AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions014_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241434
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0825	148	branched-chain amino acid ABC transporter, permease protein (braD-2)
#1	AF0827	285	branched-chain amino acid ABC transporter, periplasmic binding protein (braC-2)
#2	AF1299	300	transcription initiation factor IIB
#3	AF1300	85	ABC transporter, ATP-binding protein
#4	AF1391	50	branched-chain amino acid ABC transporter, periplasmic binding protein (braC-4)

Motif 1
TTTTGGTTATCCTAAAGTGCTCAAAAGGCGAATTAG	0	12	1
TGGAAAAAAACCAAAAAGGTTTTATACTTTTGCAAT	0	111	1
CACGTGGCTACCGAAAAGTTTAAATACTCTGCCGAA	2	24	1
AAATACTCTGCCGAAAACCTTATATACTGCATGAGC	2	45	1
TGCGTACATCCCCAAAATAGGGGATAAGGTTGTTAC	2	149	1
TTTAGTTAAGCCGAAAAATCTGGATAAGATAATATT	2	248	1
TTGAGGTTCGCTAAAAAAGAGAGAAAG         	3	1	0
          ** ****   *  ***
MAP Score: 8.615

Motif 2
GAATTAGTGAAACTCCATGAGGAAAAATTT	0	41	1
CCTTTTAAAGAACCTCGTTACTCTCTAAAT	1	13	1
GGATTCCCTTAACTTCGTTCACGTATTGCT	1	76	1
ATTGCTTTCTAACTTCGAGATCAACTCCAT	1	100	1
CTTCGAGATCAACTCCATGCTGCCAGAGTT	1	112	1
TTTTTTAGCGAACCTCAAGCTTTCTTTTGG	3	19	1
AGGCAGATTGGACTTCAGGCTTTTTATGAC	3	63	0
         AGACTCCGAGCTTTAGTAAAG	4	1	1
          **********
MAP Score: 6.08377

Motif 3
ATCCTAAAGTGCTCAAAAGGCGAATTAGTGAAACTCCA	0	20	1
AACTCCATGAGGAAAAATTTCACTTTCTATGATGTACA	0	51	1
GCTATTAATTGGAAAAAAACCAAAAAGGTTTTATACTT	0	102	1
AAGAACTCTCTGGAAAAGCCAGATTTAGAGAGTAACGA	1	27	0
TATAAAACTACGCAAAAAAGGAAAAGCTTATATGTAAT	1	231	1
TATGTAATAATGTAAAATCACAAATGGTGAAAAA    	1	261	1
CACGTGGCTACCGAAAAGTTTAAATACTCTGCCGAAAA	2	24	1
AAATACTCTGCCGAAAACCTTATATACTGCATGAGCAG	2	45	1
TAAAGCATATGTCAAAAACTGGAATGCTTGTGGTGACT	2	103	1
TGCGTACATCCCCAAAATAGGGGATAAGGTTGTTACAA	2	149	1
TTTAGTTAAGCCGAAAAATCTGGATAAGATAATATTTG	2	248	1
CTTGAGGTTCGCTAAAAAAGAGAGAAAG          	3	0	0
GGTGCGGAATGCCAAAAGAAAGCTTGAGGTTCGCTAAA	3	22	0
TTTATACAACGTTAAAATTTTAAAACTTTACTAAAGCT	4	18	0
          ** ****    * **  *
MAP Score: 5.10487

Motif 4
TCGTTACTCTCTAAATCTGGCTTTTCCAGA	1	27	1
AGGTGAATTACAAACTCTGGCAGCATGGAG	1	124	0
AAGCATATGTCAAAAACTGGAATGCTTGTG	2	105	1
TGTGGTGACTCTAAATCCTGCGTACATCCC	2	131	1
AGTTAAGCCGAAAAATCTGGATAAGATAAT	2	251	1
GAATGCCAAAAGAAAGCTTGAGGTTCGCTA	3	24	0
CCGAAGTCATAAAAAGCCTGAAGTCCAATC	3	58	1
TAAAACTTTACTAAAGCTCGGAGTCT    	4	6	0
          **********
MAP Score: 4.78439

Motif 5
TGGAAAAAAACCAAAAAGGTTTTATACTTTTGCAATC	0	111	1
TCTGGCTTTTCCAGAGAGTTCTTTAACCGAAGCAGGA	1	42	1
AAGCAGGATTCCCTTAACTTCGTTCACGTATTGCTTT	1	71	1
CACGTGGCTACCGAAAAGTTTAAATACTCTGCCGAAA	2	24	1
AAATACTCTGCCGAAAACCTTATATACTGCATGAGCA	2	45	1
AGATACTGGCCCGATAACGTCAGCAACAAATCCAATG	2	200	0
          **  **** **    **
MAP Score: 4.69452

Motif 6
GGTTATCCTAAAGTGCTCAAAAGGCGAATTAGTGA	0	16	1
TTAATTGGAAAAAAACCAAAAAGGTTTTATACTTT	0	106	1
TTGTGAAATAAAGAATTATAAAACTACGCAAAAAA	1	215	1
AAAACTACGCAAAAAAGGAAAAGCTTATATGTAAT	1	234	1
GTAATAATGTAAAATCACAAATGGTGAAAAA    	1	264	1
GTGGCTACCGAAAAGTTTAAATACTCTGCCGAAAA	2	27	1
TACTCTGCCGAAAACCTTATATACTGCATGAGCAG	2	48	1
AGCATATGTCAAAAACTGGAATGCTTGTGGTGACT	2	106	1
ACATCCCCAAAATAGGGGATAAGGTTGTTACAAGG	2	154	1
TTCCGCACCGAAGTCATAAAAAGCCTGAAGTCCAA	3	51	1
AAAATTTTAAAACTTTACTAAAGCTCGGAGTCT  	4	8	0
          ** *    *******
MAP Score: 4.43811

Motif 7
GAAAAAAACCAAAAAGGTTTTATACTTTTGCA	0	113	1
TTTATAATTAGTATAGTTTGAAGAGAATCGTG	1	169	1
CGCAAAAAAGGAAAAGCTTATATGTAATAATG	1	241	1
CGTGGCTACCGAAAAGTTTAAATACTCTGCCG	2	26	1
ATACTCTGCCGAAAACCTTATATACTGCATGA	2	47	1
CCGAAGTCATAAAAAGCCTGAAGTCCAATCTG	3	58	1
CCGAGCTTTAGTAAAGTTTTAAAATTTTAACG	4	15	1
          ****** ** **
MAP Score: 3.25901