AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions004_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251046
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0399	300	response regulator
#1	TM0470	82	conserved hypothetical protein
#2	TM0475	73	pyrazinamidase/nicotinamidase-related protein
#3	TM0476	34	hypothetical protein
#4	TM0477	82	outer membrane protein alpha
#5	TM0478	30	tyrosyl-tRNA synthetase
#6	TM0481	300	conserved hypothetical protein
#7	TM0703	42	competence-damage inducible protein, putative
#8	TM0852	268	conserved hypothetical protein
#9	TM1171	89	transcriptional regulator, crp family
#10	TM1183	73	oxidoreductase, aldo/keto reductase family
#11	TM1358	50	conserved hypothetical protein
#12	TM1655	36	response regulator DrrA
#13	TM1656	62	hypothetical protein
#14	TM1658	73	S-adenosylmethionine synthetase
#15	TM1666	104	succinyl-diaminopimelate desuccinylase, putative
#16	TM1674	62	conserved hypothetical protein
#17	TM1676	21	hypothetical protein
#18	TM1677	36	transposase, putative

Motif 1
CCCCTTTCTGGCTGGGAGGGGAGGACTCGAA	0	119	1
CCCGGCAAGTGCCGGGGGTTGATTTGCGGTG	2	17	0
ATGATAACACACAGGGGGATGTT        	7	2	0
CCAAGATAGAGCAGGCGGGTGTAGCTCAGTG	6	158	1
AGCTTGCCAAGCTGGGGGTCGCGGGTTCGAA	6	199	1
ATTGATAACTGCAAGGAGGTGAAAAT     	10	57	1
TACAATTAGCACAGGGAGTGGGAAA      	18	21	1
CTCAAAATCAGCTGGGGGATAACCCCGTGCG	8	169	1
TATACTTGAATCTGGGAGGTGTTTTCA    	15	87	1
    AAAAACTCGGGGGGATGATTT      	17	6	1
CTCCCAGCCAGAAAGGGGATGCAATGCATCC	0	106	0
AATTTATTCTGAGGGGAGGTAAGATGTT   	3	16	1
GGGATAGTTCAAGGGGTGGTGTTTCACGTTT	0	230	1
GTCGATAATCATAGGGGGAGGATGAAGA   	16	7	0
TGGATAAAGAAAAAGGGGATGCATTGCATCC	0	90	1
CTCTGGATCCGCTGGTGGAGGTTCGAGTCCT	0	140	0
TTCTGATTTTAAAGGGAGGGA          	13	51	1
CCCGGCACTTGCCGGGGGTTTTGTTTTGTTG	2	32	1
AAGAATTCAAGAAGGAAGAGGGATTCTCGGA	8	63	1
TGACTTTTAATCAGGGGGTCGTGGGTTCGAA	6	21	1
GAAATGCCCCGCAAGGGGGCCAGCTTTCAAA	13	23	0
TGATCAATGAGAAGGGAGGTTTGTCCC    	4	65	1
AAGATCAGCGAAAGGAGGATGGGAG      	14	58	1
GAGTGGCGGAACTGGCAGACGCGCTGGACTT	6	78	1
TTTCGTTCTAACGAGGTGATGGG        	5	17	1
CTATCTTGGTGCGAGAGGTGGGACTTGAACC	6	136	0
GCACTCAAAAGAAGGGAGTGCTAAATC    	8	6	0
AAAATCATAAACGTGGAGGTGGAAGA     	16	46	1
TTGAAAGGCCGTTGGGAGGTCGTCTAACGGT	0	182	0
AACAATTGTTACGGGGTGAGAGA        	9	76	1
TAGAAAAAATTTAGGGAGGTGTTTAC     	15	5	0
CCCCAGCTTGGCAAGCTGGTGCTCTACCACT	6	185	0
GAGGTGGCGGAATGGCAGACGCGGCTGACTC	8	141	1
AAAGCCCAGAAAAAGGAGGGAAAAGT     	9	5	0
CTCCAGACAAAAAAGAAGGGGAAATTTCCCC	6	242	1
AATCTAACGTGTGGGAGGGGATCGGT     	10	5	0
TTTCCTTTGGACGGGATGGTATAATCACCAC	4	22	1
TACTATATATAATGGAGGGCCGAGGTGGCGG	8	120	1
TTTGTATCACATCAGGAGGGAAAAACCT   	8	250	1
          ** ********
MAP Score: 42.4178

