AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_fusions011_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243248
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH442	195	excinuclease ABC subunit B
#1	MTH443	41	excinuclease ABC subunit A
#2	MTH444	133	sensory transduction histidine kinase
#3	MTH446	97	sensory transduction regulatory protein
#4	MTH447	109	sensory transduction regulatory protein
#5	MTH448	74	unknown
#6	MTH449	38	unknown
#7	MTH451	132	magnesium chelatase subunit ChlI
#8	MTH452	45	unknown
#9	MTH695	248	conserved protein
#10	MTH1093	96	ABC transporter (ATP-binding
#11	MTH1142	300	H(2)-dependent N5,N10-methylenetetrahydromethanopterin dehydrogenase 
#12	MTH1143	104	biotin synthetase (BioB)
#13	MTH1145	78	conserved protein
#14	MTH1147	38	conserved protein
#15	MTH1149	72	ABC transporter subunit Ycf16

Motif 1
CAGGATTATGGAACACGTGGGATACCCTGT	0	67	1
CGGACCTCTGGAAGAGCAGAGATCCGTGAA	2	83	0
     GACCAGAAGAGGAGAGTCAGAAAAA	2	118	0
 GCATGTCTTGAAGACCAGACACCAGTGAA	3	9	1
ACCAACCACTGAACCGGTGATAGC      	7	118	1
GATTCTAATGAAGGACCTGAGAGTCATCTG	9	43	0
TGAAGGACTGGAAAAGGAGAACACTTAGAT	9	70	0
AAGTGGCTATGAAAAGCTGGTTAAAATGAC	9	112	1
AATGGAGCATAAAGAGCAGAGATTGTCATT	9	136	0
TTTCAATCCCAAGCAGCTGAAACTGGTGTT	12	81	1
CCCCATCAAAGAACAGCAGAGAAAAACAGG	13	13	1
ATATAACAGGAAACAGCTGATCAAAA    	13	62	1
AACTTAAGGGAAAGAGCAGAAA        	14	26	1
          **********
MAP Score: 16.4836

Motif 2
TATCCCACGTGTTCCATAATCCTGTGATGAT	0	60	0
ATATATAAGTTGACCCTGAAATATAATCCCA	0	142	1
TGGAACCTCTTATCCATGAAATGATAAGAGT	2	37	0
TGGATAAGAGGTTCCATGAAACGCATGGCTC	2	52	1
GAAGAGCAGAGATCCGTGAAGAGCCATGCGT	2	72	0
GTCTGGACATTGCCCCTGATACTTTGATGTC	4	47	0
AGTGATAGCGGTTCCATAAAGGAGGTTTATC	4	88	1
      GCGTGTACCATCATAACTTCAGCCT	5	59	0
TTCCGTTAAAGATCCATAAAAGTCAACCGCT	9	164	1
GTTAGATTTTTATCCCTGATAGTATAAATTG	10	38	0
GATAAAAATCTAACCATAATACCCGATGCTT	10	55	1
CTCAGCCACAGATCCGTGATATTAATATCTT	11	51	1
TACCATCCATTATCCATATAATATTATATGA	11	99	0
TTAAATTGACTTACCCTGAAATTGCCACAGG	11	166	1
        AGGCCCCATCAAAGAACAGCAGA	13	2	1
GAGAAAAACAGGTCCATAAACAGTATGAACC	13	31	1
TAAACAGTATGAACCATATAACAGGAAACAG	13	47	1
AAGTTCATGCGTTCCATGTAC          	14	0	0
          * *********
MAP Score: 15.4333

Motif 3
GATGATACCCCCACTGAACTTGTTTTAAACA	0	35	0
CTCTGGAAGAGCAGAGATCCGTGAAGAGCCA	2	77	0
CTCTGCTCTTCCAGAGGTCCGGCTGATTTTT	2	92	1
CAAAGAGCGTCCTCTGGCCCG          	6	0	0
ATTAGACCAACCACTGAACCGGTGATAGC  	7	113	1
TCCAGATGACTCTCAGGTCCTTCATTAGAAT	9	41	1
GATGTGATTTCCACAGGGCTTAAGTTATAAT	9	202	1
CTGCTTCAATCCAGTGATCCTAACTGGAAGG	11	20	0
AGCAGCTCAGCCACAGATCCGTGATATTAAT	11	46	1
          ******* ***
MAP Score: 10.6791

