AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_fusions016_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243359
 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

Motif 1
ATTATATAACTGAATCGCAATATAACTCATAATAG	0	47	1
AATTTGAGTATGAAATCCTGATCAACTCTCCAATA	0	100	0
CGCAACCACGGGTATCTCAATTTCACCTTATCCTT	1	11	0
TTTCATCAGCGGAATTTCCAGTCAGTCCCTGCAAG	1	94	0
AAACCTCACAGGAATCCCTGCTGACTGAATCCCCA	1	133	1
CCCTGCTGACTGAATCCCCAATACGATGGTGGAAA	1	148	1
TGGTGGAAATGGAACTGCTCAAAAGAAGACATGAA	1	174	1
TTCAGTGAATGGAATCCGGTATTCATATTCTCCTT	1	207	0
TGAGTGGAAAGGAAACTCGAGATAATAAAACAGGA	2	53	1
AATAAATTGTGGTTCCCCTGATTAAGAGGGGTCTA	3	11	0
CTAATCAGATTGATTCTCCATAAAAAATCAGGGTT	5	13	1
         AGGATATTCATATTAACCTGGCTAAC	6	15	0
TGGTCCCTGTGGAATCTCATAAGAACCTTCATAGG	7	51	1
AACCTTCATAGGAATCCGCATAAAAAAGTTTGAAG	7	74	1
TCTTTAACCGTGTAGCCGGATTAAAACCACTATTC	8	101	1
CATGTCACCGTGAACTCCATGTGAGAAGAAACCTA	10	61	0
CATATCGCTGTGAACTCCATGTGAAATGTTCATGT	10	91	0
CCTCAGAATGTGATATGCCGGTGAAAGATATATAT	10	142	1
GAAGATTAAATGTAATCCAAGTTAAAAGAGTAGCT	10	188	1
          **** ***   * **
MAP Score: 14.7204

Motif 2
ATTTCCAGTCAGTCCCTGCAAGCATATGGTGTATCC	1	80	0
ACCTCACAGGAATCCCTGCTGACTGAATCCCCAATA	1	135	1
ACCGGATTCCATTCACTGAAGACCGAGATAGGTTGA	1	222	1
  AAATGATGGGCCCCGGAAAAAAGATAATCAGGGG	2	8	1
        TCATTCACTGAGGAACCTCATAATTGCC	7	2	1
ACTTACCCATGGTCCCTGTGGAATCTCATAAGAACC	7	42	1
TCATGGTCTCAATCACAGTTAAAGGAACACCATGAT	8	62	0
ACCTGTTCCCATTACCGGTAATATGATCTGATAGGT	10	30	1
GTCACCGTGAACTCCATGTGAGAAGAAACCTATCAG	10	57	0
CTCACATGGAGTTCACGGTGACATGAACATTTCACA	10	71	1
ATCGCTGTGAACTCCATGTGAAATGTTCATGTCACC	10	87	0
TTCACATGGAGTTCACAGCGATATGAACACCATATG	10	101	1
TATATATATCTTTCACCGGCATATCACATTCTGAGG	10	142	0
GATTAAATGTAATCCAAGTTAAAAGAGTAGCTTCCC	10	191	1
          * **** *  * * **
MAP Score: 14.6514

Motif 3
TTATATAACTGAATCGCAATATAACTCATAATAG	0	48	1
CCTGCTTCGGGATACACCATATGCTTGCAGGGAC	1	71	1
AATAAAACAGGAAGTGTCATATTC          	2	76	1
TAATCAGATTGATTCTCCATAAAAAATCAGGGTT	5	14	1
         AGGATATTCATATTAACCTGGCTAA	6	16	0
CATTCACTGAGGAACCTCATAATTGCCAGGAACT	7	11	1
TGGTCCCTGTGGAATCTCATAAGAACCTTCATAG	7	51	1
AATCTCATAAGAACCTTCATAGGAATCCGCATAA	7	63	1
ACCTTCATAGGAATCCGCATAAAAAAGTTTGAAG	7	75	1
ACCATGATCTTAATCGCCATGAAATGCTGAGGTC	8	36	0
CACAGTTAAAGGAACACCATGATCTTAATCGCCA	8	51	0
CATGTCACCGTGAACTCCATGTGAGAAGAAACCT	10	62	0
CATATCGCTGTGAACTCCATGTGAAATGTTCATG	10	92	0
CACAGCGATATGAACACCATATGATGAACCTCAG	10	114	1
          *** * *****  *
MAP Score: 12.1421

Motif 4
       CAAGGATAAGGTGAAATTGAGATA	1	3	1
GTGAAATTGAGATACCCGTGGTTGCGGCGGA	1	20	1
AGTCAGCAGGGATTCCTGTGAGGTTTTCTCT	1	128	0
AAGACATGAAGGAGAATATGAATACCGGATT	1	199	1
AATAAATTGTGGTTCCCCTGATTAAGAGGGG	3	15	0
TAAAGTATCTGTTAACCATGATGTTTTATTA	3	73	1
ATGTTAGCCAGGTTAATATGAATATCCT   	6	13	1
ACTTACCCATGGTCCCTGTGGAATCTCATAA	7	42	1
TTCCTATGAAGGTTCTTATGAGATTCCACAG	7	57	0
TTTTTATGCGGATTCCTATGAAGGTTCTTAT	7	69	0
ACAGTTAAAGGAACACCATGATCTTAATCGC	8	53	0
ATGGTGTTCCTTTAACTGTGATTGAGACCAT	8	65	1
TAACTGTGATTGAGACCATGATACTCTTTAA	8	77	1
ACCGGTAATGGGAACAGGTGAGTTATTTGTT	10	18	0
CTCACATGGAGTTCACGGTGACATGAACATT	10	71	1
CAGAATGTGATATGCCGGTGAAAGATATATA	10	145	1
          *** *******
MAP Score: 8.71951