Motif 2
AGGTTCGAGTCCTCCCCTCCCAGCCAGAAAG	0	122	0
      AAATCATCCCCCCGAGTTTTT    	17	6	0
        AACATCCCCCTGTGTGTTATCAT	7	2	1
      TCTTCATCCTCCCCCTATGATTATC	16	4	1
CACCGCAAATCAACCCCCGGCACTTGCCGGG	2	17	1
        CCCATCACCTCGTTAGAACGAAA	5	17	0
TTCGAACCCGCGACCCCCAGCTTGGCAAGCT	6	199	0
GAAGGGGAAATTTCCCCTTCTTTTTTGTCTG	6	245	0
GAAGGGGAAATTTCCCCTTCTTCTTTTTCTT	6	256	1
         ACGATCCCTCCTCAGTGATATG	7	30	0
        ACCGATCCCCTCCCACACGTTAG	10	2	1
CGCACGGGGTTATCCCCCAGCTGATTTTGAG	8	169	0
GGATGCATTGCATCCCCTTTCTGGCTGGGAG	0	106	1
       AATTTATCCCTCCCACTTTTAGTT	11	3	1
TTCGAACCCACGACCCCCTGATTAAAAGTCA	6	21	0
        ATTTTCACCTCCTTGCAGTTATC	10	60	0
ACGTGAAACACCACCCCTTGAACTATCCCTG	0	228	0
        TCTCTCACCCCGTAACAATTGTT	9	76	0
      AGGTTTTTCCCTCCTGATGTGATAC	8	253	0
        ACTTTTCCCTCCTTTTTCTGGGC	9	2	1
GGTTCAAGTCCCACCTCTCGCACCAAGATAG	6	136	1
         TCTTCCACCTCCACGTTTATGA	16	50	0
GTGATTATACCATCCCGTCCAAAGGAAATTC	4	19	0
TACCACTGAGCTACACCCGCCTGCTCTATCT	6	161	0
       TGAAAACACCTCCCAGATTCAAGT	15	90	0
        GTAAACACCTCCCTAAATTTTTT	15	2	1
GGATGCAATGCATCCCCTTTTTCTTTATCCA	0	90	0
CGCGGGTTCGAATCCCGTCGCCCGCTCCAGA	6	218	1
      AACATCTTACCTCCCCTCAGAATAA	3	19	0
CAACAAAACAAAACCCCCGGCAAGTGCCGGG	2	32	0
TGCGGGTTCAAGTCCCGCCCTCGGCACCACA	8	196	1
AGGACTCGAACCTCCACCAGCGGATCCAGAG	0	140	1
          * *********
MAP Score: 37.9645

Motif 3
TGCATCCCCTTTCTGGCTGGGAGGGGAGGACTCGA	0	114	1
GGACTCTGGATCCGCTGGTGGAGGTTCGAGTCCTC	0	139	0
ATAATTTGAAAGGCCGTTGGGAGGTCGTCTAACGG	0	183	0
TGTTGTATAATTTAAAACTGGAGGC          	2	58	1
ACCAAAATTTATTCTGAGGGGAGGTAAGATGTT  	3	11	1
CTTGAATTTCCTTTGGACGGGATGGTATAATCACC	4	16	1
AACTGTGATCAATGAGAAGGGAGGTTTGTCCC   	4	60	1
CCTGCTCTATCTTGGTGCGAGAGGTGGGACTTGAA	6	138	0
TTCTTTTTCTTTATGTCGTGGAGGTAGAAGAGCC 	6	276	1
GATATGATAACACACAGGGGGATGTT         	7	1	0
TGTGTTATCATATCACTGAGGAGGGATCGT     	7	22	1
TATTAGCACTCAAAAGAAGGGAGTGCTAAATC   	8	7	0
AGCTGGTACTATATATAATGGAGGGCCGAGGTGGC	8	114	1
TTTATTTTGTATCACATCAGGAGGGAAAAACCT  	8	245	1
AGTGGAAAGCCCAGAAAAAGGAGGGAAAAGT    	9	6	0
TGATAAAATCTAACGTGTGGGAGGGGATCGGT   	10	7	0
CGTTAGATTTTATCATTGTGGAGTGATAAAATTGA	10	27	1
ATAAAATTGATAACTGCAAGGAGGTGAAAAT    	10	52	1
TAATGATAAACTAAAAGTGGGAGGGATAAATT   	11	7	0
TAGTTTATCATTAAATAGTGGAGGATAGATT    	11	29	1
GGCATTTCTGATTTTAAAGGGAGGGA         	13	46	1
TGTTATAAGATCAGCGAAAGGAGGATGGGAG    	14	52	1
ATTGATAGAAAAAATTTAGGGAGGTGTTTAC    	15	6	0
TAGGATATACTTGAATCTGGGAGGTGTTTTCA   	15	82	1
ACTGTCGATAATCATAGGGGGAGGATGAAGA    	16	6	0
CGTTTAAAATCATAAACGTGGAGGTGGAAGA    	16	41	1
       AAAAACTCGGGGGGATGATTT       	17	3	1
TGTGTTACAATTAGCACAGGGAGTGGGAAA     	18	16	1
          **   *  *******
MAP Score: 32.594

