AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions011_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251298
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0107	76	conserved hypothetical protein
#1	TM0110	107	transcriptional regulator, XylR-related
#2	TM0593	38	amino acid ABC transporter, periplasmic amino acid-binding protein
#3	TM0594	54	conserved hypothetical protein
#4	TM0595	94	sugar ABC transporter, periplasmic sugar-binding protein, putative
#5	TM0957	73	hypothetical protein
#6	TM0958	57	ribose ABC transporter, periplasmic ribose-binding protein
#7	TM0960	207	ribokinase
#8	TM1132	155	moxR protein, putative
#9	TM1135	83	branched chain amino acid ABC transporter, periplasmic amino acid-binding protein
#10	TM1136	78	branched chain amino acid ABC transporter, permease protein

Motif 1
GTTGAAAATGTGGAGGGAGGATTCG     	0	5	0
   ACAGCCAAAAAAGGAGAAAATAACAGA	1	7	1
TATTGAGATCCAAAAGGAGGAATCGAAG  	1	89	1
AACAAAAGAAAAGCGGGAGGAACAGCCTCC	3	13	0
GAAAACATCGAGAAGGGAGGGATTCCT   	4	77	1
GAGCTAATCTAGACAGGGGGACCCGCGACC	5	15	1
CCTCCTTTCTAAAAGGGGGCACCCGCTCAT	5	46	0
GCCCCCTTTTAGAAAGGAGGATGGAAT   	5	56	1
AAATTTCCTTAGGGAGGTGGGTTTT     	6	42	1
TCATCAAGACACAAGGGAGG          	7	197	1
ATCATTCTCATGAGGGGAGGGAAGAGAT  	9	65	1
TGAAACAAGCAAAAGCGAGGCCCCTCAGGG	10	20	1
CTTTGATTGAAGAAAGGAAGGTGAAAGA  	10	60	1
          **********
MAP Score: 18.1714

Motif 2
TACCACGTTGAAAATGTGGAGGGAGGATTCG     	0	5	0
AGTTTATTATACTGACAATTGGGGGTGCTCAAC   	0	53	1
CATAATATTGAGATCCAAAAGGAGGAATCGAAG   	1	84	1
GCATTGTGTTATAATAAATCGGAGGTGATAAT    	2	16	1
GTTTTAAACAAAAGAAAAGCGGGAGGAACAGCCTCC	3	13	0
TTGATTGTGAAGAAACTCAAGGAAAGAGAGGTCTGA	4	12	0
CAAGGGGAAAACATCGAGAAGGGAGGGATTCCT   	4	71	1
TCACTGAGCTAATCTAGACAGGGGGACCCGCGACCT	5	10	1
GGGGGACCCGCGACCTATGAGCGGGTGCCCCCTTTT	5	30	1
CGGGTGCCCCCTTTTAGAAAGGAGGATGGAAT    	5	51	1
TTTTACCTCAAATTTCCTTAGGGAGGTGGGTTTT  	6	33	1
TTTTCACAAGAATGGTAACACGAAGGAAAATGAAAA	7	144	0
ACGATTTCATCAAGACACAAGGGAGG          	7	191	1
TCAGAAGAAAAGATATTCCAGGAGGT          	8	0	0
GTATGCAAATACTTCTATCTGGAGGGATCCTCGG  	8	131	1
TATAAAAATCATTCTCATGAGGGGAGGGAAGAGAT 	9	58	1
TTCCATTGAAACAAGCAAAAGCGAGGCCCCTCAGGG	10	14	1
GCTTTCTTTGATTGAAGAAAGGAAGGTGAAAGA   	10	55	1
          * *   *  *******
MAP Score: 13.6056

Motif 3
TAATAAACTTCAGAAATATTCTACCACGTTGAA	0	29	0
ATATTATGTTCACATTAATTATATGCAGGAAAT	1	59	0
ATTATCACCTCCGATTTATTATAACACAATGCT	2	15	0
AGTTTCTTCACAATCAAATTATAACCTATGCGG	4	31	1
ATAACCTATGCGGTATAATTCAAGGGGAAAACA	4	51	1
ACTCATGTTACCATGAAATTCTATATTATGAAA	7	12	1
TGGATATTATCCAAAAAATTCATTTATCATCGA	7	56	1
GATCATAAAACCCAATAATTCTTATTAATCGAT	7	84	0
ATCTTTTCTTCTGAAAAATTATACACCAGTACT	8	22	1
GAAATTTCTGCATTAAAATTCAACGTGTATTCG	8	58	1
ACCAGTTTTTCTATCAAATTCTCAATTTTTCGA	8	88	0
CGTGGTGAGCCTGTAAAATACTTATAAAAATCA	9	36	1
          *  * ********
MAP Score: 9.62157

Motif 4
ACCACGTTGAAAATGTGGAGGGAGGATTCG   	0	7	0
AATAATTTAAAATCAAGGTCGGATATCTGTTAT	1	29	0
TAAACAAAAGAAAAGCGGGAGGAACAGCCTCCC	3	12	0
AACTCAAGGAAAGAGAGGTCTGAGT        	4	2	0
GGAAAACATCGAGAAGGGAGGGATTCCT     	4	76	1
CCCCTTTTAGAAAGGAGGATGGAAT        	5	58	1
CAAATTTCCTTAGGGAGGTGGGTTTT       	6	41	1
AATCATTCTCATGAGGGGAGGGAAGAGAT    	9	64	1
TCTTTGATTGAAGAAAGGAAGGTGAAAGA    	10	59	1
          *** * *** ***
MAP Score: 9.17352

