AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons020_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252381
 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	TM1266	140	hypothetical protein
#6	TM1270	50	cystathionine gamma-synthase
#7	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
ATATCCACCACCTCCAGATCGTTTGATTCAAT	3	132	0
  AAGTATCACCTCCACATTTGAGATGGTGTA	4	8	1
  TCTCTCCACCTCCCGTGATAAAATTTTCTG	4	115	0
AAATCACAAACCTCCTGAGGTGGAGGGGAAAA	5	48	1
CCATCCATCCCCTCCCCCGGTGTCAGGATTTT	5	76	0
ACGAAAACCCCCTCTCCACGTGCCGGGAGAGG	5	117	0
   GAGTAGGCCTCCTGTTGTGATTGTGTACC	6	31	0
GTCCCCGATTCCTCCCCTGATGGGACAGCCTA	7	79	0
GTGCAGAGTTCCTCCCGCTCTGCATGCCTGGG	7	136	1
ATTCCCCATACCCCCAGGCATGCAGAGCGGGA	7	148	0
          ******* * **
MAP Score: 32.3168

Motif 2
TTCAGAGGCAACAAGAAGGAGGAAAGATGAC   	0	279	1
AGTATATTAACACAGGAGGAGGGATATTTCA   	3	7	0
ACCTTTTCATCACAGAAAGGTGAACCTCTTCACT	3	63	0
GAATCAAACGATCTGGAGGTGGTGGATATGGTAT	3	135	1
ACCATCTCAAATGTGGAGGTGATACTT       	4	3	0
AAAATTTTATCACGGGAGGTGGAGAGA       	4	118	1
        CTCTCAGAAGGTGGTATAATATGAAC	5	2	1
GTATAATATGAACAGAAAGTGAGAAAAATCACAA	5	23	1
AATCACAAACCTCCTGAGGTGGAGGGGAAAATCC	5	49	1
AAAATCCTGACACCGGGGGAGGGGATGGATGGAA	5	76	1
TCTCCACGTGCCGGGAGAGGGGTATACTTCCATC	5	103	0
CCTCTCCCGGCACGTGGAGAGGGGGTTTTCGTT 	5	117	1
ATAGTCATTGACCCGACGGAGGCGCGCCCGAGAT	7	42	1
AGTAGGCTGTCCCATCAGGGGAGGAATCGGGGAC	7	77	1
GGGGAGGAATCGGGGACGGCTGAAAGGCGAGGGC	7	94	1
GACGGCTGAAAGGCGAGGGCGCCGAAGGGTGCAG	7	108	1
CCCAGGCATGCAGAGCGGGAGGAACTCTGCACCC	7	134	0
GGAGAGACCTCCGTGACAGTGGTATGGGTATTCC	7	175	0
          * * ***** ** *
MAP Score: 24.6596

Motif 3
CTCAGAAAACCGGGAGGTGTTTCTC     	1	152	1
TGTGAAAAAAGTGAAGAGGTTCACCTTTCT	3	54	1
ATCAAACGATCTGGAGGTGGTGGATATGGT	3	137	1
CATCTCAAATGTGGAGGTGATACTT     	4	5	0
AATTTTATCACGGGAGGTGGAGAGA     	4	120	1
ACCTCCTGAGGTGGAGGGGAAAATCCTGAC	5	57	1
ATCCTGACACCGGGGGAGGGGATGGATGGA	5	79	1
CTCCACGTGCCGGGAGAGGGGTATACTTCC	5	106	0
CTCCCGGCACGTGGAGAGGGGGTTTTCGTT	5	120	1
GCTGTCCCATCAGGGGAGGAATCGGGGACG	7	82	1
CTGCATGCCTGGGGGTATGGGGAATACCCA	7	155	1
          **********
MAP Score: 16.8639

Motif 4
GTCGATGTAGCCTGGCGTGAAAACAAAATGAT	0	14	1
TTGTTTATCTCATTGTGTGGGGCTTTTATCTT	0	121	1
ACTTAGTGTTCCTGTTGGTGCGATTCTGCTCT	0	215	1
GTACAGTTGTTCTGAAGAGCAGAATCGCACCA	0	230	0
GCTCAGAAAACCGGGAGGTGTTTCTC      	1	151	1
TATATTAACACAGGAGGAGGGATATTTCA   	3	7	0
ATCAAACGATCTGGAGGTGGTGGATATGGTAT	3	137	1
AATTTTATCACGGGAGGTGGAGAGA       	4	120	1
TCACAAACCTCCTGAGGTGGAGGGGAAAATCC	5	51	1
AATCCTGACACCGGGGGAGGGGATGGATGGAA	5	78	1
TCTCCACGTGCCGGGAGAGGGGTATACTTCCA	5	105	0
TCTCCCGGCACGTGGAGAGGGGGTTTTCGTT 	5	119	1
GAGTAGGCCTCCTGTTGTGATTGTGTACCGCA	6	28	0
CGATTCCTCCCCTGATGGGACAGCCTACTCAT	7	74	0
GCTCTGCATGCCTGGGGGTATGGGGAATACCC	7	152	1
GAGGTCTCTCCGTGGAGAGCCGATCGGGTCTG	7	198	1
AGATTTCAGACCTGATTTGGCGTCTCTTCGGG	7	241	1
GGCGTCTCTTCGGGGAGCGAAGAGACGCTTTT	7	259	1
          ******* ** *
MAP Score: 16.465

