AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_operons027_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944245244
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH170	141	phosphoribosylaminoimidazolesuccinocarboxamide synthase
#1	MTH600	300	conserved protein
#2	MTH602	90	precorrin-3 methylase
#3	MTH1014	127	conserved protein
#4	MTH1015	63	methyl coenzyme M reductase system, component A2 
#5	MTH1016	65	conserved protein
#6	MTH1018	31	conserved protein
#7	MTH1020	109	conserved protein
#8	MTH1022	172	biopolymer transport protein
#9	MTH1023	35	ribonuclease HII
#10	MTH1025	222	unknown
#11	MTH1348	139	precorrin-2 methyltransferase
#12	MTH1403	78	precorrin-3 methylase
#13	MTH1404	82	unknown
#14	MTH1514	125	precorrin-6Y methylase

Motif 1
AGGTGAAATTGAGATACCCGTGGTTGCGGCGGA	1	18	1
GGACTGACTGGAAATTCCGCTGATGAAAGAGAA	1	101	1
TCAGTCAGCAGGGATTCCTGTGAGGTTTTCTCT	1	128	0
      AAATGATGGGCCCCGGAAAAAAGATAA	2	4	1
TAAATAAATTGTGGTTCCCCTGATTAAGAGGGG	3	15	0
TGGCAATTATGAGGTTCCTCAGTGAATGA    	7	6	0
AGGTTCTTATGAGATTCCACAGGGACCATGGGT	7	46	0
TTCTCACATGGAGTTCACGGTGACATGAACATT	10	69	1
ATTTCACATGGAGTTCACAGCGATATGAACACC	10	99	1
AACACCATATGATGAACCTCAGAATGTGATATG	10	126	1
CTCAGAATGTGATATGCCGGTGAAAGATATATA	10	143	1
CTTTAATGGAGAGATTGCTGAGACCCAGTGAAT	14	62	1
          ***** ** * **
MAP Score: 9.60907

Motif 2
AGAAAACCTCACAGGAATCCCTGCTGACTGA	1	130	1
ATGAAGGAGAATATGAATACCGGATTCCATT	1	204	1
ATCTGAGTGGAAAGGAAACTCGAGATAATAA	2	50	1
 TGTCAGTAAACATGAATCTGTATATTCTTT	4	43	0
AGCCAGGTTAATATGAATATCCT        	6	18	1
  TCATTCACTGAGGAACCTCATAATTGCCA	7	8	1
CCATGGTCCCTGTGGAATCTCATAAGAACCT	7	48	1
AAGAACCTTCATAGGAATCCGCATAAAAAAG	7	71	1
AATCACAGTTAAAGGAACACCATGATCTTAA	8	57	0
GTTCACAGCGATATGAACACCATATGATGAA	10	111	1
GAACACCATATGATGAACCTCAGAATGTGAT	10	125	1
TCACTGGGTCTCAGCAATCTCTCCATTAAAG	14	62	0
          * *********
MAP Score: 9.27986

Motif 3
AGTATTGGAGAGTTGATCAGGATTTCATACTCA	0	98	1
CCCGGAAAAAAGATAATCAGGGGATGATAATCT	2	21	1
 ATAGACCCCTCTTAATCAGGGGAACCACAATT	3	9	1
TACTATTAATAAAACATCATGGTTAACAGATAC	3	77	0
GATTCTCCATAAAAAATCAGGGTTGCTGATAGC	5	24	1
AGGGTTGCTGATAGCATAAGGGTCCTGGCCCCC	5	42	1
TTCATGGCGATTAAGATCATGGTGTTCCTTTAA	8	47	1
ACACGGTTAAAGAGTATCATGGTCTCAATCACA	8	81	0
AACTCTGTAGACATGATGATGGTCTGGTCATCC	11	101	0
TGCGACAGCTTCATGATCAGTGTCCTTCTTAGA	12	20	1
          * *  ********
MAP Score: 9.09979

