AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions008_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944240729
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yitV	120	similar to hypothetical proteins
#1	yitW	63	similar to hypothetical proteins
#2	yitX	54	yitX
#3	yitY	57	similar to L-gulonolactone oxydase
#4	yitZ	44	similar to multidrug resistance protein
#5	argC	206	N-acetylglutamate gamma-semialdehyde dehydrogenase
#6	carA	70	carbamoyl-phosphate transferase-arginine (subunit A)
#7	ileS	300	isoleucyl-tRNA synthetase
#8	ylyA	77	alternate gene name: ylmK; similar to hypothetical proteins from B. subtilis
#9	lsp	102	signal peptidase II
#10	pyrR	273	transcriptional attenuator and uracil phosphoribosyltransferase activity (minor)
#11	pyrP	171	uracil permease
#12	pyrB	145	aspartate carbamoyltransferase
#13	yunH	174	similar to allantoinase

Motif 1
   GTTCCCTCACTCCTTTTTTCTACAGTATA	1	44	0
ACATGTCAGGCTGTCCTTTTTTGTT       	2	3	0
ACATGTGAGGCTGTCCTTTTTTACAGCTGAAA	2	29	1
ATAGTGCTCTCCCTGCTGTTTTTATGACCA  	3	8	0
TATGGGATGAGAGGGCTTTTTTTATTTTCTGA	7	255	1
TTCATTCCTCCACTGCATTTTTTCAGAAAATA	7	277	0
GGCTTTTACGCCGGGCTCTTTTGCA       	8	3	0
GGCGTAAAAGCCGGGCTTTTTTTGTGCCAAGA	8	23	1
TTCTTTACTCCAGTGCTTTTTATTGATAAAAT	9	40	1
CTCAGCCTCTCTGGACTGTTTTAAAGAATCTA	10	139	0
GCTCTGGCAGGAGGGGTTTTTTCTTCTATATG	10	232	1
AAAAAAACCTCTTTGCTTTTTTACGCAAAGAG	11	95	0
CTATCTTAGACCGGGGTTTTTTTTCAGCCTTA	12	99	1
GTAACACAACCAGTTCTATTTTCAACAGTTTA	13	107	0
          * ***** ****
MAP Score: 25.8149

Motif 2
TTATACTGTAGAAAAAAGGAGTGAGGGAAC       	1	43	1
        AACAAAAAAGGACAGCCTGACATGTGAGG	2	2	1
AGAGCACTATGAAAAAGAAATTGCTTGCATTCGCGCT	3	30	1
ATTTCAGCCGCATAAAAAAACAGGCTGACCGCG    	5	6	0
GAATTCCGCTCAAAAAAAATCAGCACGACTCCAGCAC	5	65	0
AAATTCAGATGAAAAAACGGTTGAAAGGGACAGTCAT	7	21	1
TGCTCAAGAGGAAAAAGTGTATGCTTGCTTTTTCTAA	7	183	1
CCTCTCATCCCATAAGGGACGAGAAAGCTTATCTCGC	7	232	0
TTTATTTTCTGAAAAAATGCAGTGGAGGAATGAAA  	7	275	1
ACTCTTGGCACAAAAAAAGCCCGGCTTTTACGCCGGG	8	20	0
GAAAACCTCAGAAAAAACGGTTGACAGAGGGTTTCTT	10	77	1
AACAAAGGCCCAAAAAGTATTCGGCAGGTCTTTGTAT	11	56	1
GCCTTAAGTTGAAAAGAGAGGGGAAAGAAC       	12	125	1
TGTTTTTATAGAAAAGGAGAATGCGCT          	13	0	0
GTAAACTGTTGAAAATAGAACTGGTTGTGTTACATAA	13	106	1
          ******* *   *   *
MAP Score: 24.6122

