AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_sum_all112_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944235634
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ykvJ	300	similar to hypothetical proteins
#1	spoVK	300	alternate gene name: spoVJ; disruption leads to the production of immature spores (stage V sporulation)
#2	ynbA	220	similar to GTP-binding protein protease modulator
#3	ynbB	187	similar to hypothetical proteins
#4	glnR	110	transcriptional regulator
#5	glnA	60	glutamine synthetase
#6	nrgA	281	ammonium transporter

Motif 1
CTGACTTTTTTATTGTCAAGAAAAACATCATTATGGT	0	56	1
CCGGCGTTTTTATTGCGGAGAAGGAGAGGAATC    	0	277	1
AAATCAGCCCGTTGTATGAAAAAGAAATAATGAGAAA	1	58	1
ATTCCTTATTGTTCCCGAAAAAAGCAATTGTTTCGAC	1	206	1
TACTGCCCAATATGCAAAAGAAAGGAACATCCATTTG	2	109	1
AACAAGAAACGATTCAGGAGAAAGCCATTTTAGTCGG	2	150	1
CCGCTTCTATTTTAATGAAGAAAATGAACAGTATGAC	3	83	1
CATATCCGGCTATGTCCAAGAAGAGCAAAGTATCATC	3	119	1
ATTAAAGAAGTATATGTAGGAAGGAAATATAAAGAC 	3	161	1
AAACTATTCATATGAGCTGAAAAGGGAATTGACATTA	6	70	0
CAAAGTCTTATATCGCAAAAAATGCCATTCTCCTTCC	6	119	1
GTTATCGAGGGATGGAAAGGAAGGAGAATGGCATTTT	6	137	0
TCCTGACATGGTTTTTGAGAAATGTTATCGAGGGATG	6	160	0
CTTCATTATAGAGAAAAAAGAATGATAAAACATTTTC	6	207	0
CTTTTTTCTCTATAATGAAGAAATATAATAATTGCTT	6	224	1
TATTCTGAAAGATACGGAGGAATGAGAC         	6	263	1
          ***    ***** *  *
MAP Score: 15.7743

Motif 2
TTTTATTGTCAAGAAAAACATCATTATGGT	0	63	1
TATTGCGGAGAAGGAGAGGAATC       	0	287	1
          AAGAAAAACACTTCAGGTAT	1	0	1
AGCCCGTTGTATGAAAAAGAAATAATGAGA	1	63	1
AAAAGAAATAATGAGAAAGAAGCTCACTAT	1	77	1
CCAATATGCAAAAGAAAGGAACATCCATTT	2	115	1
CGATTTGATTCTGGAAAGGAGCTTCCCTTC	3	39	0
TATTTTAATGAAGAAAATGAACAGTATGAC	3	90	1
GGCTATGTCCAAGAAGAGCAAAGTATCATC	3	126	1
AAACTAAGTTAAGAAAAGGAGGAAATTGAG	4	90	1
TTTACCTTTTAAGAGGAGGAATTTTACCAA	5	40	1
TTATCGAGGGATGGAAAGGAAGGAGAATGG	6	143	0
ATCTTTCAGAATAAAAAGCAATTATTATAT	6	246	0
          **********
MAP Score: 13.6747

Motif 3
TAGGAACCGGGGACTGACTTTTTTATTGTCAAGA	0	43	1
TCTTACCATAATGATGTTTTTCTTGACAATAAAA	0	63	0
CCCGCATATCGCACGGATTTTCTTCAATTTTTTC	0	107	0
GTATCCTTGGATACGGCCTTTTTTATGTTTTTCT	0	184	1
ACCTTCCGAAAAAAGGTGTTTTTTTGCGTGAATT	0	223	1
TAAGATACCTGAAGTGTTTTTCTT          	1	0	0
TCAGAGTATTATAGTGAGCTTCTTTCTCATTATT	1	83	0
TTCCCGAGAAATACTTTATTTCTTATTGTATTCA	1	164	0
ATGTGTCGAAACAATTGCTTTTTTCGGGAACAAT	1	213	0
CGTTCAAATGGATGTTCCTTTCTTTTGCATATTG	2	116	0
ACATCCGACTAAAATGGCTTTCTCCTGAATCGTT	2	157	0
CACCGATGATACTTTGCTCTTCTTGGACATAGCC	3	126	0
AAAGGAAGGAGAATGGCATTTTTTGCGATATAAG	6	125	0
          * * **  ******
MAP Score: 10.7558

Motif 4
GAACCGGGGACTGACTTTTTTATTGTCAAGAAAAA	0	46	1
TCTTACCATAATGATGTTTTTCTTGACAATAAAAA	0	62	0
GTGCGATATGCGGGAGAGGTTCTAGCTACACCCTC	0	127	1
ATGTCTCTCGCCGGCGTTTTTATTGCGGAGAAGGA	0	267	1
TTTTCATACAACGGGCTGATTTTTGTACGAAACGT	1	45	0
CGGGAAAGCGCAGGATTCCTTATTGTTCCCGAAAA	1	192	1
CAGTTTTTGAGAGGTCTGTTTTTTGCTCGTATTTC	2	16	1
TGGCTTTCTCCTGAATCGTTTCTTGTTCGTTCAAA	2	142	0
CCGCATATCACGGATGAGCATTTTGAAAATTCT  	2	197	1
ACCATCGTTTCCGATTTGATTCTGGAAAGGAGCTT	3	45	0
GTAAGATTTCCTGACATGGTTTTTGAGAAATGTTA	6	170	0
          * **  ** ** ***
MAP Score: 10.2624