Motif 5
    GTCATCTTTCCTCCTTCTTGTTGCCTC	0	283	0
      ACGAATACCTCCTTTTTCAATTGTT	1	4	1
AAATGAGGAAATCCTTCTTTCAAACGAGTTC	1	91	1
    TGAAATATCCCTCCTCCTGTGTTAATA	3	6	1
TGTTCATATTATACCACCTTCTGAGAG    	5	6	0
GTCAGGATTTTCCCCTCCACCTCAGGAGGTT	5	56	0
GGAGAGGGGTATACTTCCATCCATCCCCTCC	5	93	0
ATGGAAGTATACCCCTCTCCCGGCACGTGGA	5	104	1
GCCGTCCCCGATTCCTCCCCTGATGGGACAG	7	83	0
GGGAATACCCATACCACTGTCACGGAGGTCT	7	174	1
          ******** **
MAP Score: 7.61874

Motif 6
TGTAGCCTGGCGTGAAAACAAAATGATGTCGGTG	0	19	1
GGTGGATATACTTGTGAAGAAATTCTCCGAAAGA	0	49	1
GTGTAACCCACGTGTAGCTAAAGTTCGGTATCCC	0	183	0
TTTTCAATTGTTTGACGATAAAATTCTATACTCT	1	23	1
TATACTCTTCTTTGTGAAAAAAGTGTGAATTTCT	1	49	1
TCCCTCCTCCTGTGTTAATATACTACACAAAGGC	3	17	1
CACAAAGGCTTTTGTGAAAAAAGTGAAGAGGTTC	3	42	1
TTCACCTTTCTGTGATGAAAAGGTTTCTTTGGTT	3	73	1
GTTTCAGAGGTGTGTAAGAAATATTTTACACCAT	4	32	0
CTCTGAAACATTTGACACGAAGATATAGTAAGGT	4	57	1
CTCCACCTCCCGTGATAAAATTTTCTGATGTCCT	4	108	0
          ***** ** **  *
MAP Score: 5.56526

Motif 7
AGGTTTGTGATTTTTCTCACTTTCTGTTCA	5	31	0
TGAAAGAAGGATTTCCTCATTTTGCATGTG	1	83	0
GAAATTCACACTTTTTTCACAAAGAAGAGT	1	52	0
AACCTCTTCACTTTTTTCACAAAAGCCTTT	3	45	0
CTTTCGGAGAATTTCTTCACAAGTATATCC	0	52	0
CAAAGAAACCTTTTCATCACAGAAAGGTGA	3	74	0
GCCTTCATTGTTTATCTCATTGTGTGGGGC	0	114	1
ACATCAGAAAATTTTATCACGGGAGGTGGA	4	111	1
AGAAGTAGCATTTTTATCATGAAAATGTAA	2	129	1
     GTCATCTTTCCTCCTTCTTGTTGCC	0	285	0
TAGATTTAGTATTACCTTACTATATCTTCG	4	74	0
GTCTGAAATCTTTTTCTGATTCCAGACCCG	7	222	0
CGCATCATATTTTACCTTATGT        	6	2	0
CGAAGAGACGCTTTTTTTATTAATTCAAGG	7	276	1
CGACATCATTTTGTTTTCACGCCAGGCTAC	0	20	0
AGAATAGTGAATTACCTTATCATTCTTGCC	0	87	1
AAAAAGTGTGAATTTCTCACATGCAAAATG	1	66	1
          **********
MAP Score: 5.49918

Motif 8
        TCCTCTCGGAGATTGAATGATTATACCAGA	2	2	1
AGAGGTTCACCTTTCTGTGATGAAAAGGTTTCTTTGGT	3	68	1
ATCAAACGATCTGGAGGTGGTGGATATGGTATCGGG  	3	137	1
ATATTTTACACCATCTCAAATGTGGAGGTGATACTT  	4	8	0
AAATCACAAACCTCCTGAGGTGGAGGGGAAAATCCTGA	5	48	1
GGGGAAAATCCTGACACCGGGGGAGGGGATGGATGGAA	5	72	1
AACCCCCTCTCCACGTGCCGGGAGAGGGGTATACTTCC	5	106	0
AGTCATTGACCCGACGGAGGCGCGCCCGAGATGAGTAG	7	44	1
GTAGGCTGTCCCATCAGGGGAGGAATCGGGGACGGCTG	7	78	1
ATTCCCCATACCCCCAGGCATGCAGAGCGGGAGGAACT	7	142	0
TCACGGAGGTCTCTCCGTGGAGAGCCGATCGGGTCTGG	7	193	1
          **  * * ** * *  **
MAP Score: 5.24976