Motif 4
TTGGTCTGTGGATAAAGAAAAAGGGGATGCATTGCAT	0	82	1
ACGACATAAAGAAAAAGAAGAAGGGGAAATTTCCCCT	6	258	0
GCCCGCTCCAGACAAAAAAGAAGGGGAAATTTCCCCT	6	237	1
CAGAGCACCTGACTTTTAATCAGGGGGTCGTGGGTTC	6	12	1
TCAGTGATATGATAACACACAGGGGGATGTT      	7	4	0
TAGAGCACCAGCTTGCCAAGCTGGGGGTCGCGGGTTC	6	190	1
CTCCTGATGTGATACAAAATAAAGGGGCTCTTCGGAG	8	231	0
CAAGAACAGGGATAGTTCAAGGGGTGGTGTTTCACGT	0	222	1
ACTATTATTAGCACTCAAAAGAAGGGAGTGCTAAATC	8	10	0
GGGCATTTCTGATTTTAAAGGGAGGGA          	13	45	1
CGCGGCTGACTCAAAATCAGCTGGGGGATAACCCCGT	8	160	1
AATTGATTGATAGAAAAAATTTAGGGAGGTGTTTAC 	15	9	0
CTCGCACCAAGATAGAGCAGGCGGGTGTAGCTCAGTG	6	152	1
ATAAAATTGATAACTGCAAGGAGGTGAAAAT      	10	52	1
GGGAGGACTCGAACCTCCACCAGCGGATCCAGAGTCC	0	137	1
    AAATCTGAGTAAAAAAGAGTGGATCAACATAAT	1	6	1
AGTCCTCCCCTCCCAGCCAGAAAGGGGATGCAATGCA	0	109	0
ATAGTGGAAAGCCCAGAAAAAGGAGGGAAAAGT    	9	6	0
AGACGCGCTGGACTTAGAATCCAGTGGGCTGAAGCCC	6	94	1
ACTTTTAGTTTATCATTAAATAGTGGAGGATAGATT 	11	24	1
 TAACAGCTTTCGTTCTAACGAGGTGATGGG      	5	9	1
ATCAATCAATTATATAAAATCTTGGGGTATCATTTCA	15	35	1
GGCGGGACTTGAACCCGCACGGGGTTATCCCCCAGCT	8	178	0
CTTGACTTTAGAAAGAGAAAGCTGGTACTATATATAA	8	95	1
          ** *   **   *****
MAP Score: 27.7242

Motif 5
CCCCTTTCTGGCTGGGAGGGGAGGACTCGAACCTCCACC	0	119	1
TCGTCTAACGGTAGGACGGCGGACTCTGGATCCGCTGGT	0	155	0
TTGAAAGGCCGTTGGGAGGTCGTCTAACGGTAGGACGGC	0	174	0
CCCGGCAAGTGCCGGGGGTTGATTTGCGGTGGTGTGGA 	2	9	0
TGGTGACCCGGGTGGGATTCGAACCCACGACCCCCTGAT	6	30	0
GTGCGAGAGTGGCGGAACTGGCAGACGCGCTGGACTTAG	6	72	1
TGGTGCGAGAGGTGGGACTTGAACCCACACGGGCTTCAG	6	122	0
AGATAGAGCAGGCGGGTGTAGCTCAGTGGTAGAGCACCA	6	161	1
AGCTTGCCAAGCTGGGGGTCGCGGGTTCGAATCCCGTCG	6	199	1
CTTCTTTTTTGTCTGGAGCGGGCGACGGGATTCGAACCC	6	221	0
AAGAATTCAAGAAGGAAGAGGGATTCTCGGAACTTGACT	8	63	1
TATATATAATGGAGGGCCGAGGTGGCGGAATGGCAGACG	8	123	1
GTGGCGGAATGGCAGACGCGGCTGACTCAAAATCAGCTG	8	144	1
CTCAAAATCAGCTGGGGGATAACCCCGTGCGGGTTCAAG	8	169	1
TTCGGAGCCCCTGTGGTGCCGAGGGCGGGACTTGAACCC	8	199	0
          *  *** *  *  * * **
MAP Score: 21.5736

Motif 6
GGATGGTATAATCACCACAGGATTTAACTG	4	35	1
AAGCTGGTGCTCTACCACTGAGCTACACCC	6	174	0
        GATTTAGCACTCCCTTCTTTTG	8	2	1
CTAAACTATTATTAGCACTCAAAAGAAGGG	8	21	0
CTAATAATAGTTTAGCACACATTTTAAAAG	8	36	1
       AGGTTTTTCCCTCCTGATGTGAT	8	255	0
CACGTTAGATTTTATCATTGTGGAGTGATA	10	25	1
AGTTATCAATTTTATCACTCCACAATGATA	10	37	0
        AATTTATCCCTCCCACTTTTAG	11	2	1
GCCTTGATAGTTTATCACAATCTTTCTTAA	14	22	0
CTGTGTTACAATTAGCACAGGGAGTGGGAA	18	15	1
          TTTCCCACTCCCTGTGCTAA	18	26	0
          **********
MAP Score: 3.21176