AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_fusions011_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236601
 numcols =     	10
 undersample = 	1
 oversample = 	1

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

Motif 1
    TGCACTAAAAAATTGGAAAAAATAACA	0	6	1
GGAAAACGATAAAAAAAGGGCGAATAATTTC	0	48	0
TCCTTTCCCGAAAAGCATCGCCAAAACGGCG	0	76	1
ATTATAGCAAAAAATCGCCGTTTTGGCGATG	0	91	0
TTTTGTAAATAAAAATTGGGCGAGATTATAG	0	115	0
ACAAAGGTGGAAAAGAAGGGAACCCAATTTG	1	33	0
GGAAACAAGGAAAAGTAGGGTCGCCTTTCTT	1	147	1
AAAGTAAGTAAAAAGAAAGGCGACCCTACTT	1	159	0
TCGCCAAAGAAAAAGTAAGTAAAAAGAAAGG	1	170	0
GAAGCAAAGAAAAAGTAAGGCGCCATCAGGC	1	199	1
ATTATAGCATAAAATTGTGGATATGTGGTTT	1	246	0
TTTTTGATCAAAAATTGTGGCGGATTATAGC	1	269	0
TTGAATAACCAAAATTGTGGCGATTTTACCA	2	26	1
AATTCTATCAAAAAGTGCGGTGATATTCGAC	3	17	0
TCAAATTTAAAAAATTAACGAATAACCTCAC	3	51	1
          ******* ***
MAP Score: 26.782

Motif 2
TATGGGGCGAAATTATTCGCCCTTTTTTTATCGTTT	0	40	1
AGATTATAGCAAAAAATCGCCGTTTTGGCGATGCTT	0	88	0
TTTTTGCTATAATCTCGCCCAATTTTTATTTACAAA	0	109	1
GGTGGAAAAGAAGGGAACCCAATTTGTCCTTTATCC	1	23	0
GGCTACGCTCAAACAGACGAAAATTTCCTACAAATT	1	71	0
AGTAAAAAGAAAGGCGACCCTACTTTTCCTTGTTTC	1	148	0
ATCAAAAACCACATATCCACAATTTTATGCTATAAT	1	241	1
TTTATGCTATAATCCGCCACAATTTTTGATCAAAAA	1	264	1
       TTTAAAATCTCTCTATTTGAATAACCAAA	2	3	1
AGTTGTGGTAAAATCGCCACAATTTTGGTTATTCAA	2	26	0
TGGCGATTTTACCACAACTCAAATTTACGATAAACT	2	43	1
AGTGCGGTCGAATATCACCGCACTTTTTGATAGAAT	3	11	1
CTTTTTGATAGAATTTTCTCAAATTTAAAAAATTAA	3	33	1
AATTAATCTCAGCAAATCCGAATTTTAATAAATTAA	4	14	1
          **     * *******
MAP Score: 19.4455

Motif 3
CCCATAACTTGTTATTTTTTCCAATTTTTTAGTGCA    	0	6	0
AAGTTATGGGGCGAAATTATTCGCCCTTTTTTTATCGTTT	0	36	1
GCGATTTTTTGCTATAATCTCGCCCAATTTTTATTTACAA	0	104	1
TCGGATAAAGGACAAATTGGGTTCCCTTCTTTTCCACCTT	1	21	1
AAGGAAACAAGGAAAAGTAGGGTCGCCTTTCTTTTTACTT	1	145	1
ACAATTTTATGCTATAATCCGCCACAATTTTTGATCAAAA	1	259	1
TTTGAGTTGTGGTAAAATCGCCACAATTTTGGTTATTCAA	2	26	0
TCAAATTTACGATAAACTACGCCCCTAACTTAC       	2	61	1
  AAGTGCGGTCGAATATCACCGCACTTTTTGATAGAATT	3	8	1
CGCACTTTTTGATAGAATTTTCTCAAATTTAAAAAATTAA	3	29	1
          *  * * *  ** *   ***
MAP Score: 8.99739

Motif 4
TGGCGATGCTTTTCGGGAAAGGAAAACGATAAAAAA	0	63	0
TATCTCATTCTTTTGTAAATAAAAATTGGGCGAGAT	0	120	0
CTTTTCCACCTTTGTGGAATTGAATTTGTAGGAAAT	1	49	1
GGTCCGGCAATTTCCGTTAAGGAAATTCAATGGAAC	1	108	1
TTACTTTTTCTTTGGCGAAGCAAAGAAAAAGTAAGG	1	183	1
 TGGTATTCCTTTTTTGATCAAAAATTGTGGCGGAT	1	275	0
AATCTCTCTATTTGAATAACCAAAATTGTGGCGATT	2	15	1
TGTGGCGATTTTACCACAACTCAAATTTACGATAAA	2	41	1
TTGATAGAATTTTCTCAAATTTAAAAAATTAACGAA	3	37	1
AAAATTCGGATTTGCTGAGATTAATTTAGT      	4	4	0
CAAATCCGAATTTTAATAAATTAAGAATATATCAAT	4	26	1
          ****   **   ****
MAP Score: 6.00642