AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions008_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251212
 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
        ATTGTCACCTCCAGATTTCAAA	0	2	1
TAGTCGATTATAACACCTCTCACTGTCATA	0	108	0
CTGATATTTTTTTCACATTCACCATAGTCG	0	132	0
TGAATCTAATTGTTACCTTTTGCTTTACTT	1	113	1
AATTTCATTATATCACCCTTATGGACATAA	1	174	0
        AGTATCACCTCCGGGTCTTCCA	1	203	0
CACAAACCCTTATCACGTATTTTCCTTCGG	2	48	0
CTGATGGTCTTTTCACACTCGAAATGACGA	2	165	1
       ATGTTTCACCTCCTTAGCTTTTG	3	3	1
GTTTCTATTATATCACGTTTTTACAGTCAT	3	82	1
TGCTCTATGTTGTTACCTACTTCACAAGTT	3	167	0
TCGTGAACCTTTTCACGTTATATTTTTCAC	3	222	0
          **********
MAP Score: 10.3737

Motif 2
CTGAAAAATAGTGAAAAATATAACGTGAAAAGG	3	212	1
AAAATATAACGTGAAAAGGTTCACGATTTGAAA	3	226	1
TATGGTGAATGTGAAAAAAATATCAGATAAAAA	0	136	1
GCCCGATCGTGTGAAGGATCTCATAGATAGACT	2	262	1
TCATATGACAGTGAGAGGTGTTATAATCGACTA	0	105	1
TTGAACATTTCTGAAAGATGTTATGTCCATAAG	1	154	1
CATTTCGAGTGTGAAAAGACCATCAGAAGTGGT	2	158	0
TCTACAACCGGTGAAATATCCATGATACAATTT	1	57	0
GTTGCATGTAGTGATAGAATCAAATGGGGATTA	0	45	0
TACAAAACTTGTGAAGTAGGTAACAACATAGAG	3	162	1
AGGAAAATACGTGATAAGGGTTTGTGAGAGTCT	2	52	1
TGCTTTACTTCTGAGAGAACTTTGAACATTTCT	1	133	1
GGTAAAGCACTTGAAATATATGACTGTAAAAAC	3	98	0
CGAAAACATGGTGTAGAACGTCAACACCTCGT 	2	9	0
          ********  * *
MAP Score: 8.46845

Motif 3
        ATTGTCACCTCCAGATTTCAAA	0	2	1
TAGTCGATTATAACACCTCTCACTGTCATA	0	108	0
        TTTTTTCCCTCCTTTCGAGAAA	1	2	1
TTACCTTTTGCTTTACTTCTGAGAGAACTT	1	125	1
        AGTATCACCTCCGGGTCTTCCA	1	203	0
TGTAGAACGTCAACACCTCGT         	2	1	0
TTATCACGTATTTTCCTTCGGTTTTGTCGA	2	39	0
GCTTTGACCACTTCTCTTCCGTTTTCAACA	2	94	0
       ATGTTTCACCTCCTTAGCTTTTG	3	3	1
TACCATGTTACTTTCCTTCCATATCAAAAA	3	33	0
AGAGCATTCCCTTGACTTCTCCTGAAAAAT	3	191	1
          **********
MAP Score: 6.68296

Motif 4
CACTTTGTGACTGTTTCTTTTCTTTTCATCATATGA	0	77	1
TAATTGTTACCTTTTGCTTTACTTCTGAGAGAACTT	1	119	1
CTTATCACGTATTTTCCTTCGGTTTTGTCGAAAACA	2	34	0
GGCTTTGACCACTTCTCTTCCGTTTTCAACATGACA	2	89	0
    ATGTTTCACCTCCTTAGCTTTTGTTTTTGATA	3	6	1
CACTCTTACCATGTTACTTTCCTTCCATATCAAAAA	3	33	0
AAGTGCTTTACCAATAGTTTTCTTTTTAGTGAATCA	3	119	1
CAACATAGAGCATTCCCTTGACTTCTCCTGAAAAAT	3	185	1
          *   * ***  *****
MAP Score: 5.14672

Motif 5
CACTTTGTGACTGTTTCTTTTCTTTTCATCATATGA	0	77	1
TTCGGTGAATCTAATTGTTACCTTTTGCTTTACTTC	1	108	1
GGGCTTTGACCACTTCTCTTCCGTTTTCAACATGAC	2	90	0
GGACAGACCACTTCTGATGGTCTTTTCACACTCGAA	2	152	1
    ATGTTTCACCTCCTTAGCTTTTGTTTTTGATA	3	6	1
AGAGCCGTTTCTATTATATCACGTTTTTACAGTCAT	3	76	1
AAGTGCTTTACCAATAGTTTTCTTTTTAGTGAATCA	3	119	1
 CGTTCCTTTCAAATCGTGAACCTTTTCACGTTATA	3	230	0
          **  *  **  *****
MAP Score: 4.22886

Motif 6
ATCATATGACAGTGAGAGGTGTTATAATCG	0	104	1
TCCCTCCTTTCGAGAAAAGTGTCGTTTAAA	1	15	1
AAGGAAAATACGTGATAAGGGTTTGTGAGA	2	51	1
GAGAGTCTGCCGTGTCATGTTGAAAACGGA	2	77	1
GACGCCCGATCGTGTGAAGGATCTCATAGA	2	259	1
ACATGGTAAGAGTGTAATGTAAGAGCCGTT	3	55	1
GTTTACAAAACTTGTGAAGTAGGTAACAAC	3	159	1
CCTGAAAAATAGTGAAAAATATAACGTGAA	3	211	1
AAAAATATAACGTGAAAAGGTTCACGATTT	3	225	1
          **********
MAP Score: 3.911

Motif 7
TTGTGACTGTTTCTTTTCTTTTCATCATATGA	0	81	1
       TTTTTTCCCTCCTTTCGAGAAAAGT	1	3	1
TATCACGTATTTTCCTTCGGTTTTGTCGAAAA	2	36	0
CTTTGACCACTTCTCTTCCGTTTTCAACATGA	2	91	0
ACCATGTTACTTTCCTTCCATATCAAAAACAA	3	30	0
ACATAGAGCATTCCCTTGACTTCTCCTGAAAA	3	187	1
        CGTTCCTTTCAAATCGTGAACCTT	3	241	0
          ********  **
MAP Score: 2.65541

Motif 8
TAATCGACTATGGTGAATGTGAAAAAAATA	0	128	1
CCGGTGATCATGGTGAACGACGAGTATTAC	2	221	1
AGTCACAAAGTGTTGCATGTAGTGATAGAA	0	59	0
TCCTTTCAAATCGTGAACCTTTTCACGTTA	3	232	0
AAATCGAATTCGGTGAATCTAATTGTTACC	1	100	1
GAAAACATGGTGTAGAACGTCAACACCTCG	2	11	0
         ATGTTTCACCTCCTTAGCTTT	3	1	1
GTCTTTGTGGTGTTGCACCGGTGATCATGG	2	204	1
          **********
MAP Score: 1.77744