AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_fusions019_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243439
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH384	249	unknown
#1	MTH387	24	conserved protein
#2	MTH388	35	unknown
#3	MTH393	41	NADH dehydrogenase (ubiquinone), subunit 1 related protein
#4	MTH394	55	unknown
#5	MTH397	40	formate hydrogenlyase, subunit 7 
#6	MTH399	23	polyferredoxin
#7	MTH400	33	polyferredoxin
#8	MTH403	187	formylmethanofuran:tetrahydromethanopterin formyltransferase II
#9	MTH405	130	polyferredoxin
#10	MTH1106	107	ferredoxin
#11	MTH1552	139	formate dehydrogenase, alpha subunit homolog
#12	MTH1553	71	tungsten formylmethanofuran dehydrogenase, subunit H

Motif 1
GTGACTCCATAGGAACCTCCAGGACATGAT	0	21	0
GTTCCTATGGAGTCACATCCACTTACCGGT	0	35	1
CTTCTGTAGAGGGACCCTTCAGATATCAGT	0	122	1
GTTTCTGTAGAGAAACCTCCAGATATTAGT	0	160	1
TTTCTGATTAAATCCCTTCCATTTTCATTC	4	23	0
        TAAATCCCCTCTTTTCTGATTA	4	43	0
ATGATCGGGTAGTCACCTCTGAACACTCTC	8	35	0
TGAGGAGGCAGAGGACCTCCTGGACGCAAG	8	74	1
GGAGGTCAGAAAGAACATCCGGGGAGAGGA	8	107	1
TGCTGAATGTAAGCACATCCAGGGATTCAG	8	152	0
TATACATAGTAGGAACTTCCTTAAATACAC	10	44	1
TAAATTTAACAGTCCCCTTCATGTTATCTT	11	84	0
TTCAGCCTCAAGTTCCCTTCCATCTATTCT	11	113	0
          **********
MAP Score: 12.669

Motif 2
AACCTCCAGGACATGATGGGGTGGGAAT   	0	7	0
CCCATCATGTCCTGGAGGTTCCTATGGAGTC	0	18	1
TTCACAGAAACCGGTAAGTGGATGTGACTCC	0	43	0
       AAGACATGATGTGGAATGAAAATG	4	3	1
     TAAATGCGTGATGTTGATGTCCT   	6	5	1
   GGGTTTTGCTGCAGCTGGAATTTTATCA	7	15	0
ATGCTTGCGTCCAGGAGGTCCTCTGCCTCCT	8	76	0
ACGTCCTCTCCCCGGATGTTCTTTCTGACCT	8	109	0
CGGCTGAATCCCTGGATGTGCTTACATTCAG	8	149	1
TCTTTAATGTGCTGGATCCGGGAATCTGGGT	9	17	1
GTGTGCTGAGGCCTGATGTTGATCCCGTGAA	9	46	1
GATGTTGATCCCGTGAACCGGAAAAAAATTT	9	60	1
ACTGAAGATAACATGAAGGGGACTGTTAAAT	11	80	1
ATGGAAGGGAACTTGAGGCTGAACCTGGA  	11	120	1
          ** ********
MAP Score: 10.5414

Motif 3
GTTTCTGTGAATATAATCACGAAAACGACTATGA	0	63	1
TATCTGAAGGGTCCCTCTACAGAAGATTTAGTAA	0	113	0
GACCCTTCAGATATCAGTAAAAAAAAGTTTCTGT	0	134	1
GTAAAAAAAAGTTTCTGTAGAGAAACCTCCAGAT	0	150	1
AAACCTCCAGATATTAGTAAAAAAGGCCATAATT	0	172	1
    ATATAAATCTTTTTAAAAAAGGTGAGTTAG	0	229	0
AATGGAAGGGATTTAATCAGAAAAGAGGGGATTT	4	30	1
AGTTCCTACTATGTATATAAAGAATCTAATTGAT	10	27	0
TACATCTGCTGTGTATTTAAGGAAGTTCCTACTA	10	50	0
TCATGATAAAGTTTCACCATAAAAAGGACACTGA	11	51	1
TTTCTATTTGATTTTTGTAGAAAATTATTATATG	12	31	1
          ** * * ** ****
MAP Score: 9.10049