Motif 4
GATAAGGTGAAATTGAGATACCCGTGGTTGCGGCGGA	1	14	1
TGGGCCCCGGAAAAAAGATAATCAGGGGATGATAATC	2	16	1
CAGGGGATGATAATCTGAGTGGAAAGGAAACTCGAGA	2	38	1
ATTAATAGTAAATATAGTTAATAAAGGAGGACTTTGT	3	100	1
ATGAAGGTTCTTATGAGATTCCACAGGGACCATGGGT	7	46	0
GAATCCGCATAAAAAAGTTTGAAGTGGTGGTTTT   	7	85	1
   TCATTCTTTTTTTGATTTGAAGGGGCCTCCAGCA	9	7	1
AACAGGTGAGTTATTTGTTTGTAAAGG          	10	0	0
CCATTACCGGTAATATGATCTGATAGGTTTCTTCTCA	10	38	1
GCCACAGAAAAATAATGATAATAAAGGCGGGTCTGGA	11	51	1
TCATCATGTCTACAGAGTTATTAAAGGTGTTCTA   	11	115	1
GATATTATAATAAAATGTTGGTATGGGACACTCTCTT	14	28	1
GCCTCCGTGCTGATTTGATGGAATAGGGGTAATTTT 	14	99	1
          ** * ****   *  **
MAP Score: 8.60011

Motif 5
ATAAGGTGAAATTGAGATACCCGTGGTTGCGGCGGA	1	15	1
CTGCAAGCATATGGTGTATCCCGAAGCAGGATAGTA	1	65	0
CAGGGACTGACTGGAAATTCCGCTGATGAAAGAGAA	1	98	1
GATGGTGGAAATGGAACTGCTCAAAAGAAGACATGA	1	172	1
        AAATGATGGGCCCCGGAAAAAAGATAAT	2	2	1
AAATAAATAAATTGTGGTTCCCCTGATTAAGAGGGG	3	15	0
TATTCTTTTGATGAAGCGACTATTAAAATTTTCCTA	4	15	0
GCGGATTCCTATGAAGGTTCTTATGAGATTCCACAG	7	57	0
GATTAAGATCATGGTGTTCCTTTAACTGTGATTGAG	8	55	1
TCTGCCTCACCTGGTGGATATTTAAAAATCAATGGG	8	143	0
       CTGCTGGAGGCCCCTTCAAATCAAAAAAA	9	16	0
TTCTTCTCACATGGAGTTCACGGTGACATGAACATT	10	66	1
AACATTTCACATGGAGTTCACAGCGATATGAACACC	10	96	1
TGAACACCATATGATGAACCTCAGAATGTGATATGC	10	124	1
GACACTGATCATGAAGCTGTCGCAAATGACAGAC  	12	8	0
ACTCTCTTTAATGGAGAGATTGCTGAGACCCAGTGA	14	57	1
          ******   **   **
MAP Score: 8.17915

Motif 6
TCACAGTTAAAGGAACACCATGATCTTAAT	8	56	0
TTGATTTGAAGGGGCCTCCAGCAG      	9	21	1
TCATGTCACCGTGAACTCCATGTGAGAAGA	10	67	0
TCATATCGCTGTGAACTCCATGTGAAATGT	10	97	0
TCATTCACTGAGGAACCTCATAATTGCCAG	7	10	1
TGATGAAAGAGAAAACCTCACAGGAATCCC	1	121	1
TCACAGCGATATGAACACCATATGATGAAC	10	113	1
          GAAGCCACCAACCGCCTAAG	12	68	0
TGAGTGGAAAGGAAACTCGAGATAATAAAA	2	53	1
ACACCATATGATGAACCTCAGAATGTGATA	10	127	1
CTTTTTTCCGGGGCCCATCATTT       	2	3	0
AACTGTGATTGAGACCATGATACTCTTTAA	8	78	1
TCTTAATCAGGGGAACCACAATTTATTTAT	3	19	1
     TGTCAGTAAACATGAATCTGTATAT	4	48	0
TCCTGCTTCGGGATACACCATATGCTTGCA	1	70	1
          AAAACCACCACTTCAAACTT	7	99	0
TAATAACTCTGTAGACATGATGATGGTCTG	11	108	0
CTGCTCAAAAGAAGACATGAAGGAGAATAT	1	188	1
AGGTGGGCATAAAGACATCAGCAATAAATA	1	259	1
GAATCTCATAAGAACCTTCATAGGAATCCG	7	62	1
TAAAGATTTTGGTGACCTCAGCATTTCATG	8	23	1
TGGAGTTCACGGTGACATGAACATTTCACA	10	77	1
          **********
MAP Score: 7.52159

