AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions019_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251456
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0186	300	response regulator
#1	TM0402	300	ammonium transporter
#2	TM0404	47	deoxycytidylate deaminase, putative
#3	TM1358	50	conserved hypothetical protein
#4	TM1580	118	transcriptional regulator, putative

Motif 1
GGTGAAGTACACACCTTCTGGAAGAGTGGTTCTC	0	89	1
GTAATAACCCTTCCCCTCAGGAGGGATAAAA   	0	279	1
CGGGTTGTATAATCGTCAGGGAGG          	1	0	0
CCTGACGATTATACAACCCGGAGTGTTAACAATC	1	14	1
TTTTCGGGAATAAATTTCTGGAGGATTTTATATG	1	111	0
TAAATATCTAATCCAACATGGGGTTTGTGCCCTC	1	152	1
AACAAAAAACAAACACCATGGGGTTCTTTTTTTT	1	187	0
ACAAACATATTTACCAAAAGGAGGTGTTTTT   	1	279	1
       GGTTTCCTTTCGGGAGGAGAAACCTCC	2	3	1
GGAGGCCGAAAAAAGGGGAGGAGGTTTCTCCTCC	2	22	0
ATTTAATGATAAACTAAAAGTGGGAGGGATAAAT	3	11	0
TAGTTTATCATTAAATAGTGGAGGATAGATT   	3	29	1
AAATCTTACCACACGAAAGGGAGGAAAGAGGAAC	4	13	0
AACGGGGCTGATACCGTGTTGAGGGTCCTCATCA	4	65	1
          ****   * *****
MAP Score: 13.3005

Motif 2
ATGGAAGTCATAAAAAAGGACGGGACCACATTCGT	0	246	1
AATGATAAACTAAAAGTGGGAGGGATAAATT    	3	6	0
TTTGAAGGAACAAAACGGATTTGGACTCTTCACAG	0	179	1
  GGGAGGCCGAAAAAAGGGGAGGAGGTTTCTCCT	2	24	0
ACGAAAGGGAGGAAAGAGGAACGGA          	4	0	0
      ACATCGAAATGGAATTCGACGAACTCGAA	0	4	1
GAGTGGTTCTCAAAATAGAAAAGAAAAATGATAAA	0	112	1
TAGTTTATCATTAAATAGTGGAGGATAGATT    	3	29	1
CTCCGGGTTGTATAATCGTCAGGGAGG        	1	2	0
TCGACGAACTCGAAATCGACAAAGATGCTTTCCTC	0	25	1
GAATTAATCTTAAAAGAGTCAACAAACATATTTAC	1	258	1
CACCGCGTTTGAAAACAGGTTCAAAACCAGTGCGA	0	58	0
          *****  **   ***
MAP Score: 10.7293

Motif 3
TCTCAAAATAGAAAAGAAAAATGATAAAATC	0	119	1
GACCGGGTTTGAAGGAACAAAACGGATTTGG	0	172	1
TGGTTCGATGGAAGTCATAAAAAAGGACGGG	0	239	1
CTTCCCCTCAGGAGGGATAAAA         	0	288	1
CTTTTTTTTAGAGGGCACAAACCCCATGTTG	1	165	0
GTTTCCTTTCGGGAGGAGAAACCTCCTCCCC	2	11	1
         GGGAGGCCGAAAAAAGGGGAGG	2	35	0
ACTAAAAGTGGGAGGGATAAATT        	3	2	0
CCACACGAAAGGGAGGAAAGAGGAACGGA  	4	8	0
          ******* ***
MAP Score: 10.4953

Motif 4
ATAACCCTTCCCCTCAGGAGGGATAAAA    	0	282	1
TTGAGGGTCCTCATCAGAAAGGATATTGTCAA	4	83	1
GGAGGTTTCTCCTCCCGAAAGGAAACC     	2	5	0
TGAGAACCACTCTTCCAGAAGGTGTGTACTTC	0	92	0
GGTTGTATAATCGTCAGGGAGG          	1	0	0
TCAAATCTTACCACACGAAAGGGAGGAAAGAG	4	17	0
CTGATGAGGACCCTCAACACGGTATCAGCCCC	4	68	0
TCGATGGAAGTCATAAAAAAGGACGGGACCAC	0	243	1
    GGGAGGCCGAAAAAAGGGGAGGAGGTTT	2	29	0
AAATATCTAATCCAACATGGGGTTTGTGCCCT	1	153	1
AACAAACATATTTACCAAAAGGAGGTGTTTTT	1	278	1
          ** **** ****
MAP Score: 10.2268

Motif 5
AAAGATGCTTTCCTCGCACTGGTTTTGAAC	0	45	1
TCCTTCAAACCCGGTCCTGTGTCAGAAACA	0	158	0
TTCACCAGTTTCTTCACTGTGAAGAGTCCA	0	200	0
CGAATGTGGTCCCGTCCTTTTTTATGACTT	0	250	0
TTCGTAATAACCCTTCCCCTCAGGAGGGAT	0	276	1
GTGTTAACAATCTTCCCAGTCAAACTGAAA	1	36	1
AGGAGAAACCTCCTCCCCTTTTTTCGGCCT	2	24	1
   AATTTATCCCTCCCACTTTTAGTTTAT	3	7	1
         TCCGTTCCTCTTTCCTCCCTT	4	1	1
CGTTCCTCTTTCCTCCCTTTCGTGTGGTAA	4	12	1
CAACACGGTATCAGCCCCGTTGTCCGTTGC	4	56	0
          **********
MAP Score: 9.30353

Motif 6
TATTTTGAGAACCACTCTTCCAGAAGGTGTG	0	98	0
CCGTCCTTTTTTATGACTTCCATCGAACCAT	0	238	0
CACATTCGTAATAACCCTTCCCCTCAGGAGG	0	272	1
        TTTTATCCCTCCTGAGGGGAAGG	0	287	0
CGGAGTGTTAACAATCTTCCCAGTCAAACTG	1	32	1
GGGGAGGAGGTTTCTCCTCCCGAAAGGAAAC	2	11	0
CTCCCCTTTTTTCGGCCTCCC          	2	36	1
       AATTTATCCCTCCCACTTTTAGTT	3	3	1
      TCCGTTCCTCTTTCCTCCCTTTCGT	4	4	1
GGTGTTGACAATATCCTTTCTGATGAGGACC	4	88	0
          *** *******
MAP Score: 3.94537

Motif 7
AAGATGCTTTCCTCGCACTGGTTTTGAACCTGTT	0	46	1
GAAGGTGTGTACTTCACCGCGTTTGAAAACAGGT	0	73	0
TGTTTCTGACACAGGACCGGGTTTGAAGGAACAA	0	158	1
ATAACCCTTCCCCTCAGGAGGGATAAAA      	0	282	1
          CCTCCCTGACGATTATACAACCCG	1	0	1
TGACGATTATACAACCCGGAGTGTTAACAATCTT	1	16	1
AATATCTAATCCAACATGGGGTTTGTGCCCTCTA	1	154	1
CAAAAAACAAACACCATGGGGTTCTTTTTTTTAG	1	185	0
AACATATTTACCAAAAGGAGGTGTTTTT      	1	282	1
GGCCGAAAAAAGGGGAGGAGGTTTCTCCTCCCGA	2	19	0
ATTTATCCCTCCCACTTTTAGTTTATCATTAAAT	3	11	1
GTTCCTCTTTCCTCCCTTTCGTGTGGTAAGATTT	4	13	1
CCCCGTTGTCCGTTGCTTCCGTTTCAAATCTTAC	4	38	0
          **  ** * *****
MAP Score: 1.21191