AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions007_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241228
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0433	122	conserved hypothetical protein
#1	AF0438	79	3-ketoacyl-CoA thiolase (acaB-8)
#2	AF0439	82	transcriptional regulatory protein, AsnC family
#3	AF0442	300	succinoglycan biosynthesis regulator (exsB)
#4	AF0641	51	ISA1214-3, ISORF2
#5	AF0982	300	osmoprotection protein (proX)
#6	AF1391	50	branched-chain amino acid ABC transporter, periplasmic binding protein (braC-4)
#7	AF1768	300	dipeptide ABC transporter, permease protein (dppB)

Motif 1
TCTTTGTAACCTTTGGTAACACCAAAAACCAAAATTTTAATC	0	45	1
CAAGGCAAAATTCATATTTCACGAAAACATTAAATATTACAC	1	33	1
TAAATGGCAATTTTAATTGCAATTAAAGTGTAAGTATC    	2	6	0
TTGGACATGCTTCTTGAACCTCCCAAACTCAACGAACAGAAC	3	96	1
GGGCGATGACTTCATATAACTTTGAAATCCACCTTCTAC   	3	271	1
         GTTCTGATTCCAACCAAAAAGTATTTAAGTATT	4	1	1
AAAAACCCCACTTATGGAGCAATTATACAACATTCTGGACAA	5	52	0
GCGGAAATCTTTCAGGTGACAAGGAAAATGTAATTGTAAAAT	5	190	1
GAGTCCGAACCTCAAAAAGCTTTTATAAGGGATTTATCATTT	5	248	1
      AGCGTTTATACAACGTTAAAATTTTAAAACTTTACT	6	24	0
GCCAGATACACTCAAGATACTGTTATATATCATAACACGG  	7	8	0
TACGAAACTAATCATGAAACAAGAAAAAGGAAGAGAGGCTTT	7	113	1
CATGGCACTTCTGAGAAGGCTCGAAAACGATAGTGAAAAAGA	7	212	0
          **** *   *    ***    *
MAP Score: 9.88794

Motif 2
TTATGAGAAGAAAAATTGAAAGAAAA    	0	6	0
ACCAAAAACCAAAATTTTAATCTTCAGTCT	0	65	1
ATATTTCACGAAAACATTAAATATTACACG	1	46	1
TAAAAATATAAAAATTTTATGTTTGCCATT	2	47	0
ATTAGAGAGCAAAATTTTAAAAGATGAAGA	5	93	0
ATGTAATTGTAAAATTTGAGATATCACGCT	5	217	1
TTAAAATTTTAAAACTTTACTAAAGCTCGG	6	15	0
GTAAAGTTTTAAAATTTTAACGTTGTATAA	6	25	1
TGTATCTGGCAAAAATTTAATGGGCTAATC	7	40	1
          **********
MAP Score: 8.84365

Motif 3
TCTACGCATAGAGCTGCAAGGCAAAATTCA	1	17	1
TTGAGTTTGGGAGGTTCAAGAAGCATGTCC	3	98	0
TGCGGGGGGAGGGATTCGAACCCTCGAACC	3	142	1
CTGTCCCGTAGGGGTTCGAGGGTTCGAATC	3	154	0
TATGAATATTGTGGTTTAAAGGGCGATGAC	3	251	1
GGAAGGTAATGAGGTTTAAGTTGTCCAGAA	5	32	1
AATCTTGTTGGGGGTACAAAGATATTATGG	5	135	0
AAAGCTTTTTGAGGTTCGGACTCTAGCGTG	5	241	0
GAAGTGCCATGAGCTTCAAACGTGCATCTG	7	243	1
          **********
MAP Score: 6.60129

Motif 4
TGAGAAGAAAAATTGAAAGAAAA        	0	2	0
CTTTAATTGCAATTAAAATTGCCATTTAATG	2	20	1
GAACACAGTAAGTTGAAATCAGACCAAAATG	3	12	1
ACCAAAATGGGATTGAAAGTGGACGTGTAAA	3	34	1
TGAATATTGTGGTTTAAAGGGCGATGACTTC	3	253	1
TTTGCTCTCTAATTGAAAGCGCATCCCATAA	5	110	1
TTATCATTTAAATTGAAAGAGGTGGTAAG  	5	281	1
ATCTGGCAAAAATTTAATGGGCTAATCTTTT	7	43	1
          ********* *
MAP Score: 4.29573

