AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_operons022_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944245065
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH442	195	excinuclease ABC subunit B
#1	MTH443	41	excinuclease ABC subunit A
#2	MTH1178	107	conserved protein
#3	MTH1179	67	conserved protein
#4	MTH1181	70	unknown
#5	MTH1321	184	signal recognition particle protein SRP54
#6	MTH1454	160	conserved protein
#7	MTH1455	192	threonyl-tRNA synthetase
#8	MTH1456	198	chromosome partitioning protein Soj
#9	MTH1708	300	carbon monoxide dehydrogenase, alpha subunit 
#10	MTH1710	21	carbon monoxide dehydrogenase, alpha subunit 
#11	MTH1837	128	unknown
#12	MTH1840	158	cell division inhibitor

Motif 1
GTGGGGGTATCATCACAGGATTATGGAACACGTGGGA	0	52	1
         AAATCACTTAAAATAAGAACCTCATTCT	0	177	0
AGCACCATGCAATCAGCTGAAAAGCCAGACCCCTCCC	2	36	0
GTATTCATTGAATCACTGAATCACTGAA         	3	1	0
        GGAATCACTGAACCATTGAAACCATGGCT	3	48	0
ACCTTCAGTTCATCAGCACACCTTATAAATAATAATT	4	10	1
AATGATTATCCATCACTGCAGGTGAAACC        	5	165	1
CTTCATTTTCAATCACCATATTAAAAACTGGCAGTAA	6	49	1
TTTCCATTTCAATCAGCACAGAATGTACCTCATTGAA	7	37	1
ATTTAAAAACCCTCACCTTAAAAACAATAACATTAGT	7	144	1
        GCCATCACCTTGGTAAGAATAACTAATGT	7	173	0
       TCCAATCACTATATCAAACATTCATATAAT	9	3	1
GATTAGTAATAATCACTTCAACCTTTATATTATATGA	9	31	0
TCGCCTTTTTAATTACCCTACTTTAAAGACATGTAAG	12	77	0
          *******  *  *   *
MAP Score: 15.9303

Motif 2
ATTTCAGGGTCAACTTATATATACCTTTGCCA	0	132	0
GGTGCTGGTGCAAAAACTATATATACAAGTTT	2	67	1
ACTTCATTTTCAATCACCATATTAAAAACTGG	6	48	1
GAAATAGTGACAAAAATTATATATAATTTACT	6	81	0
        TCCAATCACTATATCAAACATTCA	9	2	1
ATAATCACTTCAACCTTTATATTATATGAATG	9	28	0
CGACAATGCACAAAGTTTATATATAGATTCCA	9	218	1
CCAGAACTAACAATATTTTTATACCGGACTTA	12	49	1
ACGTGTGTAACAATATTTATATCGGAATGACT	12	113	1
          ***  *******
MAP Score: 11.0251

Motif 3
CAAGTTCAGTGGGGGTATCATCACAGGATTAT	0	44	1
AGCCATTTAGGGAGGGGTCTGGCTTTTCAGCT	2	27	1
AATGAATACCGGGCGATTCAGCCATGGTTTCA	3	29	1
TTATTTATAAGGTGTGCTGATGAACTGAAGGT	4	10	0
ACAGGGTGGTGGGCGGCAGATCCTTTGAGGAC	5	70	0
AAGAGTGGTGGATGGGCTGTGCCATATAAAGG	5	104	0
ATTAACTATTGTTGGGATCACCTTATATAATT	5	136	0
AGATAGATGGGGAGGGGACTCCAGGGATATAA	6	128	1
TAAACCAGAAGGGTGGCTGTGGAAAGACAACA	8	117	1
CTCCTGTCAAGGAGGAAAGTGCTGCTGATAGA	8	160	0
CTCCTTGACAGGAGGGTTCTTGTAATCGAC  	8	178	1
CACCCTGAGCGGAGGGATGACCATTGCCGGGG	9	98	1
GACCATTGCCGGGGGTCTCAGGGTGTATAATG	9	116	1
TTAATAAATGGTGGGGATGTGCCAGATAGGCG	9	160	0
          ** *** *****
MAP Score: 11.0203