Motif 4
CCCACGTGTTCCATAATCCTGTGATGATACCCCCAC	0	52	0
         TCCCTGCATCAGTGAGGTATCTGATCC	2	1	1
TTTCATGGAACCTCTTATCCATGAAATGATAAGAGT	2	37	0
CTCTGGAAGAGCAGAGATCCGTGAAGAGCCATGCGT	2	72	0
GTCTTGAAGACCAGACACCAGTGAAGAGCCCACAAT	3	14	1
       TTACCGGGTTTCAGTGTTGAGCGTATCAG	5	3	1
TTAGACCAACCACTGAACCGGTGATAGC        	7	114	1
TGCTCTTTATGCTCCATTCCGTTAAAGATCCATAAA	9	148	1
   TTAAGGGCAGCCTTCCAGTTAGGATCACTGGAT	11	7	1
AGCAGCTCAGCCACAGATCCGTGATATTAATATCTT	11	46	1
 TTTTGATCAGCTGTTTCCTGTTATATGGTTCATAC	13	53	0
          **    *** **** *
MAP Score: 10.5817

Motif 5
AATACCCGATGCTTCAGGGTCGCGGAGGAT	10	72	1
GTGGGATTATATTTCAGGGTCAACTTATAT	0	144	0
ACCTGTGGCAATTTCAGGGTAAGTCAATTT	11	168	0
   TTACCGGGTTTCAGTGTTGAGCGTATC	5	7	1
TGACATCAAAGTATCAGGGGCAATGTCCAG	4	46	1
 GCTATCACCGGTTCAGTGGTTGGTCTAAT	7	113	0
AGAGCCATGCGTTTCATGGAACCTCTTATC	2	54	0
GTTTAAAACAAGTTCAGTGGGGGTATCATC	0	36	1
CACTCTTATCATTTCATGGATAAGAGGTTC	2	36	1
     TCCCTGCATCAGTGAGGTATCTGAT	2	5	1
GAACGCATGAACTTAAGGGAAAGAGCAGAA	14	17	1
ACAATTTATACTATCAGGGATAAAAATCTA	10	37	1
          **********
MAP Score: 10.0443

Motif 6
         TTTATCATTACCATCCTCTGATTTATG	0	1	1
TTCAGTGGGGGTATCATCACAGGATTATGGAACACG	0	48	1
TCAACTTTATGTATCCTGGCAAAGGTATATATAAGT	0	116	1
ATGGAACCTCTTATCCATGAAATGATAAGAGTGGAT	2	33	0
TGACATCAAAGTATCAGGGGCAATGTCCAGACATTA	4	46	1
AGTGTTGAGCGTATCAGAGCAAGTATAAAGAGACGT	5	22	1
ACCCTCCACAGCATCACTATAACAATTTATACTATC	10	16	1
GGTTAGATTTTTATCCCTGATAGTATAAATTGTTAT	10	34	0
TTACCATCCATTATCCATATAATATTATATGAAAAT	11	95	0
GGTGAATAAATTCTCCTTATAAGTTTTTTGATTTGA	11	195	1
GATTTGAAAATTATCAAAAAATATATTTATATTGGA	11	224	1
ATTTATTTTTTTATCCAAGTAATTTTTACACTTCAA	12	35	1
TCTATTTATTGTATCCTACGAATAATTTATTAAAAG	15	24	1
          ******  * **   *
MAP Score: 7.16469

