AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_operons026_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944245180
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH281	259	conserved protein
#1	MTH700	110	conserved protein
#2	MTH702	27	acetyl-CoA synthetase related protein
#3	MTH708	135	thioredoxin reductase
#4	MTH1278	159	conserved protein
#5	MTH1280	66	PET112-like protein
#6	MTH1354	124	NADH oxidase
#7	MTH1496	194	amidase
#8	MTH1648	110	dihydrolipoamide dehydrogenase

Motif 1
TTCAGGATCCCTACACGGGTGTCCTATCAGCTG	0	15	1
TGGCTAGCATCTGCAGATGTAACGCCCTCCTTC	0	67	1
GCGGTGATCTCTGCAGAAGCTTCATATTACTTT	0	154	1
CAGGGAGTGCCTTCACCAGAAACAGGGATCTCA	0	197	0
   GATTACACCTCATCAGCGTCAGGAAAAATT	1	90	0
     TACTACCACACAGGGGACACCGCCTGG 	2	5	1
AAATCTTTATCTCCACCGGTGACCAAGATAATG	3	101	1
TTCTGCACTACTGCAGATGTAACCCTGCAGCTA	4	39	1
AACCCTGCAGCTACAGAAACATCACTCAAGATT	4	59	1
AACCCTGTAGCTACAGAAACATCAGTCAAGATA	4	94	1
AACTTACGGACTTCACATTTATCACGGAATTCA	4	135	1
          ** **** * ***
MAP Score: 13.4528

Motif 2
CGTGTAGGGATCCTGAATCTCA          	0	0	0
TTCACCAGAAACAGGGATCTCAAAGGATGCTT	0	187	0
    ACAGTACCTTGTACCACACAGTATATAA	0	241	0
GCTCAGCAGACCCTAAAGCTCCACCTCCTTTT	3	43	1
GCAGATGTAACCCTGCAGCTACAGAAACATCA	4	51	1
AAGATTGTAACCCTGTAGCTACAGAAACATCA	4	86	1
TTTGATGCTCCCTTATAACTACCACACAGATC	6	11	1
GAGACCTATAACCGATAACTCCTAGGAGAAGG	6	96	1
AGTTTCCGGTCCATGGACCGCCGGGACAGCCA	7	99	0
CGGTCCATGGACCGGAAACTCCACCCTCGAGG	7	111	1
GGTTGATCAGACTTATATCTCACTTCAACTTG	7	162	1
          ***** * ****
MAP Score: 10.5483

Motif 3
GCTTAAAGTAATATGAAGCTTCTGCAGAGAT	0	160	0
ACCACACAGTATATAAACCTTGTCACGCAGG	0	226	0
ATTATGTGGAACTTAAACATTTAAGATGAGA	1	15	1
TCTCTTCCCTTAATAAAGTTTCTCATCTTAA	1	35	0
CAGGAAAAATTAATAATGATTATTAATGATA	1	70	0
TCACCGGTGGAGATAAAGATTTCACATTCAG	3	92	0
CCGGTGACCAAGATAATGATTAAGGTGGT  	3	116	1
GCAGAATACTTTATAAAGTTTCATGGAGATA	4	14	0
GATGTTCAATATTTAAAGATTGGTAGATTGA	7	16	0
ACTAATGTTTAGATAAAGATCCGTCACATAT	8	52	1
GATCCGTCACATATAAAGATTTGTGGGAAAC	8	69	1
          * *********
MAP Score: 10.4296

Motif 4
GTGGAACTTAAACATTTAAGATGAGAAACTT	1	20	1
TTAAGATGAGAAACTTTATTAAGGGAAGAGA	1	35	1
TAAGGGAAGAGACATTTATCATTAATAATCA	1	54	1
AGCGTCAGGAAAAATTAATAATGATTATTAA	1	75	0
        ACCACCTTAATCATTATCTTGGT	3	122	0
TATCTCCATGAAACTTTATAAAGTATTCTGC	4	14	1
TTACGGACTTCACATTTATCACGGAATTCAA	4	138	1
TTGATGTATCCAAATTTATAAATATATCTGA	6	45	1
TTGAACATCTCACATTTATTAGTGTTGGAAA	7	38	1
AAGTCTGATCAACCTTAATAGCTGCCATGAC	7	145	0
TAACCCTCTCCAAATTAATAGGATTAAAGTC	8	14	1
          ********* *
MAP Score: 9.54286