Motif 3
TAGACCGGGGTTTTTTTTCAGCCTTAAGTTG	12	105	1
CCTCACTCCTTTTTTCTACAGTATAACGTAA	1	38	0
CAAAGAGGTTTTTTTATACAGTCATTGAGTC	11	112	1
ATATTTAATATTTTTATTCATTTATAAATTT	5	114	0
ATTGAATTAATTTTTATTCATGTTATAATGT	5	148	1
CGCATCAACGTTTTTGTGCTGGAGTCGTGCT	5	50	1
GTCGTGCTGATTTTTTTTGAGCGGAATTCCC	5	73	1
TCAGCCTGTTTTTTTATGCGGCTGAAATGCG	5	15	1
CCTCTTTGCTTTTTTACGCAAAGAGGCATAC	11	89	0
CAGGAGGGGTTTTTTCTTCTATATGAACTGT	10	239	1
AGCCGGGCTTTTTTTGTGCCAAGAGTGACAT	8	31	1
CTGTCAACCGTTTTTTCTGAGGTTTTCGATT	10	73	0
          TTTTTTTTCGATATAAAGGCA	6	0	1
ATTTATAAATTTTCTGTTCAATGGGAATTCC	5	95	0
TAAAAATGAATTTTTATGCCTTTATATCGAA	6	16	0
TGAGGCTGTCCTTTTTTACAGCTGAAAGGA 	2	34	1
ACTCCAGTGCTTTTTATTGATAAAATGCATA	9	46	1
TGACAGAGGGTTTCTTTTCTGAAATAATAAA	10	98	1
AAGCATACACTTTTTCCTCTTGAGCATCGTA	7	178	0
 TAGATCACCTTTTTAAGCAATCCAGAGAGG	11	9	1
TTAACCAATGTTTTTATAGAAAAGGAGAATG	13	14	0
TTTCAACCGTTTTTTCATCTGAATTTATGAA	7	16	0
AAAAGCCCGGCTTTTACGCCGGGCTCTTTTG	8	12	0
CTCCACTGCATTTTTTCAGAAAATAAAAAAA	7	271	0
          ***** *****
MAP Score: 19.0136

Motif 4
GATTATGGTTATCCTAAGGAGGGGCACATT  	0	100	1
AGGACAGCCTGACATGTGAGGCTGTCCTTTTT	2	18	1
AATTTCACAAAGACCAAGAGGGTGAACTTGTT	5	184	1
TTAATTATTCATCAAGAGGTGGGCTGTTAG  	6	50	1
CTTCATAGCGACCCGGAGATGGTGAGAGTCCG	7	71	1
CGTCCCTTATGGGATGAGAGGGCTTTTTTTAT	7	248	1
TTCTGAAAAAATGCAGTGGAGGAATGAAA   	7	281	1
CTTTAAAACAGTCCAGAGAGGCTGAGAAGGAT	10	145	1
GAGGGGTTTTAGGACAAGGTGCGCGCCTATAC	10	197	0
CCTCCTGCCAGAGCATAGAGGGGTTTTAGGAC	10	214	0
TCTATGCTCTGGCAGGAGGGGTTTTTTCTTCT	10	227	1
TCTTCTATATGAACTGTGAGGTGTCACACA  	10	253	1
TTTTTAAGCAATCCAGAGAGGTTGCAAAGAGG	11	19	1
CAGAGAGGTTGCAAAGAGGTGCACAACAAAGG	11	32	1
TTGCTTTTTTACGCAAAGAGGCATACAAAGAC	11	83	0
TTGCGTAAAAAAGCAAAGAGGTTTTTTTATAC	11	99	1
TTTAATGAAAGTCCAGAGAGGCTTGGAAGGGT	12	15	1
TGGAAGGGTTATGAAGAGAAGGAAGCTTCAAT	12	38	1
GCCTTAAGTTGAAAAGAGAGGGGAAAGAAC  	12	125	1
TGTGTTACATAAACTGACATGGAAAATCGTCA	13	131	1
GAAAATCGTCATCCTGACATGGGGGGATCAAT	13	152	1
          * ** *******
MAP Score: 16.8517

Motif 5
CTTAGATTTTGCTTGTTTTGCCTTACTTACAGT	0	26	1
ATTAACAAGAGCTGAATTTACGTTATACTGTAG	1	21	1
CACATGTCAGGCTGTCCTTTTTTGTT       	2	3	0
GACATGTGAGGCTGTCCTTTTTTACAGCTGAAA	2	28	1
TGCTCTCCCTGCTGTTTTTATGACCA       	3	3	0
AATTAAAATGGCTGACATTATCACAAAGCAGC 	4	22	1
  CGCGGTCAGCCTGTTTTTTTATGCGGCTGAA	5	8	1
CTGGAGTCGTGCTGATTTTTTTTGAGCGGAATT	5	68	1
GTCCGGGATGGCCGGAATCATGTAGATCAGCCC	7	98	1
AAAAGTGTATGCTTGCTTTTTCTAAAAGGGTGG	7	195	1
GGATGAGAGGGCTTTTTTTATTTTCTGAAAAAA	7	259	1
CGGCTTTTACGCCGGGCTCTTTTGCA       	8	3	0
CGGCGTAAAAGCCGGGCTTTTTTTGTGCCAAGA	8	22	1
TCCAAGCCTCTCTGGACTTTCATTAAAAGGTT 	12	9	0
TCTATCTTAGACCGGGGTTTTTTTTCAGCCTTA	12	98	1
          *****  **** *
MAP Score: 8.61956

