AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions006_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251149
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0477	82	outer membrane protein alpha
#1	TM0478	30	tyrosyl-tRNA synthetase
#2	TM0481	300	conserved hypothetical protein
#3	TM0570	113	cell division protein FtsY
#4	TM0644	27	hypothetical protein
#5	TM0645	59	NH(3)-dependent NAD(+) synthetase, putative
#6	TM0671	95	M-related protein
#7	TM0711	51	hypothetical protein
#8	TM1145	300	conserved hypothetical protein
#9	TM1182	73	chromosome segregation SMC protein, putative
#10	TM1203	60	maltose ABC transporter, permease protein
#11	TM1204	300	maltose ABC transporter, periplasmic maltose-binding protein
#12	TM1726	300	alanyl-tRNA synthetase-related protein

Motif 1
    GTAAATCCCCCTCCTCTATTCACATA	5	6	1
      ATTTTCACCTCCTTGCAGTTATCA	9	4	1
   ACCACCTTCACCTCCTTGCGGGTAGAT	11	283	0
      GTTTTTCCCTCCCTGGTGTGTTCT	4	13	0
      TGTTTTCCCTCCCTGAACGTATGG	10	46	0
    ATTTGTTCCCCTCTTTTGTTTTACCA	6	6	1
     ACCGATCCCCTCCCACACGTTAGAT	9	58	0
AGGGGAAATTTCCCCTTCTTTTTTGTCTGG	2	244	0
AGGGGAAATTTCCCCTTCTTCTTTTTCTTT	2	258	1
   GGTCCATCTACCTCCCTCGGTTTCATT	6	78	0
TTTCATATTCTCACCTCTCTGGCGACGTAG	8	30	0
     CTCTTACCCCTCCCTTCGAAAGGTT	3	5	1
      GTTTTCACCTCCCATGCTGGTAAG	8	286	0
          CTCCCTCTTCAACCTTAAAA	7	41	0
TGGTCTAAATTTCCCTCTTCGTTCTCTTCG	11	98	0
GAACCCGCGACCCCCAGCTTGGCAAGCTGG	2	197	0
CGGGGCTGGGTCCCCAGCCCCTTCCATACG	10	23	1
ACGTGGTGATCCCCCAGCTCAAAGAAACGA	12	189	1
 GGGACAAACCTCCCTTCTCATTGATCACA	0	63	0
     CCTTTCTACCTCCTGGTTTCCCGAC	3	98	0
TGAGCTACACCCGCCTGCTCTATCTTGGTG	2	156	0
      CCCATCACCTCGTTAGAACGAAAG	1	16	0
GGTTCAAGTCCCACCTCTCGCACCAAGATA	2	136	1
GAACCCACGACCCCCTGATTAAAAGTCAGG	2	19	0
   GGCTCTTCTACCTCCACGACATAAAGA	2	283	0
TTCTGGATACTTACCTGTTCGTTTTACCGG	12	20	1
AGCTGGGGGATCACCACGTTCTCCAGAGCA	12	178	0
TTACCATATTTTACCATCCTTTAGGAAAAG	6	30	1
TCTGCCAGTTCCGCCACTCTCGCACCGCTG	2	67	0
          **********
MAP Score: 39.8345

Motif 2
TGATCAATGAGAAGGGAGGTTTGTCCC      	0	65	1
TGACTTTTAATCAGGGGGTCGTGGGTTCGAATC	2	21	1
TGGTGACCCGGGTGGGATTCGAACCCACGACCC	2	36	0
ACCCGGGTCACCAGCGGTGCGAGAGTGGCGGAA	2	56	1
GACTTAGAATCCAGTGGGCTGAAGCCCGTGTGG	2	104	1
GCTCTATCTTGGTGCGAGAGGTGGGACTTGAAC	2	137	0
CCAAGATAGAGCAGGCGGGTGTAGCTCAGTGGT	2	158	1
AGCTTGCCAAGCTGGGGGTCGCGGGTTCGAATC	2	199	1
TTTTTTGTCTGGAGCGGGCGACGGGATTCGAAC	2	223	0
TTCTTTATGTCGTGGAGGTAGAAGAGCC     	2	282	1
GAAACCTTTCGAAGGGAGGGGTAAGAG      	3	4	0
AGTCGGGAAACCAGGAGGTAGAAAGG       	3	97	1
ACAGAACACACCAGGGAGGGAAAAAC       	4	11	1
TGTGAATAGAGGAGGGGGATTTAC         	5	1	0
AGAATGAAACCGAGGGAGGTAGATGGACC    	6	76	1
TACTACGTCGCCAGAGAGGTGAGAATATGAAAT	8	28	1
ATCTTACCAGCATGGGAGGTGAAAAC       	8	284	1
ATTGATAACTGCAAGGAGGTGAAAAT       	9	3	0
TAAAATCTAACGTGTGGGAGGGGATCGGT    	9	54	1
CTGAACGTATGGAAGGGGCTGGGGACCCAGCCC	10	25	0
TTCCATACGTTCAGGGAGGGAAAACA       	10	44	1
ATATCTACCCGCAAGGAGGTGAAGGTGGT    	11	281	1
TGAAAGAAAGGGTGCAGGTTGGAAGAAG     	12	282	1
          ********  * *
MAP Score: 22.1164