Motif 5
        CGAATCCTCCCTCCACATTTTC	0	2	1
     CTTCGATTCCTCCTTTTGGATCTCA	1	92	0
TCTTTTGTTTAAAACTCCTTTAAAGAAAAC	3	34	1
ACTCAGACCTCTCTTTCCTTGAGTTTCTTC	4	10	1
      AGGAATCCCTCCCTTCTCGATGTT	4	80	0
      ATTCCATCCTCCTTTCTAAAAGGG	5	59	0
TTTTTACCTCAAATTTCCTTAGGGAGGTGG	6	32	1
ATATTATGAAAATTCTCGTTCATGGATATT	7	34	1
GTTGACTTTTCATTTTCCTTCGTGTTACCA	7	138	1
          AAACTTCCATTGAAACAAGC	10	0	1
     TCTTTCACCTTCCTTTCTTCAATCA	10	63	0
          **********
MAP Score: 9.01352

Motif 6
      CGAATCCTCCCTCCACATTTTCAACGTGG	0	4	1
ATAACAGATATCCGACCTTGATTTTAAATTATTTC	1	29	1
TTAAATTATTTCCTGCATATAATTAATGTGAACAT	1	52	1
AGGCTGTTCCTCCCGCTTTTCTTTTGTTTAAAACT	3	15	1
CTCAGACCTCTCTTTCCTTGAGTTTCTTCACAATC	4	11	1
TCTCGATGTTTTCCCCTTGAATTATACCGCATAGG	4	55	0
AAACAGTATTTTCTTCTTTTCAAAT          	6	0	0
AAAATACTGTTTTTACCTCAAATTTCCTTAGGGAG	6	23	1
ATGAAAATTCTCGTTCATGGATATTATCCAAAAAA	7	39	1
TCTTTGTTTTTCTCTCGTTGACTTTTCATTTTCCT	7	122	1
GGAATATCTTTTCTTCTGAAAAATTATACACCAGT	8	17	1
CTGGCGAAATTTCTGCATTAAAATTCAACGTGTAT	8	53	1
          **** * *  * ***
MAP Score: 6.84789

Motif 7
TGGTAGAATATTTCTGAAGTTTATTATACTGACAAT	0	36	1
AAATAACAGATATCCGACCTTGATTTTAAATTATTT	1	27	1
TTTTAAATTATTTCCTGCATATAATTAATGTGAACA	1	50	1
TCCTCCCGCTTTTCTTTTGTTTAAAACTCCTTTAAA	3	22	1
 ACTCAGACCTCTCTTTCCTTGAGTTTCTTCACAAT	4	9	1
AAAACAGTATTTTCTTCTTTTCAAAT          	6	0	0
ATTCTTTGTTTTTCTCTCGTTGACTTTTCATTTTCC	7	120	1
TGGAATATCTTTTCTTCTGAAAAATTATACACCAGT	8	16	1
ACTGGCGAAATTTCTGCATTAAAATTCAACGTGTAT	8	52	1
GGGGCTTCGCTTTCTTTGATTGAAGAAAGGAAGGTG	10	47	1
          *****    ** * **
MAP Score: 4.85603

Motif 8
ATTATACTGACAATTGGGGGTGCTCAAC          	0	58	1
ATATTGAGATCCAAAAGGAGGAATCGAAG         	1	88	1
AAACAAAAGAAAAGCGGGAGGAACAGCCTCCCGC    	3	6	0
CTGAGCTAATCTAGACAGGGGGACCCGCGACCTATGAG	5	13	1
ATCCTCCTTTCTAAAAGGGGGCACCCGCTCATAGGTCG	5	40	0
GCAAATACTTCTATCTGGAGGGATCCTCGG        	8	135	1
TTGAAACAAGCAAAAGCGAGGCCCCTCAGGGGCTTCGC	10	19	1
          * *   ** ** ***  *
MAP Score: 4.76127

Motif 9
ACTGACAATTGGGGGTGCTCAAC       	0	63	1
ATCGAGAAGGGAGGGATTCCT         	4	83	1
CTCATAGGTCGCGGGTCCCCCTGTCTAGAT	5	21	0
CGACCTATGAGCGGGTGCCCCCTTTTAGAA	5	40	1
AAGCCCCTGAGGGGCCTCGCTTTTGCTTGT	10	24	0
AGGCCCCTCAGGGGCTTCGCTTTCTTTGAT	10	37	1
          **********
MAP Score: 2.5963

Motif 10
GCCAAAAAAGGAGAAAATAACAGATATCCGACCT	1	13	1
ACATAATATTGAGATCCAAAAGGAGGAATCGAAG	1	83	1
TTTGATTGTGAAGAAACTCAAGGAAAGAGAGGTC	4	15	0
TATAATTCAAGGGGAAAACATCGAGAAGGGAGGG	4	64	1
AAGGAAATTTGAGGTAAAAACAGTATTTTCTTCT	6	18	0
AAGTCAACGAGAGAAAAACAAAGAATCTCGATCA	7	112	0
TCACAAGAATGGTAACACGAAGGAAAATGAAAAG	7	143	0
TCGAAAAATTGAGAATTTGATAGAAAAACTGGTA	8	88	1
ATTCTCATGAGGGGAGGGAAGAGAT         	9	68	1
GATTGAAGAAAGGAAGGTGAAAGA          	10	64	1
          *****   ** ***
MAP Score: 2.34309