AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions044_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242160
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ykvD	192	similar to two-component sensor histidine kinase
#1	spo0A	275	two-component response regulator
#2	mcpB	157	methyl-accepting chemotaxis protein
#3	yvqA	277	similar to two-component response regulator [YvqB]

Motif 1
TACATTTTAAAAAAGAAGAGAAATATTGGAAA	0	82	0
TTAAGGGAAGAAAGGAAGAGAAAAAGAGCGAG	3	140	0
TTTTCTTATTAAAGAAGAAGAAACAATGATAT	0	151	1
AGAATATGTGAAATTATGAAAATTGCCTGCCG	3	209	1
GGAGAAAAGCAAAGCACCAAAATAGAATATGT	3	89	1
AAGAGGGATCAAAATAAAAAAACTGCCGGAAA	1	19	0
AATGAAAGTTAAAAAGGCAGAAGACAGCCAAA	2	55	1
TGTGGGATAAAAATGAAAAGAATATGTGAAAT	3	191	1
TTTAAAATAAAAAATGGAAGAAGTTCTTTTTG	2	83	0
TAATAAGAAAAAATAACCAAAAAAATTAGAAA	0	130	0
TTTTTAGTCGAAAAACAGAGAAAAACATAGAA	1	131	1
ATAACCAAAAAAATTAGAAAAAGATGTTGGCA	0	118	0
ATTGTCCCAATAATGAGGAGAAAAGCAAAGCA	3	73	1
ATACCCTCTAAAAAAATCATAATCACCAATAT	1	182	0
AGGAAGAGAAAAAGAGCGAGGAAGATGTAGGA	3	128	0
TACATACGGTAAAATATACAAAAGAAGATTTT	1	63	1
AATGACGTTGAAAGGATGTGAAGAGCC     	3	260	1
          **** * *****
MAP Score: 18.5486

Motif 2
AGAGAAACATTAATAAACAAAGACCAAAATGT	0	39	1
CTTACATTTTAAAAAAGAAGAGAAATATTGGA	0	84	0
ATAACCAAAAAAATTAGAAAAAGATGTTGGCA	0	118	0
TAATAAGAAAAAATAACCAAAAAAATTAGAAA	0	130	0
TTTTCTTATTAAAGAAGAAGAAACAATGATAT	0	151	1
AAGAGGGATCAAAATAAAAAAACTGCCGGAAA	1	19	0
ATGTATTCTGAGAAGTGAAGAGGGATCAAAAT	1	36	0
ACATACGGTAAAATATACAAAAGAAGATTTTT	1	64	1
CATTTTTAGTCGAAAAACAGAGAAAAACATAG	1	129	1
AGAAAAACATAGAATAACAAAGATATGCCACT	1	149	1
GTTTTTTATAAGATATGCAAAGAGCTTGGGCA	2	24	1
TTGGGCAATGAAAGTTAAAAAGGCAGAAGACA	2	49	1
AAAAGGCAGAAGACAGCCAAAAAGAACTTCTT	2	66	1
TTTAAAATAAAAAATGGAAGAAGTTCTTTTTG	2	83	0
AATAATGAGGAGAAAAGCAAAGCACCAAAATA	3	81	1
GAAGAAAGGAAGAGAAAAAGAGCGAGGAAGAT	3	134	0
ATTGTGGGATAAAAATGAAAAGAATATGTGAA	3	189	1
          *** * ******
MAP Score: 17.7004

Motif 3
TATTGACATTTTGGTCTTTGTTTATTAATGTTTCTCTGT	0	37	0
AATAAAAATCTTTCCAATATTTCTCTTCTTTTTTAAAAT	0	72	1
TGCCAACATCTTTTTCTAATTTTTTTGGTTATTTTTTCT	0	118	1
TATTATATCATTGTTTCTTCTTCTTTAATAAGAAAAAAT	0	148	0
 CTGCCGGAGTTTCCGGCAGTTTTTTTATTTTGATCCCT	1	9	1
TTTTTTTATTTTGATCCCTCTTCACTTCTCAGAATACAT	1	29	1
CGTGAATTTGTCGAAAAATCTTCTTTTGTATATTTTACC	1	70	0
CGTTTCCTTGTTTGTCAAATTTCATTTTTAGTCGAAAAA	1	107	1
ATCTTTGTTATTCTATGTTTTTCTCTGTTTTTCGACTAA	1	134	0
AAAAAGAACTTCTTCCATTTTTTATTTTAAAACTTTTTT	2	84	1
TTACACTCCTTTAACGGTTATTCATTTATCGTTACATAT	3	14	1
CATATTCTATTTTGGTGCTTTGCTTTTCTCCTCATTATT	3	81	0
TCTTCCTCGCTCTTTTTCTCTTCCTTTCTTCCCTTAACC	3	135	1
TTCATTTTTATCCCACAATGTTTGTTTATGATATGGTTA	3	169	0
TCATAATTTCACATATTCTTTTCATTTTTATCCCACAAT	3	189	0
          **      * *** *** *
MAP Score: 15.9881