Motif 4
ATTTCAGGGTCAACTTATATATACCTTTGCCAG	0	131	0
GGTGCTGGTGCAAAAACTATATATACAAGTTTT	2	67	1
TTCATCAGCACACCTTATAAATAATAATTATAG	4	18	1
CATTTTCAATCACCATATTAAAAACTGGCAGTA	6	52	1
GAAATAGTGACAAAAATTATATATAATTTACTG	6	80	0
TCCACCGGAGCAATATTTAAAAACCCTCACCTT	7	130	1
TATAAGTTATCAGATTAAAAAAAATTA      	8	4	0
TAACTTATCACATATACTTTATAAGTTATAAAT	8	35	1
ATCAAACATTCATATAATATAAAGGTTGAAGTG	9	22	1
ACATCCCCACCATTTATTAAAAAGGTCCATGTC	9	172	1
AGCGACAATGCACAAAGTTTATATATAGATTCC	9	216	1
ATATAGATTCCATAAAATTAAAAACATCATTAT	9	238	1
CAGAGTATTCCACCTAAAATATATAGGCTTTAA	11	26	1
TAGTCATACCCATTTAATTAATAAATGCTTAAA	11	54	0
CCAGAACTAACAATATTTTTATACCGGACTTAC	12	49	1
          **  ** ******
MAP Score: 10.9415

Motif 5
GTTTAAAACAAGTTCAGTGGGGGTATCATCACAGGA	0	36	1
TGTGGGACAGCCATTTAGGGAGGGGTCTGGCTTTTC	2	19	1
TGTAACAGATAGATGGGGAGGGGACTCCAGGGATAT	6	122	1
CATCATCTGAACATTACTAGGGGTTTAAAGATCCAC	7	99	1
GCACTTTCCTCCTTGACAGGAGGGTTCTTGTAATCG	8	170	1
TAATATCGCACCCTGAGCGGAGGGATGACCATTGCC	9	90	1
GGAGGGATGACCATTGCCGGGGGTCTCAGGGTGTAT	9	108	1
GGGATGTGCCAGATAGGCGGAGGATTATTACCATTA	9	143	0
        TCAGGATAATGGAGGAATTCA       	10	2	1
GTGGAATACTCTGTTTATGGAGGCATAGT       	11	3	0
          ** *  * *****  *
MAP Score: 9.81147

Motif 6
TTATCATTACCATCCTCTGATTTATGTTTA	0	11	1
TCAGTGGGGGTATCATCACAGGATTATGGA	0	49	1
ACACGTGGGATACCCTGTCAGATATGAGAC	0	79	1
AGCACCATGCAATCAGCTGAAAAGCCAGAC	2	43	0
ATAGTTTTTGCACCAGCACCATGCAATCAG	2	57	0
ACCTTCAGTTCATCAGCACACCTTATAAAT	4	10	1
TGCCGCCCACCACCCTGTGACCTTTATATG	5	84	1
TTTCCATTTCAATCAGCACAGAATGTACCT	7	37	1
CCTTAAGGGTCATCATCTGAACATTACTAG	7	89	1
AATATTTAAAAACCCTCACCTTAAAAACAA	7	141	1
TCTCCCATCTCATCACCTGCTGGATCTAAG	8	73	0
GCCGTTAATCTATCAGCAGCACTTTCCTCC	8	152	1
GGTAATATCGCACCCTGAGCGGAGGGATGA	9	88	1
TACCATTATACACCCTGAGACCCCCGGCAA	9	121	0
CTATCTGGCACATCCCCACCATTTATTAAA	9	163	1
CCGGATCGGATATCCTGTCCAGAACTAACA	12	31	1
          **********
MAP Score: 8.74605

Motif 7
CAGTGGGGGTATCATCACAGGATTATGGAACAC	0	50	1
ACCCTGAAATATAATCCCACAATAGAATGAGGT	0	154	1
CTTAATTCTCATTACCAGAAAATGT        	1	2	0
CCTTCAGTTCATCAGCACACCTTATAAATAATA	4	11	1
TTCCATTTCAATCAGCACAGAATGTACCTCATT	7	38	1
CTTAAGGGTCATCATCTGAACATTACTAGGGGT	7	90	1
GTGGAAAGACAACAACAGCCGTTAATCTATCAG	8	135	1
CCGTTAATCTATCAGCAGCACTTTCCTCCTTGA	8	153	1
AGGGTGCGATATTACCACAATATAAGGGAAACC	9	71	0
AATGGTAATAATCCTCCGCCTATCTGGCACATC	9	144	1
TATCTGGCACATCCCCACCATTTATTAAAAAGG	9	164	1
CTATGCCTCCATAAACAGAGTATTCCACCTAAA	11	11	1
          ATAATCACTCCTTTAATACTTGC	11	115	0
CCTCCAGATAATAATCAGTCATTCCGATATAAA	12	128	0
          **** *** * **
MAP Score: 6.85375