Motif 5
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
          * *  ********
MAP Score: 8.54222

Motif 6
CTAAGAAGCATGAATCTGATTTCGCAAGATTA	0	19	1
ATTATATAACTGAATCGCAATATAACTCATAA	0	47	1
CGCAACCACGGGTATCTCAATTTCACCTTATC	1	14	0
TCCTGCTTCGGGATACACCATATGCTTGCAGG	1	70	1
ATTCCGCTGATGAAAGAGAAAACCTCACAGGA	1	114	1
CCCTGCTGACTGAATCCCCAATACGATGGTGG	1	148	1
AAAGAAGACATGAAGGAGAATATGAATACCGG	1	195	1
CTTAATCAGGGGAACCACAATTTATTTATTTA	3	20	1
TCAGTAAACATGAATCTGTATATTCTTTTGAT	4	39	0
CTAATCAGATTGATTCTCCATAAAAAATCAGG	5	13	1
CATTCACTGAGGAACCTCATAATTGCCAGGAA	7	11	1
TGGTCCCTGTGGAATCTCATAAGAACCTTCAT	7	51	1
AACCTTCATAGGAATCCGCATAAAAAAGTTTG	7	74	1
     ATTAATGGAACACTAAAGATTTTGGTG	8	5	1
ATTGAGACCATGATACTCTTTAACCGTGTAGC	8	85	1
CACCATATGATGAACCTCAGAATGTGATATGC	10	128	1
          **** * *****
MAP Score: 6.10512

Motif 7
GAGTTGATCAGGATTTCATACTCAAATTCTTTA	0	107	1
CAGTCAGCAGGGATTCCTGTGAGGTTTTCTCTT	1	127	0
CATCGTATTGGGGATTCAGTCAGCAGGGATTCC	1	143	0
TATGAATACCGGATTCCATTCACTGAAGACCGA	1	215	1
TGATAGCATAAGGGTCCTGGCCCCC        	5	50	1
GGCAATTATGAGGTTCCTCAGTGAATGA     	7	5	0
GGTTCTTATGAGATTCCACAGGGACCATGGGTA	7	45	0
TTTTTTATGCGGATTCCTATGAAGGTTCTTATG	7	68	0
GGTGACCTCAGCATTTCATGGCGATTAAGATCA	8	33	1
CTTCTCACATGGAGTTCACGGTGACATGAACAT	10	68	1
CATTTCACATGGAGTTCACAGCGATATGAACAC	10	98	1
          ********  * *
MAP Score: 5.8754

Motif 8
CCCGTGGTTGCGGCGGATGCAGAGGATAGAATACTA	1	34	1
CCCTCTTAATCAGGGGAACCACAATTTATTTATTTA	3	16	1
   TCATTCACTGAGGAACCTCATAATTGCCAGGAA	7	7	1
CCCATGGTCCCTGTGGAATCTCATAAGAACCTTCAT	7	47	1
AAACTTTTTTATGCGGATTCCTATGAAGGTTCTTAT	7	69	0
TACTCTTTAACCGTGTAGCCGGATTAAAACCACTAT	8	98	1
AAATATCCACCAGGTGAGGCAGAAAA          	8	156	1
TGAACACCATATGATGAACCTCAGAATGTGATATGC	10	124	1
          * * *** ** **  *
MAP Score: 5.74171

Motif 9
TATAGGTGTAAATTCTATTATGAGTTATATTGCGA	0	61	0
CTCGAGTTTCCTTTCCACTCAGATTATCATCCCCT	2	39	0
GCAACCCTGATTTTTTATGGAGAATCAATCTGATT	5	15	0
CACTTCAAACTTTTTTATGCGGATTCCTATGAAGG	7	76	0
GTGACCTCAGCATTTCATGGCGATTAAGATCATGG	8	34	1
TCATGGTGTTCCTTTAACTGTGATTGAGACCATGA	8	63	1
TGATAGGTTTCTTCTCACATGGAGTTCACGGTGAC	10	58	1
GTGACATGAACATTTCACATGGAGTTCACAGCGAT	10	88	1
GGAAGCTACTCTTTTAACTTGGATTACATTTAATC	10	191	0
          * *** **   ****
MAP Score: 5.30805

Motif 10
AAGAGAAAACCTCACAGGAATCCCTGCTGAC	1	127	1
AAAGTATCTGTTAACCATGATGTTTTATTAA	3	74	1
GTTAGCCAGGTTAATATGAATATCCT     	6	15	1
CATAAGAACCTTCATAGGAATCCGCATAAAA	7	68	1
ACCTCAGCATTTCATGGCGATTAAGATCATG	8	37	1
TGGTGTTCCTTTAACTGTGATTGAGACCATG	8	66	1
CCTGTTCCCATTACCGGTAATATGATCTGAT	10	31	1
TAGGTTTCTTCTCACATGGAGTTCACGGTGA	10	61	1
TCACATGGAGTTCACGGTGACATGAACATTT	10	72	1
ACATGAACATTTCACATGGAGTTCACAGCGA	10	91	1
TCACATGGAGTTCACAGCGATATGAACACCA	10	102	1
ATATATATCTTTCACCGGCATATCACATTCT	10	146	0
AGCTACTCTTTTAACTTGGATTACATTTAAT	10	192	0
          ***** *****
MAP Score: 3.44034