AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_fusions019_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243431
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH405	130	polyferredoxin
#1	MTH1106	107	ferredoxin
#2	MTH1552	139	formate dehydrogenase, alpha subunit homolog
#3	MTH1553	71	tungsten formylmethanofuran dehydrogenase, subunit H

Motif 1
AATTTAACAGTCCCCTTCATGTTATCTTCA	2	82	0
AGCCTCAAGTTCCCTTCCATCTATTCTAAA	2	110	0
ATCTTCAGTGTCCTTTTTATGGTGAAACTT	2	59	0
TCTCTACTCATAACCTTTATCTGTGCATCA	2	24	1
GAGTTAACACAACCCTTTATTACCTTTTAA	0	103	0
TAGTAGGAACTTCCTTAAATACACAGCAGA	1	50	1
      CCACACACCTATATATATATTTTT	3	4	1
AACCCTTTATTACCTTTTAAACGTATTTAC	0	93	0
ATCAATTAGATTCTTTATATACATAGTAGG	1	27	1
TTAAACGTATTTACTTAAATTTTTTTCCGG	0	77	0
TTTAAGGAAGTTCCTACTATGTATATAAAG	1	39	0
          **********
MAP Score: 2.67254

Motif 2
TTTAAAAGGTAATAAAGGGTTGTGTTAACTCT	0	102	1
AGATTCTTTATATACATAGTAGGAACTTCCTT	1	34	1
AACTTCCTTAAATACACAGCAGATGTATTAAT	1	57	1
TTAAATTTAGAATAGATGGAAGGGAACTTGAG	2	105	1
TAGAAAAATATATATATAGGTGTGTGG     	3	5	0
GTAGAAAATTATTATATGGACGGCGGCTAAAT	3	47	1
          **** **** **
MAP Score: 2.39409

Motif 3
AAAAGGTAATAAAGGGTTGTGTTAACTCTTG	0	105	1
ACGTTGTAGTACAGAGTTCTGATGAATTAAT	1	83	0
TTCACCATAAAAAGGACACTGAAGATAACAT	2	63	1
AAGATAACATGAAGGGGACTGTTAAATTTAG	2	84	1
AGAATAGATGGAAGGGAACTTGAGGCTGAAC	2	113	1
          ****** ****
MAP Score: 2.11541

Motif 4
AAGATAACATGAAGGGGACTGTTAAATTTA	2	84	1
AGAATAGATGGAAGGGAACTTGAGGCTGAA	2	113	1
TTATTATATGGACGGCGGCTAAATGT    	3	55	1
          **********
MAP Score: 0.968722

Motif 5
ATCAATTAGATTCTTTATATACATAGTAGG	1	27	1
TCTACTCATAACCTTTATCTGTGCATCATG	2	26	1
ATCTTCAGTGTCCTTTTTATGGTGAAACTT	2	59	0
    CCACACACCTATATATATATTTTTCT	3	6	1
          **********
MAP Score: 0.574067