Motif 6
ACAGCCTCACATGTCAGGCTGTCCTTTTTTG	2	12	0
ACAGCCTGACATGTGAGGCTGTCCTTTTTTA	2	21	1
GCCGCATAAAAAAACAGGCTGACCGCG    	5	6	0
GCCTGTTTTTTTATGCGGCTGAAATGCGGCA	5	18	1
TTCACAAAGACCAAGAGGGTGAACTTGTT  	5	187	1
TAATTATTCATCAAGAGGTGGGCTGTTAG  	6	51	1
AGCAAGGAAACTAAAGGGCTGATCTACATGA	7	115	0
CTTGCTTTTTCTAAAAGGGTGGTACCGCGAG	7	206	1
AAACCTCAGAAAAAACGGTTGACAGAGGGTT	10	79	1
TAAAACAGTCCAGAGAGGCTGAGAAGGATAA	10	148	1
ATGCTCTGGCAGGAGGGGTTTTTTCTTCTAT	10	230	1
TCTATATGAACTGTGAGGTGTCACACA    	10	256	1
TTAAGCAATCCAGAGAGGTTGCAAAGAGGTG	11	22	1
CGTAAAAAAGCAAAGAGGTTTTTTTATACAG	11	102	1
TGAAAGTCAACAATCAGGGGGAAATCATC  	11	152	1
AATGAAAGTCCAGAGAGGCTTGGAAGGGTTA	12	18	1
CCTTAAGTTGAAAAGAGAGGGGAAAGAAC  	12	126	1
          * *********
MAP Score: 6.12269

Motif 7
          GAAAAGCTCCTTTAACCTTA	0	0	1
         AACAAAAAAGGACAGCCTGAC	2	1	1
    TGGTCATAAAAACAGCAGGGAGAGCA	3	6	1
TGACATTATCACAAAGCAGC          	4	34	1
CAGCCGCATAAAAAAACAGGCTGACCGCG 	5	9	0
CGACTCCAGCACAAAAACGTTGATGCGGTG	5	47	0
AAATAATTTCACAAAGACCAAGAGGGTGAA	5	180	1
AAATTCAGATGAAAAAACGGTTGAAAGGGA	7	21	1
TCAGAAAATAAAAAAAGCCCTCTCATCCCA	7	257	0
         TGCAAAAGAGCCCGGCGTAAA	8	1	1
CTTGGCACAAAAAAAGCCCGGCTTTTACGC	8	24	0
TTTTATCAATAAAAAGCACTGGAGTAAAGA	9	41	0
GAAAACCTCAGAAAAAACGGTTGACAGAGG	10	77	1
TTATTTCAGAAAAGAAACCCTCTGTCAACC	10	95	0
TCCTGCCAGAGCATAGAGGGGTTTTAGGAC	10	214	0
CATATAGAAGAAAAAACCCCTCCTGCCAGA	10	234	0
CAGAGAGGTTGCAAAGAGGTGCACAACAAA	11	32	1
GAGGTGCACAACAAAGGCCCAAAAAGTATT	11	47	1
AAAGAGGCATACAAAGACCTGCCGAATACT	11	71	0
GCTTTTTTACGCAAAGAGGCATACAAAGAC	11	83	0
GCGTAAAAAAGCAAAGAGGTTTTTTTATAC	11	101	1
GAAGGGTTATGAAGAGAAGGAAGCTTCAAT	12	40	1
TAAGGCTGAAAAAAAACCCCGGTCTAAGAT	12	101	0
CTTAAGTTGAAAAGAGAGGGGAAAGAAC  	12	127	1
TATTACATCAGCAAAACCGCTAGAATTCCT	13	62	0
          **********
MAP Score: 4.07186