Motif 7
TCACAGGATTATGGAACACGTGGGATACCCTG	0	64	1
TTATCATTTCATGGATAAGAGGTTCCATGAAA	2	41	1
AAGAGGTTCCATGAAACGCATGGCTCTTCACG	2	57	1
AACCTCCTTTATGGAACCGCTATCACTGAGGA	4	83	0
ATGAAAAAACATGACACGCATGGAGGTGTGA 	8	24	1
AAATAATTTAATGAAAAAGGGAGTT       	9	3	0
TAAGCTCCAGATGACTCTCAGGTCCTTCATTA	9	36	1
CTAAGTGGCTATGAAAAGCTGGTTAAAATGAC	9	110	1
GGAGGATAAAATGAAAACATTGCTTAAATTGA	11	143	1
TCCCAAGCAGCTGAAACTGGTGTTAAA     	12	87	1
ACCATATAACAGGAAACAGCTGATCAAAA   	13	59	1
      GTACATGGAACGCATGAACTTAAGGG	14	4	1
          ******* * **
MAP Score: 6.32817

Motif 8
GGTTCCATAAAGGAGGTTTATC         	4	97	1
      GTCCAGGACATTGAAGTCAAAGAGC	6	23	0
GAGAGTCATCTGGAGCTTAAAAATAATTTAA	9	24	0
GATGACTCTCAGGTCCTTCATTAGAATCTAA	9	45	1
GGCTATGAAAAGCTGGTTAAAATGACAATCT	9	116	1
TTTAACGGAATGGAGCATAAAGAGCAGAGAT	9	143	0
ATTCCGTTAAAGATCCATAAAAGTCAACCGC	9	163	1
TCTGTGGCTGAGCTGCTTCAATCCAGTGATC	11	32	0
GGCTTCCCAAAGGAGGATAAAATGAAAACAT	11	132	1
AAATTGCCACAGGTGAATAAATTCTCCTTAT	11	184	1
TTCAATCCCAAGCAGCTGAAACTGGTGTTAA	12	82	1
AGAGAAAAACAGGTCCATAAACAGTATGAAC	13	30	1
AAGAAATAGGTGGTGGTTTAA          	15	61	1
          ******** **
MAP Score: 5.48821

Motif 9
ACAATAGAATGAGGTTCTTATTTTAAGTGATTT     	0	172	1
TTAATACAGTCAGGTACATATTAGTAATACTCATCTTT	7	53	1
AGATGACTCTCAGGTCCTTCATTAGAATCTAAGTGTTC	9	44	1
TCCAGTCCTTCAGCTTCCCTTTCTAAGTGGCTATGAAA	9	88	1
TTATATGATGGAGGTTCCTATTATAACTTAAGCCCTGT	9	214	0
GCACCCTCCACAGCATCACTATAACAATTTATACTATC	10	14	1
ATCTGTGGCTGAGCTGCTTCAATCCAGTGATCCTAACT	11	26	0
AGCTCAGCCACAGATCCGTGATATTAATATCTTAATAA	11	49	1
CAGAGAAAAACAGGTCCATAAACAGTATGAACCATATA	13	29	1
          ***** * *  *   * *
MAP Score: 5.47933

Motif 10
ATTAAGGCAGGATTAAAGAGTT          	1	29	1
AAATTTCCAGGCTTAAGGTGTCTTGAGCTCAT	3	51	1
GCAGAATAAGGTTTAATGTGACGCCGTGACCA	4	12	0
ATCAGAGCAAGTATAAAGAGACGTCAGGCTGA	5	34	1
ATGAAAAGCTGGTTAAAATGACAATCTCTGCT	9	120	1
ATCCCTGATAGTATAAATTGTTATAGTGATGC	10	26	0
TCCCAAAGGAGGATAAAATGAAAACATTGCTT	11	136	1
TGAAAACATTGCTTAAATTGACTTACCCTGAA	11	154	1
TGCCACAGGTGAATAAATTCTCCTTATAAGTT	11	188	1
ATTGGAAACCGATTAATCTGTACTACTAATAA	11	254	1
AGCTGCTTGGGATTGAAAAGTCAGTAAATTGA	12	67	0
          * ***** ****
MAP Score: 3.58267