AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_fusions005_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243017
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH1522	116	nitrogenase alpha chain (NifD) related protein
#1	MTH1584	112	phosphomannomutase
#2	MTH1591	30	phosphonopyruvate decarboxylase
#3	MTH1592	21	conserved protein
#4	MTH1593	205	ribosomal protein S3a
#5	MTH1759	70	mannose-1-phosphate guanyltransferase
#6	MTH1762	159	DNA mismatch recognition protein MutS
#7	MTH1791	23	glucose-1-phosphate thymidylyltransferase
#8	MTH1792	116	dTDP-4-dehydrorhamnose reductase

Motif 1
AAGCTTCTAAATGAATATTAATCAATCCATGG	0	19	1
TAATCAATCCATGGATATGAATCATGGGATGG	0	37	1
GAATCATGGGATGGATTTGCATCATGGTTCCA	0	55	1
TCAAATGTCTGTGGTTATGCAACATGGCTGGA	0	83	0
TTGAGGTAATGTGATTAAAAATTCATACGGAG	1	19	1
ATCCATATTGGTGATTAACAATTCAAATATTA	1	66	1
GCCCCATTCACTGGATAATATTTGAATTGTTA	1	81	0
GGGGTGCTGTGTGGTCATGAATATGAACAGCC	4	21	0
TCATATTTAACTGGTTAACCATGATTTAGAGT	4	123	0
        TTCTGGTTATTATAATGTAATTGC	5	2	1
TGCATATTCGCTGGAAAAAAATACTTATTAGT	5	31	1
ATAAATTTCCCTGGATATATATGGATTCAGAG	6	130	0
TGGTTTTATTCTGGATATCTTTCATGATAACA	8	33	0
GCACCTCTCTCTGGTCTTTTATTGTTAGAGGG	8	90	0
          ********  **
MAP Score: 13.3435

Motif 2
GCCATGTTGCATAACCACAGACATTTGAGGTGA	0	87	1
GGATAAAGTCAGACCTTCACTCCGTATGAATTT	1	37	0
  TTTTTAACAGCCCCATTCACTGGATAATATT	1	91	0
ATGACCACACAGCACCCCAAACCACCATGTCAA	4	35	1
AAGATTTAAATACTCCCTTATCCTATTATAGAG	4	66	1
       TATATCACCTTAATCTTTAACACCGT	4	189	0
ATTGCACCTAATATCCCCACTCTTTCTGAAGTA	6	52	1
     GCTTCACCTCCTCAGACTTTCAT     	7	5	0
TCATGATAACAAATCCCTTATCTGATTGCAGGA	8	11	0
TCTTAATACAAACCCCTCTTTCCCTGGTTTTAT	8	56	0
       CTGAGCACCTCTCTCTGGTCTTTTAT	8	100	0
          * * ***** ***
MAP Score: 9.16787

Motif 3
TGAATCATGGGATGGATTTGCATCATGGTT	0	54	1
GGTCGCTGCTGATGGGTATGGCAGTTATA 	6	9	0
TTAATCAATCCATGGATATGAATCATGGGA	0	36	1
ACCAGGGAAAGAGGGGTTTGTATTAAGATC	8	61	1
CGTAAAAACAGCTGGATTTAACATAAATTC	4	162	0
GCAATCAGATAAGGGATTTGTTATCATGAA	8	15	1
TTCCATACTGGCGGTGTATGTAACTCTAAA	4	101	1
TATAAATTTCCCTGGATATATATGGATTCA	6	133	0
GCTGTGTGGTCATGAATATGAACAGCCAGT	4	18	0
AACCCACCTTCCTAGATTTATGATCT    	2	6	0
CCCCTCTTTCCCTGGTTTTATTCTGGATAT	8	47	0
          **********
MAP Score: 8.82926

Motif 4
ATATTAATCAATCCATGGATATGAATCATGGG	0	33	1
CATGTTGCATAACCACAGACATTTGAGGTGAC	0	89	1
TTCAAATATTATCCAGTGAATGGGGCTGTTAA	1	87	1
AATCATGGTTAACCAGTTAAATATGAATTTTT	4	129	1
ATCCATATATATCCAGGGAAATTTATAGTTGG	6	136	1
TCCAGAATAAAACCAGGGAAAGAGGGGTTTGT	8	50	1
AACAATAAAAGACCAGAGAGAGGTGCTCAG  	8	96	1
          ****** ** **
MAP Score: 7.92785

Motif 5
ATTGATTAATATTCATTTAGAAGCTTACATATA	0	12	0
CCATCCCATGATTCATATCCATGGATTGATTAA	0	36	0
TGGAACCATGATGCAAATCCATCCCATGATTCA	0	54	0
GTCTGACTTTATCCATATTGGTGATTAACAATT	1	56	1
ATAACTGGCTGTTCATATTCATGACCACACAGC	4	15	1
AATTCAAAAAATTCATATTTAACTGGTTAACCA	4	134	0
AGGTGCAATAATTCACATCGAAGGTCGCTGCTG	6	28	0
CGCACTCTGAATCCATATATATCCAGGGAAATT	6	126	1
          ** *****  ***
MAP Score: 6.9297

Motif 6
TTTTTAACAGCCCCATTCACTGGATAATATTT	1	90	0
CACCTAATATCCCCACTCTTTCTGAAGTAAAA	6	56	1
AGAATACTTTCCACACGCACTCTGAATCCATA	6	111	1
AATACAAACCCCTCTTTCCCTGGTTTTATTCT	8	53	0
     CTGAGCACCTCTCTCTGGTCTTTTATT	8	99	0
          ** ***** ***
MAP Score: 1.66754

Motif 7
CCTAATATCCCCACTCTTTCTGAAGTAAAA	6	58	1
TTAATACAAACCCCTCTTTCCCTGGTTTTA	8	57	0
     CTGAGCACCTCTCTCTGGTCTTTTA	8	101	0
          **********
MAP Score: 1.06078