Motif 3
TGTGATCAATGAGAAGGGAGGTTTGTCCC 	0	63	1
CTTTCGTTCTAACGAGGTGATGGG      	1	16	1
GACTTTTAATCAGGGGGTCGTGGGTTCGAA	2	22	1
CACCAGCGGTGCGAGAGTGGCGGAACTGGC	2	64	1
ATCTTGGTGCGAGAGGTGGGACTTGAACCC	2	135	0
CACCAAGATAGAGCAGGCGGGTGTAGCTCA	2	156	1
GCTTGCCAAGCTGGGGGTCGCGGGTTCGAA	2	200	1
GGAGCGGGCGACGGGATTCGAACCCGCGAC	2	216	0
TCTTTTTTGTCTGGAGCGGGCGACGGGATT	2	228	0
AAAGAAAAAGAAGAAGGGGAAATTTCCCCT	2	258	0
TCTTTATGTCGTGGAGGTAGAAGAGCC   	2	283	1
AAACCTTTCGAAGGGAGGGGTAAGAG    	3	6	0
GTCGGGAAACCAGGAGGTAGAAAGG     	3	98	1
CAGAACACACCAGGGAGGGAAAAAC     	4	12	1
TATGTGAATAGAGGAGGGGGATTTAC    	5	6	0
TCCTTCTCCGGAGAATCTGGTGAAACTCGC	8	182	1
TGATAACTGCAAGGAGGTGAAAAT      	9	4	0
AATCTAACGTGTGGGAGGGGATCGGT    	9	57	1
TAAAACTTTTACGGGGCTGGGTCCCCAGCC	10	12	1
GAACGTATGGAAGGGGCTGGGGACCCAGCC	10	26	0
TCCATACGTTCAGGGAGGGAAAACA     	10	45	1
ATCTACCCGCAAGGAGGTGAAGGTGGT   	11	283	1
CAATGCTCTGGAGAACGTGGTGATCCCCCA	12	175	1
          **********
MAP Score: 8.36319

Motif 4
TTAATCAGGGGGTCGTGGGTTCGAATCCCACCCGGGTCA	2	27	1
AAGCCCGTGTGGGTTCAAGTCCCACCTCTCGCACCAAGA	2	125	1
CCAAGCTGGGGGTCGCGGGTTCGAATCCCGTCGCCCGCT	2	205	1
AAAAGAAGAAGGGGAAATTTCCCCTTCTTTTTTGTCTGG	2	244	0
TGGTTTCAGGGGAAAAGCGTTCCTTCTCCGGAGAATCTG	8	162	1
CAGTTCCAAGGGATCAACGTTCAATACCTTGGCGAGTTT	8	204	0
AAACTTTTACGGGGCTGGGTCCCCAGCCCCTTCCATACG	10	14	1
GGACTCTTTTGGTCTAAATTTCCCTCTTCGTTCTCTTCG	11	98	0
          **    * ****    ***
MAP Score: 4.53395

