGAGAGGA         	2	1	0
ATAAATAAATCACGGGGGGTTTTTAGGAAT	2	49	1
TATATTAACACAGGAGGAGGGATATTTCA 	3	9	0
ACCTTTTCATCACAGAAAGGTGAACCTCTT	3	67	0
ATCAAACGATCTGGAGGTGGTGGATATGGT	3	137	1
AATACTAAATCTAAAAGAGGACATCAGAAA	4	91	1
AATTTTATCACGGGAGGTGGAGAGA     	4	120	1
AGAGACACCTCCACATCAGGATTTTACCAC	5	11	1
TGTGAAATCACACAAAGAAAACCTGGAAAC	5	47	0
ACTCTTCGTTCTGAAAGAGAACGATTTTGT	5	102	1
ATAATTCGTTCCAGAGGAGGTGCATACT  	5	206	1
      CTCTCAGAAGGTGGTATAATATGA	6	4	1
ATAATATGAACAGAAAGTGAGAAAAATCAC	6	25	1
TTCCCCTCCACCTCAGGAGGTTTGTGATTT	6	48	0
AAAATCCTGACACCGGGGGAGGGGATGGAT	6	76	1
TCTCCACGTGCCGGGAGAGGGGTATACTTC	6	107	0
TCTCCCGGCACGTGGAGAGGGGGTTTTCGT	6	119	1
TACACAATCACAACAGGAGGCCTACTC   	7	33	1
AGTCATTGACCCGACGGAGGCGCGCCCGAG	8	44	1
TAGGCTGTCCCATCAGGGGAGGAATCGGGG	8	79	1
GGCGAGGGCGCCGAAGGGTGCAGAGTTCCT	8	119	1
CAGGCATGCAGAGCGGGAGGAACTCTGCAC	8	136	0
ATCGGCTCTCCACGGAGAGACCTCCGTGAC	8	192	0
CTCTTCGCTCCCCGAAGAGACGCCAAATCA	8	253	0
          **********
MAP Score: 2.03776

Motif 11
GAATCAAACGATCTGGAGGTGGTGGATATGGTATCG	3	135	1
AGAAAATTTTATCACGGGAGGTGGAGAGA       	4	116	1
AATCACAAACCTCCTGAGGTGGAGGGGAAAATCCTG	6	49	1
GGAAAATCCTGACACCGGGGGAGGGGATGGATGGAA	6	74	1
GTATACCCCTCTCCCGGCACGTGGAGAGGGGGTTTT	6	110	1
GACGGAGGCGCGCCCGAGATGAGTAGGCTGTCCCAT	8	56	1
AGTAGGCTGTCCCATCAGGGGAGGAATCGGGGACGG	8	77	1
AGGCGAGGGCGCCGAAGGGTGCAGAGTTCCTCCCGC	8	118	1
TTCCCCATACCCCCAGGCATGCAGAGCGGGAGGAAC	8	143	0
GATTTGGCGTCTCTTCGGGGAGCGAAGAGACGCTTT	8	254	1
          * *  **** *  ***
MAP Score: 1.36548