AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions014_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241428
 numcols =     	10
 undersample = 	1
 oversample = 	1

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

Motif 1
TTTTGGTTATCCTAAAGTGCTCAAAAGGCGAATTAG	0	12	1
TGGAAAAAAACCAAAAAGGTTTTATACTTTTGCAAT	0	111	1
CACGTGGCTACCGAAAAGTTTAAATACTCTGCCGAA	1	24	1
AAATACTCTGCCGAAAACCTTATATACTGCATGAGC	1	45	1
TGCGTACATCCCCAAAATAGGGGATAAGGTTGTTAC	1	149	1
TTTAGTTAAGCCGAAAAATCTGGATAAGATAATATT	1	248	1
TTGAGGTTCGCTAAAAAAGAGAGAAAG         	2	1	0
          ** ****   *  ***
MAP Score: 11.5694

Motif 2
CTTTTGAGCACTTTAGGATAACCAAAATC        	0	2	0
TATAAAACCTTTTTGGTTTTTTTCCAATTAATAGCAT	0	100	0
AACTGGAATGCTTGTGGTGACTCTAAATCCTGCGTAC	1	119	1
GACTCTAAATCCTGCGTACATCCCCAAAATAGGGGAT	1	137	1
TCCCCCTACGCTTTAGTTAAGCCGAAAAATCTGGATA	1	237	1
CAAAAGAAAGCTTGAGGTTCGCTAAAAAAGAGAGAAA	2	11	0
CTCAAGCTTTCTTTTGGCATTCCGCACCGAAGTCATA	2	32	1
AGACTCCGAGCTTTAGTAAAGTTTTAAAATTTTAACG	3	10	1
          **** **    **  **
MAP Score: 6.67589

Motif 3
TCCTAAAGTGCTCAAAAGGCGAATTAGTGAAACTCCA	0	21	1
TGGTTTTTTTCCAATTAATAGCATTAGACTCCCACTG	0	87	0
TGCCGAAAACCTTATATACTGCATGAGCAGGTTGCGG	1	53	1
GCGTACATCCCCAAAATAGGGGATAAGGTTGTTACAA	1	150	1
TTAGTTAAGCCGAAAAATCTGGATAAGATAATATTTG	1	249	1
GTGCGGAATGCCAAAAGAAAGCTTGAGGTTCGCTAAA	2	22	0
          * ****    * ** **
MAP Score: 5.21498

Motif 4
TTTTGGTTATCCTAAAGTGCTCAAAAGGCGAATTAG	0	12	1
TGGAAAAAAACCAAAAAGGTTTTATACTTTTGCAAT	0	111	1
TCACGTGGCTACCGAAAAGTTTAAATACTCTGCCGA	1	23	1
AAATACTCTGCCGAAAACCTTATATACTGCATGAGC	1	45	1
TTTAGAGTCACCACAAGCATTCCAGTTTTTGACATA	1	110	0
TTGGGGATGTACGCAGGATTTAGAGTCACCACAAGC	1	128	0
TTTAGTTAAGCCGAAAAATCTGGATAAGATAATATT	1	248	1
TTTTAGCGAACCTCAAGCTTTCTTTTGGCATTCCGC	2	21	1
GGCATTCCGCACCGAAGTCATAAAAAGCCTGAAGTC	2	47	1
TCCGAGCTTTAGTAAAGTTTTAAAATTTTAACGTTG	3	14	1
          ** ****  **  * *
MAP Score: 0.806122