Motif 5
CAGAGTGTATCAGAAACAGCTGATAGGACACCCGTGTAGGGA	0	22	0
CTGGATTGGCTAGCATCTGCAGATGTAACGCCCTCCTTCCTG	0	61	1
CGGTAATAAGCTGATGGTGCGGTGATCTCTGCAGAAGCTTCA	0	136	1
TTTGAGATCCCTGTTTCTGGTGAAGGCACTCCCTGCGTGACA	0	195	1
TTAATTTTTCCTGACGCTGATGAGGTGTAATC          	1	88	1
GGGTGCTCAGCAGACCCTAAAGCTCCACCTCCTTTTTAATAT	3	39	1
AGTGATGTTTCTGTAGCTGCAGGGTTACATCTGCAGTAGTGC	4	43	0
ACTGATGTTTCTGTAGCTACAGGGTTACAATCTTGAGTGATG	4	78	0
ACTGTCATGGCTGTCCCGGCGGTCCATGGACCGGAAACTCCA	7	92	1
GCTGCCATGACTGCCTCGAGGGTGGAGTTTCCGGTCCATGGA	7	114	0
          ***   **** *        **
MAP Score: 9.3116

Motif 6
CTGCAGATGTAACCCTGCAGCTACAGAAACATCACT	4	49	1
TCAAGATTGTAACCCTGTAGCTACAGAAACATCAGT	4	84	1
GGCGGTCCATGGACCGGAAACTCCACCCTCGAGGCA	7	109	1
GTGCTCAGCAGACCCTAAAGCTCCACCTCCTTTTTA	3	41	1
    GATTACACCTCATCAGCGTCAGGAAAAATTAA	1	88	0
TTCTGCAGAGATCACCGCACCATCAGCTTATTACCG	0	136	0
CCTTTTTATGATCCGGTGAACTTCAGAGTATATTAT	5	23	0
GGGACTTTGAGACCCTAAAGAATCAGATGGCCAGGA	0	98	0
       ACAGTACCTTGTACCACACAGTATATAAA	0	240	0
ACTGAATGTGAAATCTTTATCTCCACCGGTGACCAA	3	91	1
CACAGTATATAAACCTTGTCACGCAGGGAGTGCCTT	0	217	0
AATCCAGAGTGTATCAGAAACAGCTGATAGGACACC	0	32	0
          * *** * * *  ***
MAP Score: 8.5463

Motif 7
GAGTGTATCAGAAACAGCTGATAGGACACCCGTGTAGGG	0	23	0
GGAGGGCGTTACATCTGCAGATGCTAGCCAATCCAGAGT	0	58	0
GTAATATGAAGCTTCTGCAGAGATCACCGCACCATCAGC	0	145	0
TGAGATCCCTGTTTCTGGTGAAGGCACTCCCTGCGTGAC	0	197	1
TGGAGCTTTAGGGTCTGCTGAGCACCCTCAATAATAAAA	3	27	0
AGTATTCTGCACTACTGCAGATGTAACCCTGCAGCTACA	4	35	1
ATGTAACCCTGCAGCTACAGAAACATCACTCAAGATTGT	4	55	1
TTGTAACCCTGTAGCTACAGAAACATCAGTCAAGATAAA	4	90	1
ACTACCACACAGATCTATTGATGTATCCAAATTTATAAA	6	28	1
          *   *******     * *
MAP Score: 7.24235

Motif 8
ATCAGCTTATTACCGCAGGGACTTTGAGAC	0	121	0
AATATGAAGCTTCTGCAGAGATCACCGCAC	0	152	0
CAGTACCTTGTACCACACAGTATATAAACC	0	238	0
       TACTACCACACAGGGGACACCGC	2	3	1
TATTCTGCACTACTGCAGATGTAACCCTGC	4	37	1
CCCTTATAACTACCACACAGATCTATTGAT	6	20	1
          **********
MAP Score: 6.56124

Motif 9
GATTCTTTAGGGTCTCAAAGTCCCTGCGGT	0	110	1
CAGAAACAGGGATCTCAAAGGATGCTTAAA	0	184	0
CAGTACCTTGTACCACACAGTATATAAACC	0	238	0
       TACTACCACACAGGGGACACCGC	2	3	1
TGGAGATAAAGATTTCACATTCAGTTAACC	3	86	0
ACAACTTACGGACTTCACATTTATCACGGA	4	133	1
CCCTTATAACTACCACACAGATCTATTGAT	6	20	1
AAATATTGAACATCTCACATTTATTAGTGT	7	33	1
ATCAGACTTATATCTCACTTCAACTTGAAA	7	167	1
          **********
MAP Score: 4.69523

