AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions012_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944240912
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yirY	300	similar to DNA exonuclease
#1	mcpC	134	methyl-accepting chemotaxis protein
#2	yknT	136	alternate gene name: cse15; similar to sporulation protein sigma-E-controlled
#3	yomK	300	yomK
#4	yomJ	81	similar to phage-related immunity protein
#5	yomI	53	yomI
#6	ytwP	196	ytwP
#7	yttA	194	yttA
#8	yukB	27	yukB
#9	yukD	143	yukD
#10	yukE	300	yukE

Motif 1
ATATGGATAAAGCCCGGGTGCGCCTTCCGCAGC	0	100	0
AAAAACAAACTGGCGGTGCGGTGCCGGATGAAG	0	222	1
TGCCGGATGAAGAAATGGTGAGGCTGTTTTTAG	0	243	1
TATAGAAATTAGGAGGGGATTGGT         	1	120	1
TAAACAGACAAGCAGTAGCGTTGAGCCTTTGCT	2	47	0
AAAGTAATATTGCCAGAGAGTTCGGGTTGGACA	3	41	0
ATCATGTTAGAGTAGGTGTGCTGAAATAATTCA	3	97	0
GTCGATAATATGGAGAGGTGATGAAA       	3	284	1
ACTTCCTTTCAGTAGGGGAGAGGACAAAGAAAA	5	21	0
TACCTTAATCTGTCAGGGTGTTTTATTTATTCA	6	154	0
TAAGGTAAACAGCAAGGGGGCTCATT       	6	180	1
TTTTTAGGTAAGAAAGGGGGATGAGT       	7	3	0
TAAAATAAATAGAAAAAGGGGTCATATTATGGA	7	170	1
ACCCTTACATAGAAAGAGCGCCGTCTTCTTTTG	9	112	0
GCTCTTTCTATGTAAGGGTGATCCTAA      	9	126	1
TGAACCTTTCAGAAATGGTGCTGTAGCATCAAA	10	33	1
          ** ***** * **
MAP Score: 15.3469

Motif 2
TATCAGGCCGGTTTTTGAAGAACAGAACAA	0	130	1
TCTCCTTATGTTGTTTCATTATAACGAAGA	1	13	1
TTATAATTTATTTTTTGATTATTCATTTTT	1	74	1
TGCAAAATAATTTTTTGAATTATTTCAGCA	3	82	1
AACATGATTCTTTTTTGATTTACATAAAAA	3	122	1
AATGACTCAATTTTTCGATTTTTTATGTAA	3	141	0
AATTGAGTCATTTTTCCTTGGAGAATGACT	3	159	1
 CTGAGTGGCTTTTTTCTTTGTCCTCTCCC	5	9	1
GATTTGACTATTTTTTCATGGGGTGACATC	6	11	0
TGCACAAAAAGTTTTTGATTTCTGGTCAAA	6	51	1
GTAACAAACATTTTTTGACCAGAAATCAAA	6	64	0
TAGGTTTCGTTTTTTTCATGAGCTTTTTTA	7	30	0
ATTTGTTAGATTTTTTCACGCTCATCAGTT	7	125	0
AAAGGTTCAGTTTTTTCTTTCCTTAATTAG	10	12	0
TAAAACATATTTGTTTGACTATGCCGAAAA	10	223	1
          **********
MAP Score: 13.5366

Motif 3
AGTTTGTTTTTCATAAAATTTCTTAAAGCGG	0	202	0
TATAAGAAAATCGGAATATATTTACTGAAAA	1	48	0
AAATGAATAATCAAAAAATAAATTATAAGAA	1	71	0
GCCCTTTCGTTTGAAAAATGAATAATCAAAA	1	86	0
AAAAATTATTTTGCAATATGATTAAAGTAAT	3	66	0
CTGAAATAATTCAAAAAATTATTTTGCAATA	3	79	0
ACATAAAAAATCGAAAAATTGAGTCATTTTT	3	143	1
TCATTTTTCCTTGGAGAATGACTGTGTATAA	3	166	1
TTTCTCTAATTTTCAAAATGAATGAATAGTC	3	208	0
TGGTATAATGTAGGAAAATGATACCGGCGGT	4	54	1
TGATTTCTGGTCAAAAAATGTTTGTTACATG	6	66	1
CGCTCATCAGTTGAAAAATGTGAGAGAGACA	7	106	0
CAAATATTGTTTGAAAAATGTAAAATAAATA	7	150	1
AAAAAACCTTTCAGAAAATTTGATGCTACAG	10	53	0
TTTGGATTATTCGGAGAATGAAGAGAAGATT	10	111	1
AAGAGAAGATTAAGAAAATAAACCTATTTAC	10	131	1
TGTTTTAATTTTACAAAATGAGTCCAATGGT	10	199	0
          *** *******
MAP Score: 12.1527