Motif 5
ATACTTACACTTTAATTGCAATTAAAATTGC	2	11	1
AAAATTGCCATTTAATGGCAAACATAAAATT	2	34	1
CCCATTTTGGTCTGATTTCAACTTACTGTGT	3	14	0
AAAAGATATCTCTGATGACGAAAAGAAGATT	3	63	0
CAACCCCCGCTCAGATGAAAAATTCTGCATA	3	215	1
        GTTCTGATTCCAACCAAAAAGTA	4	2	1
AATTTTGCTCTCTAATTGAAAGCGCATCCCA	5	107	1
CGGAAATCTTTCAGGTGACAAGGAAAATGTA	5	191	1
GATTTATCATTTAAATTGAAAGAGGTGGTAA	5	278	1
CAAACGTGCATCTGATGAAATACAATCTTCA	7	259	1
          ******* ***
MAP Score: 3.77867

Motif 6
AAATTTACTGTTCTTTGTAACCTTTGGTAACA	0	34	1
ATCCCATAATATCTTTGTACCCCCAACAAGAT	5	132	1
CATGTTTGTTAGCTTTCTCACGTGGCAATCTT	5	159	0
CAATTACATTTTCCTTGTCACCTGAAAGATTT	5	194	0
TAATGGGCTAATCTTTTTATCGCTCCGGCTGG	7	57	1
AAGCCTCTCTTCCTTTTTCTTGTTTCATGATT	7	122	0
CTTCCGTTAATTATTTCTCCCGAAATCGACAT	7	177	1
ATCGACATGGTTCTTTTTCACTATCGTTTTCG	7	201	1
  ATTGTTGTACCTTTATCGCCTGAAGATTGT	7	280	0
          ****** ** **
MAP Score: 3.52308

Motif 7
TAAGTTGAAATCAGACCAAAATGGGATTGAA	3	20	1
CAACCCCCGCTCAGATGAAAAATTCTGCATA	3	215	1
CGGAAATCTTTCAGGTGACAAGGAAAATGTA	5	191	1
CTTGAGTGTATCTGGCAAAAATTTAATGGGC	7	34	1
CATGTCGATTTCGGGAGAAATAATTAACGGA	7	179	0
CAAACGTGCATCTGATGAAATACAATCTTCA	7	259	1
AATACAATCTTCAGGCGATAAAGGTACAACA	7	277	1
          ** ********
MAP Score: 1.69782

Motif 8
AAAGAACAGTAAATTTATGAGAAGAAAAATTGAAAGAAAA   	0	7	0
GCAAGGCAAAATTCATATTTCACGAAAACATTAAATATTACAC	1	32	1
TCCAAGTAAAAGATATCTCTGATGACGAAAAGAAGATTTACAC	3	58	0
       GTTAAGTATATCCATAGAAATACTTAAATACTTTTT	4	25	0
AAACATGCGGAAATCTTTCAGGTGACAAGGAAAATGTAATTGT	5	184	1
    CTTACCACCTCTTTCAATTTAAATGATAAATCCCTTATA	5	271	0
CTCTTCCGTTAATTATTTCTCCCGAAATCGACATGGTTCTTTT	7	175	1
  ATTGTTGTACCTTTATCGCCTGAAGATTGTATTTCATCAGA	7	269	0
          *  * * **    ****     *
MAP Score: 1.37043

Motif 9
ACCAAAAACCAAAATTTTAATCTTCAGTCTGCC	0	65	1
GCTGCAAGGCAAAATTCATATTTCACGAAAACA	1	29	1
AATTGCAATTAAAATTGCCATTTAATGGCAAAC	2	24	1
TGGCAAACATAAAATTTTTATATTTTTAGTTTA	2	49	1
TGTAATTGTAAAATTTGAGATATCACGCTAGAG	5	218	1
GTAAAGTTTTAAAATTTTAACGTTGTATAAACG	6	25	1
          *******  ** *
MAP Score: 0.719814

Motif 10
AAAGAACAGTAAATTTATGAGAAGAAAAATTGAAAGA	0	13	0
TATTTCACGAAAACATTAAATATTACACGACTACTTT	1	47	1
TGGCAAACATAAAATTTTTATATTTTTAGTTTACTTT	2	49	1
ATTAGAGAGCAAAATTTTAAAAGATGAAGAAAAACCC	5	86	0
AAACATGCGGAAATCTTTCAGGTGACAAGGAAAATGT	5	184	1
CGAACCTCAAAAAGCTTTTATAAGGGATTTATCATTT	5	253	1
ATACAACGTTAAAATTTTAAAACTTTACTAAAGCTCG	6	16	0
TGTATCTGGCAAAAATTTAATGGGCTAATCTTTTTAT	7	40	1
          ***  *** * * *  *
MAP Score: 0.0290677