Motif 5
TTTTTTATTGTCAAGAAAAACATCATTATGGTAAGATA	0	61	1
ATAGCAGAAGTGAAAAAATTGAAGAAAATCCGTGCGAT	0	96	1
TACACCCTCTATAAAAAACTAAGGACGAGCTGTATCCT	0	153	1
CGGAAGGTGCTCTAGAAAAACATAAAAAAGGCCGTATC	0	193	0
          AAGAAAAACACTTCAGGTATCTTAGGGC	1	0	1
AGCCCGTTGTATGAAAAAGAAATAATGAGAAAGAAGCT	1	63	1
CGTGAATACAATAAGAAATAAAGTATTTCTCGGGAAAG	1	162	1
CCCAATATGCAAAAGAAAGGAACATCCATTTGAACGAA	2	114	1
ATTTGAACGAACAAGAAACGATTCAGGAGAAAGCCATT	2	141	1
TCTATTTTAATGAAGAAAATGAACAGTATGACATATCC	3	88	1
CATCAAATCCAGGAGAAATTTTTAAAAAAT        	4	2	0
TGAAACTAAGTTAAGAAAAGGAGGAAATTGAG      	4	88	1
TTGTATCTATAAAAGAAACTATTCATATGAGCTGAAAA	6	84	0
TTATAGAGAAAAAAGAATGATAAAACATTTTCATGTAA	6	201	0
TTCTCTATAATGAAGAAATATAATAATTGCTTTTTATT	6	229	1
          * ******   *  *  *
MAP Score: 9.75378

Motif 6
ACTTTTTTATTGTCAAGAAAAACATCATTATGG	0	59	1
AAGTGAAAAAATTGAAGAAAATCCGTGCGATAT	0	103	1
TGCTCTAGAAAAACATAAAAAAGGCCGTATCCA	0	191	0
CGGCGTTTTTATTGCGGAGAAGGAGAGGAATC 	0	278	1
AATCAGCCCGTTGTATGAAAAAGAAATAATGAG	1	59	1
ATGAAAAAGAAATAATGAGAAAGAAGCTCACTA	1	73	1
TTCCTTATTGTTCCCGAAAAAAGCAATTGTTTC	1	207	1
ACAAATCGATTGCTTTGAAAAGGCGGAAATACG	2	43	0
ACTGCCCAATATGCAAAAGAAAGGAACATCCAT	2	110	1
ACAAGAAACGATTCAGGAGAAAGCCATTTTAGT	2	151	1
CTTCTATTTTAATGAAGAAAATGAACAGTATGA	3	86	1
TTAACATCAAATCCAGGAGAAATTTTTAAAAAA	4	11	0
AATGAAACTAAGTTAAGAAAAGGAGGAAATTGA	4	86	1
ACTATTCATATGAGCTGAAAAGGGAATTGACAT	6	72	0
AAAGTCTTATATCGCAAAAAATGCCATTCTCCT	6	120	1
AGGGATGGAAAGGAAGGAGAATGGCATTTTTTG	6	134	0
TCAGGAAATCTTACATGAAAATGTTTTATCATT	6	191	1
TTTCTTCATTATAGAGAAAAAAGAATGATAAAA	6	214	0
          **  * *******
MAP Score: 8.29233

Motif 7
GTAGCTAGAACCTCTCCCGCATATCGCACG	0	126	0
 GATTCCTCTCCTTCTCCGCAATAAAAACG	0	281	0
CTCATTATTTCTTTTTCATACAACGGGCTG	1	62	0
GGAATCCTGCGCTTTCCCGAGAAATACTTT	1	181	0
AAAAAACAGACCTCTCAAAAACTGAGAGGT	2	10	0
CGTATTTCCGCCTTTTCAAAGCAATCGATT	2	43	1
ATGTTCCTTTCTTTTGCATATTGGGCAGTA	2	109	0
       CGTCTTTTGAAGCACATGTGCCG	3	3	1
AAGGGAAGCTCCTTTCCAGAATCAAATCGG	3	40	1
TCAATTTCCTCCTTTTCTTAACTTAGTTTC	4	89	0
TACATTTTTACCTTTTAAGAGGAGGAATTT	5	34	1
ATGTCAATTCCCTTTTCAGCTCATATGAAT	6	72	1
CATTCTCCTTCCTTTCCATCCCTCGATAAC	6	144	1
          **********
MAP Score: 4.92465

Motif 8
ATTGCGGAGAAGGAGAGGAATC         	0	288	1
TCAGGTATCTTAGGGCGGGTAATACGTTTCG	1	22	1
ATTGCTTTGAAAAGGCGGAAATACGAGCAAA	2	37	0
TGTGCCGGCAAGTGAAGGGAAGCTCCTTTCC	3	26	1
CTTCTATTTTAATGAAGAAAATGAACAGTAT	3	86	1
GAAGTATATGTAGGAAGGAAATATAAAGAC 	3	167	1
TAAGTTAAGAAAAGGAGGAAATTGAG     	4	94	1
TTACCTTTTAAGAGGAGGAATTTTACCAA  	5	41	1
AATGTTATCGAGGGATGGAAAGGAAGGAGAA	6	146	0
ATTTCTTCATTATAGAGAAAAAAGAATGATA	6	217	0
TTCTGAAAGATACGGAGGAATGAGAC     	6	265	1
          ** ********
MAP Score: 2.57617