AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions011_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251291
 numcols =     	10
 undersample = 	1
 oversample = 	1

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

Motif 1
    ACAGCCAAAAAAGGAGAAAATAACAG	0	6	1
TATTGAGATCCAAAAGGAGGAATCGAAG  	0	89	1
AACAAAAGAAAAGCGGGAGGAACAGCCTCC	2	13	0
GAAACTCAAGGAAAGAGAGGTCTGAGT   	3	7	0
GAAAACATCGAGAAGGGAGGGATTCCT   	3	77	1
GAGCTAATCTAGACAGGGGGACCCGCGACC	4	15	1
CCTCCTTTCTAAAAGGGGGCACCCGCTCAT	4	46	0
GCCCCCTTTTAGAAAGGAGGATGGAAT   	4	56	1
TCATCAAGACACAAGGGAGG          	6	197	1
TTCTCATGAGGGGAGGGAAGAGAT      	8	69	1
TGAAACAAGCAAAAGCGAGGCCCCTCAGGG	9	20	1
TTCAATCAAAGAAAGCGAAGCCCCTGAGGG	9	41	0
CTTTGATTGAAGAAAGGAAGGTGAAAGA  	9	60	1
          **********
MAP Score: 16.3251

Motif 2
TCTGTTATTTTCTCCTTTTTTGGCTGT   	0	7	0
GCTGTTCCTCCCGCTTTTCTTTTGTTTAAA	2	17	1
 ACTCAGACCTCTCTTTCCTTGAGTTTCTT	3	9	1
   AGGAATCCCTCCCTTCTCGATGTTTTC	3	77	0
   ATTCCATCCTCCTTTCTAAAAGGGGGC	4	56	0
     AAAACCCACCTCCCTAAGGAAATTT	5	42	0
CGTTGACTTTTCATTTTCCTTCGTGTTACC	6	137	1
CCTCCTGGAATATCTTTTCTTCTGAAAAAT	7	11	1
         ATCTCTTCCCTCCCCTCATGA	8	72	0
CTCAGGGGCTTCGCTTTCTTTGATTGAAGA	9	43	1
  TCTTTCACCTTCCTTTCTTCAATCAAAG	9	60	0
          **********
MAP Score: 9.86324

Motif 3
TCACATTAATTATATGCAGGAAATAATTTAAAATC	0	48	0
ATATAATTAATGTGAACATAATATTGAGATCCAAA	0	68	1
GAAAATACTGTTTTTACCTCAAATTTCCTTAGGGA	5	22	1
   TTACTCATGTTACCATGAAATTCTATATTATG	6	7	1
CATGAAATTCTATATTATGAAAATTCTCGTTCATG	6	23	1
CGTTCATGGATATTATCCAAAAAATTCATTTATCA	6	50	1
TGGAATATCTTTTCTTCTGAAAAATTATACACCAG	7	16	1
ACTGGCGAAATTTCTGCATTAAAATTCAACGTGTA	7	52	1
AAATTCAACGTGTATTCGAAAAATTGAGAATTTGA	7	73	1
AGTATACCAGTTTTTCTATCAAATTCTCAATTTTT	7	91	0
          * * * * * *****
MAP Score: 5.25127