AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions017_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251423
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0398	300	conserved hypothetical protein
#1	TM0429	28	methyl-accepting chemotaxis protein
#2	TM0431	80	sugar ABC transporter, permease protein
#3	TM0432	246	sugar ABC transporter, periplasmic sugar-binding protein, putative
#4	TM0863	82	ribosomal protein L9
#5	TM0868	29	glutaredoxin-related protein

Motif 1
AAAGGCCGTTGGGAGGTCGTCTAACGGTAG	0	10	1
GTCGTCTAACGGTAGGACGGCGGACTCTGG	0	25	1
CTTTCTGGCTGGGAGGGGAGGACTCGAACC	0	68	0
CACCTCCTGAAGGAGAAAAGCATGAATATA	0	274	0
TTTCTCCTTCAGGAGGTGAATGCC      	0	286	1
ACTATGGAAGAGGAGGAGAAAGC       	1	15	1
ATTGCCTTCGGGGAGGGTATCCTCCCTCCC	2	19	1
AATAAATATGGGGAGGGAGGATACCCTCCC	2	29	0
AAACAAAACAGGGAGGAGAGTGG       	2	67	1
CAGATATCTCAGTAGGGAGGG         	3	1	0
ATCTTATGTTAGGAGGGGAGAGTT      	3	232	1
TCTTGAAAAGAGGAGGTGTGAAGT      	4	4	0
AAAAATTTTCAGGAGGTGATTTGTT     	4	67	1
AGAATTATATCGGAGGTGAAAAA       	5	16	1
          **********
MAP Score: 27.4261

Motif 2
TGGAGGTTCGAGTCCTCCCCTCCCAGCCAGA	0	64	1
AGGGGATGCATTGCATCCCCTTTCTGGCTGG	0	86	0
       GGCATTCACCTCCTGAAGGAGAAA	0	286	0
      GCTTTCTCCTCCTCTTCCATAGTTA	1	13	0
GGAGGGAGGATACCCTCCCCGAAGGCAATCA	2	17	0
GAGGGTATCCTCCCTCCCCATATTTATTTGC	2	31	1
      CCACTCTCCTCCCTGTTTTGTTTTC	2	65	0
ATCACCGAATTTTCATCCGTGTCAAGTTTGA	3	165	0
       AACTCTCCCCTCCTAACATAAGAT	3	232	0
       ACTTCACACCTCCTCTTTTCAAGA	4	3	1
      AACAAATCACCTCCTGAAAATTTTT	4	67	0
        TTTTTCACCTCCGATATAATTCT	5	16	0
          * *********
MAP Score: 12.3531

Motif 3
AGGGGAGGACTCGAACCTCCACCAGCGGATCCAGAGTCC	0	46	0
GAGGTTCGAGTCCTCCCCTCCCAGCCAGAAAGGGGATGC	0	66	1
        GCTTTCTCCTCCTCTTCCATAGTTAGAG   	1	7	0
GGGGAGGGTATCCTCCCTCCCCATATTTATTTGCCACGA	2	28	1
       ACTTCACACCTCCTCTTTTCAAGATTATATCA	4	3	1
          **   ***** * *    *
MAP Score: 1.43356

Motif 4
CGTTAGACGACCTCCCAACGGCCTTT     	0	5	0
CAGAGTCCGCCGTCCTACCGTTAGACGACCT	0	23	0
GAGGACTCGAACCTCCACCAGCGGATCCAGA	0	50	0
TGGAGGTTCGAGTCCTCCCCTCCCAGCCAGA	0	64	1
ATGCATTGCATCCCCTTTCTGGCTGGGAGGG	0	81	0
TTAATTTTTATGCCATAACTGGAATAATTAC	0	139	1
TACACGGATGTTTCATAACAGACTTTTACTT	0	167	1
 GCTTTCTCCTCCTCTTCCATAGTTAGAG  	1	8	0
GGAGGGAGGATACCCTCCCCGAAGGCAATCA	2	17	0
GGGAGGGTATCCTCCCTCCCCATATTTATTT	2	29	1
      CCACTCTCCTCCCTGTTTTGTTTTC	2	65	0
         CCCTCCCTACTGAGATATCTGA	3	1	1
  AACTCTCCCCTCCTAACATAAGATTTTCG	3	227	0
          ********* *
MAP Score: 0.444928