Motif 5
GGGGTCGTGGGTTCGAATCCCACCCGGGTCA	2	35	1
GCCCACTGGATTCTAAGTCCAGCGCGTCTGC	2	92	0
GCCCGTGTGGGTTCAAGTCCCACCTCTCGCA	2	127	1
GGGGTCGCGGGTTCGAATCCCGTCGCCCGCT	2	213	1
       CCTTTCTACCTCCTGGTTTCCCGA	3	99	0
        GTTTTTCCCTCCCTGGTGTGTTC	4	14	0
TATTCTACATGTTAAAATCCCAGAGGGTGAC	5	34	1
TTTACCATATTTTACCATCCTTTAGGAAAAG	6	29	1
AGGGATCAACGTTCAATACCTTGGCGAGTTT	8	204	0
        GTTTTCACCTCCCATGCTGGTAA	8	287	0
        ATTTTCACCTCCTTGCAGTTATC	9	2	1
     ACCACCTTCACCTCCTTGCGGGTAGA	11	284	0
          ****** ****
MAP Score: 4.26668

Motif 6
ATTTCCTTTGGACGGGATGGTATAATCACC	0	21	1
TCGTTCTAACGAGGTGATGGG         	1	19	1
TTTAATCAGGGGGTCGTGGGTTCGAATCCC	2	26	1
CCGCTGGTGACCCGGGTGGGATTCGAACCC	2	43	0
CGGGTCACCAGCGGTGCGAGAGTGGCGGAA	2	59	1
GGAACTGGCAGACGCGCTGGACTTAGAATC	2	85	1
TGGGCTGAAGCCCGTGTGGGTTCAAGTCCC	2	118	1
ATCTTGGTGCGAGAGGTGGGACTTGAACCC	2	135	0
ACCAAGATAGAGCAGGCGGGTGTAGCTCAG	2	157	1
GCACCAGCTTGCCAAGCTGGGGGTCGCGGG	2	194	1
GAAACCTTTCGAAGGGAGGGGTAAGAG   	3	7	0
GTTTTCACCTCCCATGCTGGTAAGATAAAA	8	280	0
GATAAAATCTAACGTGTGGGAGGGGATCGG	9	52	1
TAAAACTTTTACGGGGCTGGGTCCCCAGCC	10	12	1
TTCCATACGTTCAGGGAGGGAAAACA    	10	44	1
TTCGAAGAGAACGAAGAGGGAAATTTAGAC	11	96	1
          **********
MAP Score: 1.81521

Motif 7
TGTGGTGATTATACCATCCCGTCCAAAGGAAA	0	22	0
GTGGGTTCGAATCCCACCCGGGTCACCAGCGG	2	41	1
GTGGGACTTGAACCCACACGGGCTTCAGCCCA	2	118	0
TGGGTTCAAGTCCCACCTCTCGCACCAAGATA	2	134	1
CACTGAGCTACACCCGCCTGCTCTATCTTGGT	2	157	0
CGAATCCCGTCGCCCGCTCCAGACAAAAAAGA	2	226	1
       CTCTTACCCCTCCCTTCGAAAGGTT	3	3	1
      GTTTTTCCCTCCCTGGTGTGTTCTGT	4	11	0
     GTAAATCCCCCTCCTCTATTCACATAT	5	5	1
   GGTCCATCTACCTCCCTCGGTTTCATTCT	6	76	0
TTTCATATTCTCACCTCTCTGGCGACGTAGTA	8	28	0
AAGCGTACAGAACCCGCACTAGATCCTCTAAA	8	68	0
GGGAAAAGCGTTCCTTCTCCGGAGAATCTGGT	8	171	1
GGGGCTGGGGACCCAGCCCCGTAAAAGTTTTA	10	12	0
CGGGGCTGGGTCCCCAGCCCCTTCCATACGTT	10	23	1
      TGTTTTCCCTCCCTGAACGTATGGAA	10	44	0
AGCACACCAGATCTTTCTCCGGTAAAACGAAC	12	36	0
  CTTCTTCCAACCTGCACCCTTTCTTTCAAT	12	280	0
          * *** ******
MAP Score: 1.66629

Motif 8
TGGTGACCCGGGTGGGATTCGAACCCACGACCCCCTGATTAAAAG	2	24	0
CTGAAGCCCGTGTGGGTTCAAGTCCCACCTCTCGCACCAAGATAG	2	122	1
TGGAGCGGGCGACGGGATTCGAACCCGCGACCCCCAGCTTGGCAA	2	202	0
AGACAAAAAAGAAGGGGAAATTTCCCCTTCTTCTTTTTCTTTATG	2	246	1
TGAACGTATGGAAGGGGCTGGGGACCCAGCCCCGTAAAAGTTTTA	10	12	0
          *  ***       ***    * * *
MAP Score: 1.3793