AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions009_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251245
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0278	300	sugar ABC transporter, permease protein
#1	TM1222	55	oligopeptide ABC transporter, permease protein
#2	TM1223	131	oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
#3	TM1234	42	sugar ABC transporter, permease protein
#4	TM1235	22	conserved hypothetical protein
#5	TM1375	166	spermidine/putrescine ABC transporter, periplasmic spermidine/putrescine-binding protein

Motif 1
TTTTTTAAAACCCCGCCCCGAGGGGCGGGG	1	18	0
  AATGATGACCCCGCCCCTCGGGGCGGGG	1	8	1
ATCCGAGAGTTCCCGCCCTCGAGGTAACGT	0	87	1
CGAATCCCACCGCCGCCTCCAGAGAGCCAG	5	103	1
GGGTGGGGATCCCCACCCCGGGTA      	3	4	0
GGGTGGGGATCCCCACCCCTTTTCCGGGGG	3	16	1
TTTTGCAGACCCCCGCCTTTGACCGCTTGG	5	57	0
AGAGGGGGCGCTCTGCCCCCTTTTGCC   	0	283	1
TCTGGAGAACTCCCGCTCTCCATGGAAACG	0	200	1
GGGCAGAGCGCCCCCTCTTCACCTCCTTAT	0	271	0
CGCTTGGCTACGCCGCCATCCACATAGAAT	5	34	0
       GACTCCTACCTCCTTCTTTTTTT	1	42	0
GGATCAGCGGCCCTCACCTCGGGATCCTGG	0	61	0
ACATTCCAAATCCAGTCTCCCGGGATTATC	2	45	0
        GGTGCACCCCCGGAAAAGGGGT	3	30	0
TCCTGAGATTCGCCGTCGCTCCTGCCAGAA	0	21	1
AGTATGAGATCGCTATCTCCACGTGTAAAT	2	92	0
          **********
MAP Score: 29.1816

Motif 2
GTTACCTCGAGGGCGGGAACTCTCGGATCAG	0	84	0
AGGAGGTGAAGAGGGGGCGCTCTGCCCCCTT	0	274	1
CGCCCCGAGGGGCGGGGTCATCATT      	1	4	0
CCGCCCCTCGGGGCGGGGTTTTAAAAAAAGA	1	20	1
ACTCTTTTAAGGGGGTGTTCTT         	2	119	1
     TACCCGGGGTGGGGATCCCCACCCCT	3	5	1
CCCCGGAAAAGGGGTGGGGATCCCCACCCCG	3	14	0
CCCCTTTTCCGGGGGTGCACC          	3	31	1
 GGTGAGAAAGTGGTTGTTTTTC        	4	9	1
AGCGGTCAAAGGCGGGGGTCTGCAAAATCCC	5	60	1
CTCTGGAGGCGGCGGTGGGATTCGAACCCAC	5	96	0
          ******** **
MAP Score: 19.666

Motif 3
TCCGAGAGTTCCCGCCCTCGAGGTAACGTA	0	88	1
CTGGAGAACTCCCGCTCTCCATGGAAACGC	0	201	1
AGAGGGGGCGCTCTGCCCCCTTTTGCC   	0	283	1
   AATGATGACCCCGCCCCTCGGGGCGGG	1	7	1
TTTTTTTAAAACCCCGCCCCGAGGGGCGGG	1	19	0
GGGTGGGGATCCCCACCCCTTTTCCGGGGG	3	16	1
ATTTTGCAGACCCCCGCCTTTGACCGCTTG	5	58	0
TGGGTTCGAATCCCACCGCCGCCTCCAGAG	5	97	1
          **********
MAP Score: 4.54738

Motif 4
CCTCGGGATCCTGGAGTGTTGAGATTCTGGC	0	44	0
GCCGCTGATCCGAGAGTTCCCGCCCTCGAGG	0	80	1
GAGACCTTCTCCAAGATCCTCTCTGGAGAAC	0	179	1
CCATGGAGAGCGGGAGTTCTCCAGAGAGGAT	0	194	0
AAGGAGGTGAAGAGGGGGCGCTCTGCCCCCT	0	273	1
GCCCCTCGGGGCGGGGTTTTAAAAAAAGAAG	1	22	1
ATCCAGTCTCCCGGGATTATCAAGATTTATT	2	35	0
TACTCTTTTAAGGGGGTGTTCTT        	2	118	1
       TACCCGGGGTGGGGATCCCCACCC	3	3	1
ACCCCCGGAAAAGGGGTGGGGATCCCCACCC	3	16	0
CACCCCTTTTCCGGGGGTGCACC        	3	29	1
CGGTCAAAGGCGGGGGTCTGCAAAATCCCTA	5	62	1
AATCCCTATTCGTGGGTTCGAATCCCACCGC	5	85	1
TCTCTGGAGGCGGCGGTGGGATTCGAACCCA	5	97	0
          ******** **
MAP Score: 0.250243