Motif 8
GAGGTTCTTATTTTAAGTGATTT        	0	182	1
TCAGCACACCTTATAAATAATAATTATAGAG	4	22	1
GTGACAAAAATTATATATAATTTACTGCCAG	6	76	0
AGGTGAGGGTTTTTAAATATTGCTCCGGTGG	7	131	0
ATGTGATAAGTTATAAGTTATCAGATTAAAA	8	17	0
AATTTATAACTTATAAAGTATATGTGATAAG	8	38	0
ACTTTATAAGTTATAAATTATAACTTAGATC	8	50	1
ATGTTTTTAATTTTATGGAATCTATATATAA	9	234	0
AAAAACATCATTATAAATCATTAATAATTGT	9	257	1
          ******** **
MAP Score: 5.91592

Motif 9
          AAATCACTTAAAATAAGAACCTCATT	0	179	0
TCATCAGCACACCTTATAAATAATAATTATAGAGAA	4	19	1
TTGCAGCGGTACTTCATTTTCAATCACCATATTAAA	6	38	1
AACTGGCAGTAAATTATATATAATTTTTGTCACTAT	6	74	1
GAGACAGGACATTTCCATTTCAATCAGCACAGAATG	7	26	1
AAAAACCCTCACCTTAAAAACAATAACATTAGTTAT	7	148	1
    GCCATCACCTTGGTAAGAATAACTAATGTTAT	7	170	0
ATAAGTTATCAGATTAAAAAAAATTA          	8	0	0
TTAATCTGATAACTTATAACTTATCACATATACTTT	8	19	1
TATCACATATACTTTATAAGTTATAAATTATAACTT	8	40	1
GGGAAACCGAAGATTAGTAATAATCACTTCAACCTT	9	43	0
GTTTATATATAGATTCCATAAAATTAAAAACATCAT	9	232	1
AAAATTAAAAACATCATTATAAATCATTAATAATTG	9	251	1
          *  *** **  *** *
MAP Score: 4.69412

Motif 10
TTGAGTCTGGAGTCTCATATCTGACAGGGTATCCCA	0	84	0
TCAGCTGAAAAGCCAGACCCCTCCCTAAATGGCTGT	2	25	0
TCAAAGGATCTGCCGCCCACCACCCTGTGACCTTTA	5	74	1
GACCTTTATATGGCACAGCCCATCCACCACTCTTAA	5	102	1
TCATATATGTAGTCACATACCTTGCAGCGGTACTTC	6	17	1
ATATCCCTGGAGTCCCCTCCCCATCTATCTGTTACA	6	122	0
TCCGCCTATCTGGCACATCCCCACCATTTATTAAAA	9	158	1
          ** * ** ***   **
MAP Score: 4.38618

Motif 11
        TTCAGTGATTCAGTGATTCAATGAATACC	3	2	1
GCGATTCAGCCATGGTTTCAATGGTTCAGTGATTCC 	3	41	1
AATTTACTGCCAGTTTTTAATATGGTGATTGAAAATG	6	52	0
GAGGGGACTCCAGGGATATAACGAGTGAGGT      	6	139	1
TGTCCTGTCTCTGCGATTGAAAGGATC          	7	0	0
TACCTCATTGAAGAGGTTCAGGAGATCCCTTAAGGGT	7	62	1
ACATCCCCACCATTTATTAAAAAGGTCCATGTCTTTA	9	172	1
TAAAAAGGTCCATGTCTTTATGTGTTCAGCGACAATG	9	189	1
AGGCTTTAAGCATTTATTAATTAAATGGGTATGACTA	11	50	1
TTGATTCCAGCAAGTATTAAAGGAGTGATTAT     	11	106	1
CAGATAAGGTCAACTGTTGCCCGGATCGGATATCCTG	12	11	1
          **  * ** *  ** **
MAP Score: 1.97703

Motif 12
GTATCCTGGCAAAGGTATATATAAGTTGACCC	0	126	1
TGCTGGTGCAAAAACTATATATACAAGTTTTG	2	69	1
AATTTATTGATGAGATATATAGGCTT      	4	54	1
CACCACCCTGTGACCTTTATATGGCACAGCCC	5	91	1
TCCACCACTCTTAATTATATAAGGTGATCCCA	5	124	1
AAACTGGCAGTAAATTATATATAATTTTTGTC	6	73	1
GTATATGTGATAAGTTATAAGTTATCAGATTA	8	20	0
TTATAACTTATAAAGTATATGTGATAAGTTAT	8	34	0
ATAATCACTTCAACCTTTATATTATATGAATG	9	28	0
CGACAATGCACAAAGTTTATATATAGATTCCA	9	218	1
AATGATGTTTTTAATTTTATGGAATCTATATA	9	237	0
GTATTCCACCTAAAATATATAGGCTTTAAGCA	11	30	1
ACGTGTGTAACAATATTTATATCGGAATGACT	12	113	1
          ***  *******
MAP Score: 0.625524