Motif 4
TCCACTTACCGGTTTCTGTGAATATAATCACG	0	52	1
AGTAAAAAAAAGTTTCTGTAGAGAAACCTCCA	0	149	1
ATATATAGATGATTACTGGTGA          	1	12	1
ATCATTCCGGTGTTAATGGTGATGAG      	3	25	1
          GGGTTTTGCTGCAGCTGGAATT	7	21	0
CGATCATAACGGTTATTGAGGAGGCAGAGGAC	8	58	1
ACATTCAGCATGGTTGTGATGCTCA       	8	172	1
TCCGGGAATCTGGGTGTGCTGAGGCCTGATGT	9	33	1
AGGTAATAAAGGGTTGTGTTAACTCTTGAAGC	9	108	1
TTGTAGTACAGAGTTCTGATGAATTAATACAT	10	79	0
TTCAGTGTCCTTTTTATGGTGAAACTTTATCA	11	54	0
ATAACATGAAGGGGACTGTTAAATTTAGAATA	11	87	1
TTTTCTATTTGATTTTTGTAGAAAATTATTAT	12	30	1
          ***** ** ***
MAP Score: 8.70727

Motif 5
AACCTCCAGGACATGATGGGGTGGGAAT   	0	7	0
       AAGACATGATGTGGAATGAAAATG	4	3	1
AATAAAGAGCAAATGCTGAGGTAAAGAA   	5	22	1
     TAAATGCGTGATGTTGATGTCCT   	6	5	1
GTTCAGGAGAGTGTTCAGAGGTGACTACCCG	8	29	1
CGGTTATTGAGGAGGCAGAGGACCTCCTGGA	8	67	1
GGGAATCTGGGTGTGCTGAGGCCTGATGTTG	9	36	1
TTGTAGTACAGAGTTCTGATGAATTAATACA	10	80	0
GTAGAGAGTGAGGTGAAGAGG          	11	0	0
ACTGAAGATAACATGAAGGGGACTGTTAAAT	11	80	1
          * *********
MAP Score: 8.5697

Motif 6
TGTAGAGGGACCCTTCAGATATCAGTAAAAA	0	126	1
CTGTAGAGAAACCTCCAGATATTAGTAAAAA	0	164	1
         GGCTTCCATGTTCTCATTCAGG	2	1	1
TGATTAAATCCCTTCCATTTTCATTCCACAT	4	18	0
GTTCTTTCTGACCTCCATGCTTGCGTCCAGG	8	92	0
CCCTGGATGTGCTTACATTCAGCATGGTTGT	8	158	1
GTAGGAACTTCCTTAAATACACAGCAGATGT	10	52	1
TTTAACAGTCCCCTTCATGTTATCTTCAGTG	11	79	0
CCTCAAGTTCCCTTCCATCTATTCTAAATTT	11	107	0
CATTTAGCCGCCGTCCATATAATAATTTTCT	12	49	0
          ******** **
MAP Score: 4.22578

Motif 7
TACTAAATCTTCTGTAGAGGGACCCTTCAGA	0	114	1
CCTTCAGATATCAGTAAAAAAAAGTTTCTGT	0	137	1
AAAAAAAGTTTCTGTAGAGAAACCTCCAGAT	0	153	1
CCTCCAGATATTAGTAAAAAAGGCCATAATT	0	175	1
 AAGACATGATGTGGAATGAAAATGGAAGGG	4	9	1
AGGGATTTAATCAGAAAAGAGGGGATTTA  	4	36	1
TGAACTTCAATCAATAAAGAGCAAATGCTGA	5	10	1
GTGGATGAGTTCAGGAGAGTGTTCAGAGGTG	8	21	1
ATCCAGGGATTCAGCCGAGGGATCCGACGTC	8	135	0
CTAATTGATCTCATGAGAGGGTCACG     	10	5	0
ATAAAGGTTATGAGTAGAGAGTGAGGTGAAG	11	13	0
CTATTTGATTTTTGTAGAAAATTATTATATG	12	34	1
          **** ******
MAP Score: 4.02246

Motif 8
TAAATTTAACAGTCCCCTTCATGTTATCTTCA	11	82	0
      ATTCCCACCCCATCATGTCCTGGAGG	0	4	1
        TAAATCCCCTCTTTTCTGATTAAA	4	41	0
      TGAGCATCACAACCATGCTGAATGTA	8	171	0
ACTCTCTACTCATAACCTTTATCTGTGCATCA	11	22	1
TTTCTGATTAAATCCCTTCCATTTTCATTCCA	4	21	0
CTGCCTCCTCAATAACCGTTATGATCGGGTAG	8	53	0
TTTAGGTCTAACTCACCTTTTTTAAAAAGATT	0	222	1
CCTCAAGTTCCCTTCCATCTATTCTAAATTTA	11	106	0
          CCACACACCTATATATATATTT	12	0	1
AAGAGTTAACACAACCCTTTATTACCTTTTAA	9	103	0
        CTCATCACCATTAACACCGGAATG	3	27	0
TATTTAAGGAAGTTCCTACTATGTATATAAAG	10	39	0
TTCCATTTTCATTCCACATCATGTCTT     	4	5	0
          * ***** ****
MAP Score: 1.5572