AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions017_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251410
 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
AGGTTCGAGTCCTCCCCTCCCAGCCAGAAA	0	67	1
GGATGCATTGCATCCCCTTTCTGGCTGGGA	0	84	0
GGATGCAATGCATCCCCTTTTTCTTTATCC	0	99	1
   GCTTTCTCCTCCTCTTCCATAGTTAGA	1	11	0
GGAGGGAGGATACCCTCCCCGAAGGCAATC	2	18	0
GGGAGGGTATCCTCCCTCCCCATATTTATT	2	29	1
      CCACTCTCCTCCCTGTTTTGTTTT	2	66	0
       AACTCTCCCCTCCTAACATAAGA	3	233	0
    ACTTCACACCTCCTCTTTTCAAGATT	4	6	1
          **********
MAP Score: 12.7544

Motif 3
GTTTCATAACAGACTTTTACTTTTCTCAAACGAAA	0	176	1
TATAACATTTATACCATATGTGTTCTCTCAATCAA	0	229	0
ACAAGATTTTATATTCATGCTTTTCTCCTTCAGGA	0	265	1
        GCTTTCTCCTCCTCTTCCATAGTTAGA	1	11	0
GTCAGTGATGTTACCACATCTTTTCGATTCAAGTC	3	48	1
TTATATCCAATTATTGTGTGTGTTCTTATGAAACC	3	90	0
     ACTTCACACCTCCTCTTTTCAAGATTATAT	4	5	1
CCTGAAAATTTTTCCTTATCTATTCTATCATGCTT	4	45	0
          *****    ** ***
MAP Score: 3.87115

Motif 4
TACTTTTCTCAAACGAAACAATACTGATACAGTCCTT	0	193	1
ACCCTCCCCGAAGGCAATCATCATTGA          	2	0	0
TTTGCCACGAAAACAAAACAGGGAGGAGAGTGG    	2	57	1
TTGAAACATCAGATATCTCAGTAGGGAGGG       	3	3	0
TGATGTTTCAAATTTTCACGTCAGTGATGTTACCACA	3	29	1
ATTAACTTGAAGAACAATCGATTACGAGTGATTAGAA	3	129	0
ATTGTTCTTCAAGTTAATCAAACTTGACACGGATGAA	3	148	1
CTCCTAACATAAGATTTTCGATTTTGATGTCTGATAC	3	210	0
TTTCAAGATTATATCAATCAAGCATGATAGAATAGAT	4	26	1
  TTTGGTAGAATTATATCGGAGGTGAAAAA      	5	8	1
          **   *****    ***
MAP Score: 3.60566

Motif 5
TGGAATAATTACACGGATGTTTCATAACAGAC	0	158	1
CTAACTATGGAAGAGGAGGAGAAAGC      	1	12	1
          TCAATGATGATTGCCTTCGGGG	2	0	1
ATGATTGCCTTCGGGGAGGGTATCCTCCCTCC	2	16	1
CGAAAACAAAACAGGGAGGAGAGTGG      	2	64	1
AATTTTCACGTCAGTGATGTTACCACATCTTT	3	39	1
ATCAAACTTGACACGGATGAAAATTCGGTGAT	3	164	1
ATTATATCAATCAAGCATGATAGAATAGATAA	4	33	1
          *** ***** **
MAP Score: 2.64855

Motif 6
GATGCAATGCATCCCCTTTTTCTTTATCCACAGACCA	0	100	1
TCTGTTATGAAACATCCGTGTAATTATTCCAGTTATG	0	152	0
GATGTTTCATAACAGACTTTTACTTTTCTCAAACGAA	0	173	1
AAAGGACTGTATCAGTATTGTTTCGTTTGAGAAAAGT	0	194	0
TGAATATAAAATCTTGTGTATAACATTTATACCATAT	0	245	0
AGATTTTATATTCATGCTTTTCTCCTTCAGGAGGTGA	0	268	1
CGGGGAGGGTATCCTCCCTCCCCATATTTATTTGCCA	2	27	1
     CCACTCTCCTCCCTGTTTTGTTTTCGTGGCAA	2	58	0
CTACTGAGATATCTGATGTTTCAAATTTTCACGTCAG	3	16	1
CAGTGATGTTACCACATCTTTTCGATTCAAGTCAATA	3	50	1
AGTGATTAGAAACAATTATATCCAATTATTGTGTGTG	3	103	0
ATTGTTTCTAATCACTCGTAATCGATTGTTCTTCAAG	3	124	1
TCACCGAATTTTCATCCGTGTCAAGTTTGATTAACTT	3	158	0
AGACATCAAAATCGAAAATCTTATGTTAGGAGGGGAG	3	215	1
        ACTTCACACCTCCTCTTTTCAAGATTATA	4	2	1
TCCTTATCTATTCTATCATGCTTGATTGATATAATCT	4	31	0
          ***   * * ***  **
MAP Score: 0.906798

Motif 7
TTACACGGATGTTTCATAACAGACTTTTACTTT	0	166	1
TTTCTCAAACGAAACAATACTGATACAGTCCTT	0	197	1
TCCTTTGATTGAGAGAACACATATGGTATAAAT	0	225	1
ATTTGCCACGAAAACAAAACAGGGAGGAGAGTG	2	56	1
GTGAAAATTTGAAACATCAGATATCTCAGTAGG	3	15	0
AAAAGATGTGGTAACATCACTGACGTGAAAATT	3	39	0
ATTTGGTTTCATAAGAACACACACAATAATTGG	3	86	1
AATCGATTACGAGTGATTAGAAACAATTATATC	3	118	0
AATCAAGCATGATAGAATAGATAAGGAAAAATT	4	41	1
          ** **** *** *
MAP Score: 0.649968