Motif 4
TTGATTATTCATTTTTCAAACGAAAGGGCCGAT	1	88	1
GATTAAAGTAATATTGCCAGAGAGTTCGGGTTG	3	45	0
TACTTTAATCATATTGCAAAATAATTTTTTGAA	3	68	1
GTGTGCTGAAATAATTCAAAAAATTATTTTGCA	3	82	0
CTGTGTATAAATCTTAAAAAGGACTATTCATTC	3	187	1
CGTTTCTCTAATTTTCAAAATGAATGAATAGTC	3	208	0
AATCCTGCCGATTTTGCACAAAAAGTTTTTGAT	6	37	1
ACATGGTATCATAATAACAATGAAAACGACAGT	6	92	1
CCTAAAAAAGCTCATGAAAAAAACGAAACCTAA	7	28	1
TCTCTCTCACATTTTTCAACTGATGAGCGTGAA	7	108	1
TTTATTTTACATTTTTCAAACAATATTTGTTAG	7	146	0
GAAGGAGCGCCTGATTCAAAAGAAGACGGCGCT	9	96	1
CATTCTCCGAATAATCCAAAAGACCCAAATAAC	10	98	0
          ** ** **** **
MAP Score: 6.57674

Motif 5
AAATTTTATGAAAAACAAACTGGCGGTGCGGTGCCG	0	212	1
TGCAAGCTCTAAAAACAGCCTCACCATTTCTTCATC	0	248	0
TTCCTCTTTAATAAACAGACAAGCAGTAGCGTTGAG	2	55	0
TGAAAATTAGAGAAACGTACTCTCAGAAACCTAATT	3	224	1
TCTGAATAAATAAAACACCCTGACAGATTAAGGTAA	6	152	1
TTATCATAGCACATTCATTCTATCTGTCTCTCTCAC	7	82	1
CTGATGAGCGTGAAAAAATCTAACAAATATTGTTTG	7	127	1
TCCAACTCCCAAAAAAAACCTTTCAGAAAATTTGAT	10	60	0
TCATTATTATAAAAACAGTTTTTCGGCATAGTCAAA	10	236	0
          * *****  **  * *
MAP Score: 4.84657

Motif 6
CGGACCAGCTGTCACTTGAAGAGATTCACAGGCTGC	0	69	1
TCCTTATGTTGTTTCATTATAACGAAGATTGAATTT	1	15	1
CTCACCTCTAGTTTCGTTAAAAGCATAGCAAAAGCA	2	15	1
CTGCTTGTCTGTTTATTAAAGAGGAATAGCTGTTCA	2	65	1
 GCAGCCCCAGTGTATTAAATACTTACAATTTTGTC	3	9	1
TTGTTACATGGTATCATAATAACAATGAAAACGACA	6	87	1
AAAACGACAGTTTTTCTCAATACATATCCTGAAATC	6	114	1
CCCTGACAGATTAAGGTAAACAGCAAGGGGGCTCAT	6	169	1
TTAGGTTTCGTTTTTTTCATGAGCTTTTTTAGGTAA	7	25	0
TTTGAAAAATGTAAAATAAATAGAAAAAGGGGTCAT	7	159	1
GACATATACTGTAAAGTAAATAGGTTTATTTTCTTA	10	141	0
GACTCATTTTGTAAAATTAAAACATATTTGTTTGAC	10	206	1
AAAACTGTTTTTATAATAATGACGTTCTAAAAATAA	10	250	1
          ** *  * ** ** **
MAP Score: 2.77003