AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_fusions011_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236616
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0567	150	DNA gyrase, subunit B (gyrB)
#1	HI0568	95	transcription accessory protein (tex)
#2	HI1264	300	DNA gyrase, subunit A (gyrA)
#3	HI1527	84	lipid A biosynthesis lauroyl acyltransferase (htrB)
#4	HI1528	73	topoisomerase IV, subunit B (parE)
#5	HI1529	66	topoisomerase IV, subunit A (parC)

Motif 1
CTTGTTATTTTTTCCAATTTTTTAGTGCA    	0	6	0
GCGAAATTATTCGCCCTTTTTTTATCGTTTTCC	0	46	1
TGCTATAATCTCGCCCAATTTTTATTTACAAAA	0	113	1
TTCAAAAAACTTTCTTTTATTTTTATT      	1	4	0
CAGTATTCTATCTTCGTTTTTTTATAATAAAGA	1	63	1
GACAAATTGGGTTCCCTTCTTTTCCACCTTTGT	2	31	1
AAAAGTAGGGTCGCCTTTCTTTTTACTTACTTT	2	157	1
TCGCCTGATGGCGCCTTACTTTTTCTTTGCTTC	2	199	0
AAAAACCACATATCCACAATTTTATGCTATAAT	2	244	1
ATGCTATAATCCGCCACAATTTTTGATCAAAAA	2	267	1
TGTGGTAAAATCGCCACAATTTTGGTTATTCAA	3	26	0
CGGTCGAATATCACCGCACTTTTTGATAGAATT	4	15	1
GTGAGGTTATTCGTTAATTTTTTAAATTTGAGA	4	49	0
          *****  * ****
MAP Score: 25.2367

Motif 2
GAAAACGATAAAAAAAGGGCGAATAATTTCGCCCC	0	43	0
GGATTATAGCATAAAATTGTGGATATGTGGTTTTT	2	244	0
AATGGAACAAAGGAAACAAGGAAAAGTAGGGTCGC	2	136	1
TGCTTCGCCAAAGAAAAAGTAAGTAAAAAGAAAGG	2	170	0
ACAATTTTTGATCAAAAAAGGAATACCA       	2	282	1
TCCGAATTTTAATAAATTAAGAATATATCAATTAA	5	30	1
    TGCACTAAAAAATTGGAAAAAATAACAAGTT	0	6	1
         AATAAAAATAAAAGAAAGTTTTTTGA	1	1	1
TCTTTGGCGAAGCAAAGAAAAAGTAAGGCGCCATC	2	191	1
TCTTTATTATAAAAAAACGAAGATAGAATACTGGT	1	61	0
TCCACAAAGGTGGAAAAGAAGGGAACCCAATTTGT	2	32	0
ATTTTTATTTACAAAAGAATGAGATAAATT     	0	130	1
CTCAAATTTAAAAAATTAACGAATAACCTCACC  	4	50	1
ATTTTGGTTATTCAAATAGAGAGATTTTAAA    	3	6	0
TTAAGAATATATCAATTAACAGAAACAAAA     	5	46	1
CTTTGTGGAATTGAATTTGTAGGAAATTTTCGTCT	2	58	1
          *  ***  * *****
MAP Score: 14.5639

Motif 3
TGGAAAAAATAACAAGTTATGGGGCGAAATTATTCGCCCT	0	23	1
TATAGCAAAAAATCGCCGTTTTGGCGATGCTTTTCGGGAA	0	80	0
ATTCTTTTGTAAATAAAAATTGGGCGAGATTATAGCAAAA	0	110	0
AAATCGGATAAAGGACAAATTGGGTTCCCTTCTTTTCCAC	2	18	1
CAAAGGAAACAAGGAAAAGTAGGGTCGCCTTTCTTTTTAC	2	143	1
TGGCGAAGCAAAGAAAAAGTAAGGCGCCATCAGGCGAAAT	2	195	1
TCCTTTTTTGATCAAAAATTGTGGCGGATTATAGCATAAA	2	264	0
CTATTTGAATAACCAAAATTGTGGCGATTTTACCACAACT	3	22	1
AGAAAATTCTATCAAAAAGTGCGGTGATATTCGACCGCAC	4	12	0
          **  * *  *  ****   *
MAP Score: 11.812

Motif 4
CGAAATTATTCGCCCTTTTTTTATCGTTTTCCTTTCCCGA	0	47	1
ATCGCCAAAACGGCGATTTTTTGCTATAATCTCGCCCAAT	0	92	1
GCTATAATCTCGCCCAATTTTTATTTACAAAAGAATGAGA	0	114	1
AGTATTCTATCTTCGTTTTTTTATAATAAAGAAGTACGAC	1	64	1
AACCACATATCCACAATTTTATGCTATAATCCGCCACAAT	2	247	1
CTATAATCCGCCACAATTTTTGATCAAAAAAGGAATACCA	2	270	1
GGTAAAATCGCCACAATTTTGGTTATTCAAATAGAGAGAT	3	16	0
TCGAATATCACCGCACTTTTTGATAGAATTTTCTCAAATT	4	18	1
GATAGAATTTTCTCAAATTTAAAAAATTAACGAATAACCT	4	39	1
          ** *  ****      * **
MAP Score: 4.85937