Motif 7
CACCCTAAGAAGCATGAATCTGATTTCGCAAGA	0	15	1
AGATAATCAGGGGATGATAATCTGAGTGGAAAG	2	31	1
GTATCTGTTAACCATGATGTTTTATTAATAGTA	3	77	1
  TGTCAGTAAACATGAATCTGTATATTCTTTT	4	42	0
GATCTTAATCGCCATGAAATGCTGAGGTCACCA	8	32	0
TTAAAGGAACACCATGATCTTAATCGCCATGAA	8	47	0
TGTGATTGAGACCATGATACTCTTTAACCGTGT	8	81	1
AGTTCACGGTGACATGAACATTTCACATGGAGT	10	80	1
TGAACACCATATGATGAACCTCAGAATGTGATA	10	124	1
CTCTGTAGACATGATGATGGTCTGGTCATCCTT	11	99	0
AAGGACACTGATCATGAAGCTGTCGCAAATGAC	12	14	0
          * ******  ***
MAP Score: 5.5148

Motif 8
   TATTTCACCCTAAGAAGCATGAATCTGATTTC	0	7	1
GACTGGAAATTCCGCTGATGAAAGAGAAAACCTCA	1	106	1
 AAATGATGGGCCCCGGAAAAAAGATAATCAGGGG	2	9	1
 TCAATGTTAGCCAGGTTAATATGAATATCCT   	6	9	1
TTCATAGGAATCCGCATAAAAAAGTTTGAAGTGGT	7	78	1
AATGTGATATGCCGGTGAAAGATATATATACTCAT	10	148	1
TATAGTTCCACCCCCTTAAATAGGTCC        	11	2	0
TTTAGAGAGTGCCACAGAAAAATAATGATAATAAA	11	41	1
TCTGGATATTTCCAGAGAAGGATGACCAGACCATC	11	82	1
CTTGATTAAATCCCTCTAAGAAGGACACTGATCAT	12	32	0
ATCCTTCACTGCCCTGTAAGGTGGTTTTTAACATC	13	14	1
          ***   **** * **
MAP Score: 5.26061

Motif 9
ATTTCATACTCAAATTCTTTAAAAGTGATAGT      	0	119	1
TATCAGCAACCCTGATTTTTTATGGAGAATCAATCTGA	5	17	0
TTTTGGTGACCTCAGCATTTCATGGCGATTAAGATCAT	8	29	1
TAAGATCATGGTGTTCCTTTAACTGTGATTGAGACCAT	8	58	1
TTGAGACCATGATACTCTTTAACCGTGTAGCCGGATTA	8	86	1
AGAAGGGAAGCTACTCTTTTAACTTGGATTACATTTAA	10	193	0
          GGACCTATTTAAGGGGGTGGAACTATAT	11	0	1
ATCATGTCTACAGAGTTATTAAAGGTGTTCTA      	11	117	1
ATCTAATTCAGAAAGTTTTAAAATGTGTGTGCAGTAAA	13	46	1
TGGTATGGGACACTCTCTTTAATGGAGAGATTGCTGAG	14	46	1
          *    * *****  * **
MAP Score: 4.31798

Motif 10
AGTATGAAATCCTGATCAACTCTCCAATACTT	0	97	0
AGTATTCTATCCTCTGCATCCGCCGCAACCAC	1	37	0
TATTCATATTCTCCTTCATGTCTTCTTTTGAG	1	191	0
   ATAGACCCCTCTTAATCAGGGGAACCACA	3	7	1
TTAATAGTCGCTTCATCAAAAGAATATACAGA	4	25	1
CACTGAGGAACCTCATAATTGCCAGGAACTTA	7	15	1
ATTTTGGTGACCTCAGCATTTCATGGCGATTA	8	28	1
CTGCTGGAGGCCCCTTCAAATCAAAAAAAGAA	9	13	0
ATATGATGAACCTCAGAATGTGATATGCCGGT	10	132	1
ATAGTTCCACCCCCTTAAATAGGTCC      	11	4	0
ATGACCAGACCATCATCATGTCTACAGAGTTA	11	103	1
          *********  *
MAP Score: 4.19292

Motif 11
   CAAGGATAAGGTGAAATTGAGATACCCGT	1	7	1
CCCCAATACGATGGTGGAAATGGAACTGCTCA	1	163	1
AGAAGACATGAAGGAGAATATGAATACCGGAT	1	197	1
GATAGGTTGAAAGGTGGGCATAAAGACATCAG	1	248	1
ATAGTTAATAAAGGAGGACTTTGT        	3	113	1
TCTGCCTCACCTGGTGGATATTTAAAAATCAA	8	147	0
AATGATAATAAAGGCGGGTCTGGATATTTCCA	11	64	1
ACTGCCCTGTAAGGTGGTTTTTAACATCTAAT	13	21	1
ACTCTCTTTAATGGAGAGATTGCTGAGACCCA	14	57	1
          ********  **
MAP Score: 2.62974