AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions008_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251228
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0012	161	NADP-reducing hydrogenase, subunit A
#1	TM0198	215	ATP-dependent Clp protease, ATPase subunit
#2	TM0228	300	NADP-reducing hydrogenase, subunit C
#3	TM1420	255	hypothetical protein

Motif 1
        ATTGTCACCTCCAGATTTCAAACG	0	2	1
        TTTTTTCCCTCCTTTCGAGAAAAG	1	2	1
ATCATGGATATTTCACCGGTTGTAGATCCGTA	1	64	1
TGAATCTAATTGTTACCTTTTGCTTTACTTCT	1	113	1
AATTTCATTATATCACCCTTATGGACATAACA	1	172	0
        AGTATCACCTCCGGGTCTTCCAAT	1	201	0
CACAAACCCTTATCACGTATTTTCCTTCGGTT	2	46	0
       ATGTTTCACCTCCTTAGCTTTTGTT	3	3	1
GTTTCTATTATATCACGTTTTTACAGTCATAT	3	82	1
CAGTCATATATTTCAAGTGCTTTACCAATAGT	3	105	1
TGCTCTATGTTGTTACCTACTTCACAAGTTTT	3	165	0
          * ****** ***
MAP Score: 10.4746

Motif 2
AAAGAAAAGAAACAGTCACAAAGTGTTGCATGT	0	69	0
TTCATCATATGACAGTGAGAGGTGTTATAATCG	0	101	1
CGACTATGGTGAATGTGAAAAAAATATCAGATA	0	132	1
GGTTCGATTAAATTGTATCATGGATATTTCACC	1	48	1
TTATGTCCATAAGGGTGATATAATGAAATTGGA	1	174	1
CCGAAGGAAAATACGTGATAAGGGTTTGTGAGA	2	48	1
TCGTCATTTCGAGTGTGAAAAGACCATCAGAAG	2	162	0
CGACGAGTATTACGGTAACATGACGCCCGATCG	2	238	1
CATGACGCCCGATCGTGTGAAGGATCTCATAGA	2	256	1
GATATGGAAGGAAAGTAACATGGTAAGAGTGTA	3	38	1
GTAACATGGTAAGAGTGTAATGTAAGAGCCGTT	3	52	1
ATGACTGTAAAAACGTGATATAATAGAAACGGC	3	79	0
TCTCCTGAAAAATAGTGAAAAATATAACGTGAA	3	208	1
GTGAAAAATATAACGTGAAAAGGTTCACGATTT	3	222	1
          **  **** ****
MAP Score: 8.97251

Motif 3
TAATCCCCATTTGATTCTATCACTACATGCAAC	0	45	1
TTCTTTTCTTTTCATCATATGACAGTGAGAGGT	0	91	1
TTCACCATAGTCGATTATAACACCTCTCACTGT	0	112	0
TCGGTTCGATTAAATTGTATCATGGATATTTCA	1	46	1
GTCTTCCAATTTCATTATATCACCCTTATGGAC	1	178	0
AAGAGCCGTTTCTATTATATCACGTTTTTACAG	3	75	1
GTAAAGCACTTGAAATATATGACTGTAAAAACG	3	97	0
          *  *** ******
MAP Score: 8.20511

Motif 4
GTGTCGTTTAAATTCGGTTCGATTAAATTGT	1	33	1
CGAAAAATCGAATTCGGTGAATCTAATTGTT	1	96	1
CTTTTGCTTTACTTCTGAGAGAACTTTGAAC	1	129	1
AACTTTGAACATTTCTGAAAGATGTTATGTC	1	150	1
CCCTCAAAGAAATTCTGAAAATCGACTTCGG	2	123	1
CTGAAAATCGACTTCGGACAGACCACTTCTG	2	137	1
CGGACAGACCACTTCTGATGGTCTTTTCACA	2	151	1
          ******** **
MAP Score: 4.81196

Motif 5
GTGTCGTTTAAATTCGGTTCGATTAAATTGTA	1	33	1
CGAAAAATCGAATTCGGTGAATCTAATTGTTA	1	96	1
CTTTTGCTTTACTTCTGAGAGAACTTTGAACA	1	129	1
AACTTTGAACATTTCTGAAAGATGTTATGTCC	1	150	1
CCCTCAAAGAAATTCTGAAAATCGACTTCGGA	2	123	1
CTGAAAATCGACTTCGGACAGACCACTTCTGA	2	137	1
CGGACAGACCACTTCTGATGGTCTTTTCACAC	2	151	1
          * ****** ***
MAP Score: 4.77279

Motif 6
TGCAACACTTTGTGACTGTTTCTTTTCTTTTCATCATATGACAG	0	72	1
TCGAATTCGGTGAATCTAATTGTTACCTTTTGCTTTACTTCTGA	1	103	1
CACGGCAGACTCTCACAAACCCTTATCACGTATTTTCCTTCGGT	2	47	0
         ATGTTTCACCTCCTTAGCTTTTGTTTTTGATATGG	3	1	1
TACAGTCATATATTTCAAGTGCTTTACCAATAGTTTTCTTTTTA	3	103	1
TTCTTTTTAGTGAATCAGTTTGTTTACAAAACTTGTGAAGTAGG	3	138	1
GGTAACAACATAGAGCATTCCCTTGACTTCTCCTGAAAAATAGT	3	180	1
          *    **  * ***  *   *  *
MAP Score: 4.75586

Motif 7
TCACTGTCATATGATGAAAAGAAAAGAAACAGTC	0	85	0
ATAATCGACTATGGTGAATGTGAAAAAAATATCA	0	127	1
TAAGGGTGATATAATGAAATTGGAAGACCCGGAG	1	183	1
TGTCGAAAACATGGTGTAGAACGTCAACACCTCG	2	11	0
CTGCCGTGTCATGTTGAAAACGGAAGAGAAGTGG	2	83	1
CCTCAAAGAAATTCTGAAAATCGACTTCGGACAG	2	124	1
ACCGGTGATCATGGTGAACGACGAGTATTACGGT	2	220	1
CTCCTGAAAAATAGTGAAAAATATAACGTGAAAA	3	209	1
          *** **** *  **
MAP Score: 3.97001

Motif 8
TATAATGAAATTGGAAGACCCGGAGGTGATAC	1	192	1
GACAAAACCGAAGGAAAATACGTGATAAGGGT	2	41	1
CATGTTGAAAACGGAAGAGAAGTGGTCAAAGC	2	92	1
TGTTTTTGATATGGAAGGAAAGTAACATGGTA	3	31	1
TAAGAGTGTAATGTAAGAGCCGTTTCTATTAT	3	61	1
GGTTCACGATTTGAAAGGAACG          	3	243	1
          * ****** ***
MAP Score: 0.550455