Motif 10
       TGAGATTCAGGATCCCTACACGGGTGTCCTA	0	3	1
TGCGGTGATCTCTGCAGAAGCTTCATATTACTTTAAGC	0	153	1
GCCTTCACCAGAAACAGGGATCTCAAAGGATGCTTAAA	0	184	0
CCCTGTTTCTGGTGAAGGCACTCCCTGCGTGACAAGGT	0	203	1
CACCGGTGGAGATAAAGATTTCACATTCAGTTAACCGG	3	84	0
TAACCCTGCAGCTACAGAAACATCACTCAAGATTGTAA	4	58	1
TAACCCTGTAGCTACAGAAACATCAGTCAAGATAAATT	4	93	1
GTGTGGTAGTTATAAGGGAGCATCAAAC          	6	0	0
GGCGGTCCATGGACCGGAAACTCCACCCTCGAGGCAGT	7	109	1
TCATGGCAGCTATTAAGGTTGATCAGACTTATATCTCA	7	146	1
CTAATGTTTAGATAAAGATCCGTCACATATAAAGATTT	8	53	1
          * * ****  *  **  *
MAP Score: 4.49574

Motif 11
GGGTGTCCTATCAGCTGTTTCTGATACACTCTGGATTGGC	0	31	1
GGGCGTTACATCTGCAGATGCTAGCCAATCCAGAGTGTAT	0	54	0
TCAGCTTATTACCGCAGGGACTTTGAGACCCTAAAGAATC	0	110	0
ATATGAAGCTTCTGCAGAGATCACCGCACCATCAGCTTAT	0	141	0
 GATTACACCTCATCAGCGTCAGGAAAAATTAATAATGAT	1	81	0
TTGAGGGTGCTCAGCAGACCCTAAAGCTCCACCTCCTTTT	3	35	1
CAGGGTTACATCTGCAGTAGTGCAGAATACTTTATAAAGT	4	26	0
CAGATGTAACCCTGCAGCTACAGAAACATCACTCAAGATT	4	52	1
AGATTGTAACCCTGTAGCTACAGAAACATCAGTCAAGATA	4	87	1
ACAGTACTCATCCGTGGTTTTAATTTCATTTCCAACACTA	7	57	0
          ** ****   *     ** *
MAP Score: 4.28249

Motif 12
CGGTGATCTCTGCAGAAGCTTCATATTACTTTA	0	155	1
TATTAATTTTTCCTGACGCTGATGAGGTGTAAT	1	86	1
GCTCAGCAGACCCTAAAGCTCCACCTCCTTTTT	3	43	1
GCAGATGTAACCCTGCAGCTACAGAAACATCAC	4	51	1
AAGATTGTAACCCTGTAGCTACAGAAACATCAG	4	86	1
GTCATGGCTGTCCCGGCGGTCCATGGACCGGAA	7	95	1
          *** * **** **
MAP Score: 2.99768

Motif 13
CGTGTAGGGATCCTGAATCTCA        	0	2	0
GCGTTACATCTGCAGATGCTAGCCAATCCA	0	62	0
CTTCCTGGCCATCTGATTCTTTAGGGTCTC	0	96	1
CGGTGATCTCTGCAGAAGCTTCATATTACT	0	155	1
CCTTTGAGATCCCTGTTTCTGGTGAAGGCA	0	193	1
CTTCCCTTAATAAAGTTTCTCATCTTAAAT	1	33	0
TATTAATTTTTCCTGACGCTGATGAGGTGT	1	86	1
GCAGATGTAACCCTGCAGCTACAGAAACAT	4	51	1
CAATCTTGAGTGATGTTTCTGTAGCTGCAG	4	63	0
AAGATTGTAACCCTGTAGCTACAGAAACAT	4	86	1
TTATCTTGACTGATGTTTCTGTAGCTACAG	4	98	0
          **********
MAP Score: 0.643579

Motif 14
       TGAGATTCAGGATCCCTACACGGGTGTCCTATCAG	0	3	1
GTGCTCAGCAGACCCTAAAGCTCCACCTCCTTTTTAATATGA	3	41	1
ACTGAATGTGAAATCTTTATCTCCACCGGTGACCAAGATAAT	3	91	1
TAACCCTGCAGCTACAGAAACATCACTCAAGATTGTAACCCT	4	58	1
TAACCCTGTAGCTACAGAAACATCAGTCAAGATAAATTCCAC	4	93	1
GGCGGTCCATGGACCGGAAACTCCACCCTCGAGGCAGTCATG	7	109	1
          *   *   * * ****    **
MAP Score: 0.0930059