Motif 4
ATTTTTAGTCGAAAAACAGAGAAAAACATAGAATAA	1	130	1
AGTGAAGAGGGATCAAAATAAAAAAACTGCCGGAAA	1	19	0
AACATTGTGGGATAAAAATGAAAAGAATATGTGAAA	3	186	1
AATGAAATTTGACAAACAAGGAAACGTGAATTTGTC	1	97	0
TAAGGGAAGAAAGGAAGAGAAAAAGAGCGAGGAAGA	3	135	0
TAAAAAAGAAGAGAAATATTGGAAAGATTTTTATTG	0	71	0
AAAGTTTTAAAATAAAAAATGGAAGAAGTTCTTTTT	2	84	0
AACATTAATAAACAAAGACCAAAATGTCAATAAAAA	0	44	1
TCTGTTTTTCGACTAAAAATGAAATTTGACAAACAA	1	114	0
GAAAAACATAGAATAACAAAGATATGCCACTAATAT	1	150	1
ATTAAAGAAGAAGAAACAATGATATAATACCTCTAA	0	158	1
AAATAACCAAAAAAATTAGAAAAAGATGTTGGCAAG	0	116	0
CAATTGTCCCAATAATGAGGAGAAAAGCAAAGCACC	3	71	1
TTGTACATGCGATGAATATGTAACGATAAATGAATA	3	32	0
GAGCTTGGGCAATGAAAGTTAAAAAGGCAGAAGACA	2	45	1
          **  ** *  **** *
MAP Score: 13.6071

Motif 5
CGTTACAGAGAAACATTAATAAACAAAGACCAAAATGTCAATAA	0	33	1
GTTGGCAAGCTTACATTTTAAAAAAGAAGAGAAATATTGGAAAG	0	81	0
TTTAATAAGAAAAAATAACCAAAAAAATTAGAAAAAGATGTTGG	0	120	0
TTCTCAGAATACATACGGTAAAATATACAAAAGAAGATTTTTCG	1	54	1
TTTTTAGTCGAAAAACAGAGAAAAACATAGAATAACAAAGATAT	1	131	1
CAATGAAAGTTAAAAAGGCAGAAGACAGCCAAAAAGAACTTCTT	2	54	1
TCGGCTGCTTAAAAAAGTTTTAAAATAAAAAATGGAAGAAGTTC	2	89	0
TATCATAAACAAACATTGTGGGATAAAAATGAAAAGAATATGTG	3	175	1
          *** *      ** * *    * *
MAP Score: 2.51317

Motif 6
GAAACCGTTACAGAGAAACATTAATAAACAAAGACCAAAATG	0	28	1
CATTTTAAAAAAGAAGAGAAATATTGGAAAGATTTTTATTGA	0	70	0
AACCAAAAAAATTAGAAAAAGATGTTGGCAAGCTTACATTTT	0	106	0
TTCTTCTTTAATAAGAAAAAATAACCAAAAAAATTAGAAAAA	0	128	0
TTTTTCTTATTAAAGAAGAAGAAACAATGATATAATACCTCT	0	150	1
AAGAGGGATCAAAATAAAAAAACTGCCGGAAACTCCGGCAG 	1	9	0
CGGTAAAATATACAAAAGAAGATTTTTCGACAAATTCACGTT	1	69	1
CTGTTTTTCGACTAAAAATGAAATTTGACAAACAAGGAAACG	1	107	0
AGTCGAAAAACAGAGAAAAACATAGAATAACAAAGATATGCC	1	136	1
TATACCCTCTAAAAAAATCATAATCACCAATATTAGTGGCAT	1	173	0
TGCATATCTTATAAAAAACAAGGGGGGCTAAAC         	2	1	0
ATATCGGCTGCTTAAAAAAGTTTTAAAATAAAAAATGGAAGA	2	94	0
CCCAATAATGAGGAGAAAAGCAAAGCACCAAAATAGAATATG	3	78	1
GGAAGAAAGGAAGAGAAAAAGAGCGAGGAAGATGTAGGATGA	3	125	0
AACCATATCATAAACAAACATTGTGGGATAAAAATGAAAAGA	3	170	1
TTTCAACGTCATTATAAACTAGTTTTAACATACGGCAGGCAA	3	231	0
          *  *******         * *
MAP Score: 1.75313