AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_sum_all106_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944235375
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ygaG	300	similar to transcriptional regulator (Fur family)
#1	lysA	105	diaminopimelate decarboxylase
#2	spoVAA	121	mutants lead to the production of immature spores (stage V sporulation)
#3	spoIIAA	95	anti-anti-sigma factor (antagonist of SpoIIAB)
#4	dacF	154	D-alanyl-D-alanine carboxypeptidase (penicilin binding protein)
#5	drm	160	phosphodeoxyribomutase
#6	ripX	300	integrase/recombinase
#7	yqkL	112	similar to transcriptional regulator (Fur family)
#8	spoIIM	100	spoIIM
#9	yqkK	99	yqkK
#10	yqkI	140	similar to Na+/H+ antiporter
#11	ansB	44	L-aspartase
#12	ansA	181	L-asparaginase
#13	yqfV	137	similar to transcriptional regulator (Fur family)
#14	yqfU	115	similar to hypothetical proteins from B. subtilis
#15	yutL	122	similar to diaminopimelate epimerase
#16	yutK	136	similar to Na+/nucleoside cotransporter
#17	yuzB	262	yuzB

Motif 1
CGCTTGGAAAAAATAAAAAGGATTATGAAAT	4	119	1
ATAGACGTATAGAAAAAAAGGAGGCTTTCAA	5	138	1
AATGGATCAGGATGAAAAAGGCGGATGGTTC	6	236	1
TTACTATGAAAATAAAAAAGGGAGTGATCAC	9	78	1
TGTACGGCAAAATAAAAAAGGGCCTGTCCAG	16	20	0
CTGTCGCTCTAAACAAAAAAGCCGCAGCCAC	5	16	0
ATCAGCTCAAGGTGAAAAAGGAGCGGAAGTT	12	11	0
TGTCAACGGGAATGAAAACGGTTTATACTTG	5	82	1
ATAAACTGATAAATAAAATGGTTTTCTTTTA	7	19	0
TATCTGCAGTAAAGAAAATGGCTTGCTGGAC	13	48	1
CATGTATGAAAAAGAAAATGGCAGCTGTCTG	13	78	0
ACAATGATAAGAAAAAAACAGCACCTGCTAC	9	32	0
ATCCATAAGCGGAGAAAGAGGGAATGACA  	1	86	1
CTTCTTTATCAATTAAAAAAGTGGAACGCTC	0	68	0
TAGCATAATAGAACAAAGCGGTAAAACCGGT	6	130	0
TCCCCGTTTTGGTAAAAAAAGATCAACCGGT	6	268	0
AGAGCGGGCGGGAGGAAACGGT         	8	88	1
TACTAAGAAAAAGAAAAAAAGTTGGAGGCAC	15	99	1
TTCTTAAGCAAAGCGAAAAGGGGGACCCTTC	13	116	1
TAACCAGCAAAGAGAAAGAAGGTTAAAGATT	11	23	1
TAGATTGTATGAAAGAAACAGAAAAACATGC	8	42	0
ACTATTCGTCAAAGACAACGGATGATTCAAA	17	201	0
          *** *******
MAP Score: 21.5887

Motif 2
ATAAAACTGTCCTTTCATCCATAAGCGGAG	1	70	1
GATTTTGTTCTCATTCATCCGCTCGAAAAG	2	59	0
AGTATAAACCGTTTTCATTCCCGTTGACAA	5	81	0
TGCATTGAAAGTTTTCATCCTGTTTACCGG	6	105	1
ACCGATGATAGTTTTCATACTCTTGATTCA	6	170	0
GAGCTTCCGGTTTATCATACCGATGATAGT	6	188	0
ACCATCCGCCTTTTTCATCCTGATCCATTT	6	235	0
TTTTTCTGTTTCTTTCATACAATCTATTAA	8	47	1
TGTAAACAGCTTATTCATCCGACTATTCGG	10	39	0
TGCCATTTTCTTTTTCATACATGTGATACG	13	86	1
TTATCCCCCGTTTTTCATACATAAAAGCTC	15	39	0
GCTTATAATAGCTTTTATACTAAGAAAAAG	15	82	1
TAAAAAAATATCTTTTATACGATAACAATA	16	87	0
CTTCAATGTATCTATCATACTCTTCGGATT	17	24	0
          **********
MAP Score: 20.0989

Motif 3
GAAAAACTTCGGAAAAGAGTATATGGGAATCGAGC	0	37	1
ATTAAAGAATGGAGAAAAGTAAAAGTAAAGGACCA	0	107	1
CATCACGCTTGGAAAAAATAAAAAGGATTATGAAA	4	114	1
TACAATAGACGTATAGAAAAAAAGGAGGCTTTCAA	5	134	1
CCATGACTCATTATAACAAAATACGCGCAGAGTTC	7	64	0
ATCATTACTATGAAAATAAAAAAGGGAGTGATCAC	9	74	1
TAGGGATGAGGAAGTATAGTATACGTGTTGCACTA	10	72	1
CCCCCTTCATGTAAAAGCTAAAACGCTTTCAATAT	10	108	0
TTATAGACACGGAAAATAAAATACGCAAGACATTA	12	83	0
CCCATAAAATGAATAAAAGTAAATGAAAGC     	13	5	0
AATTTTATCTGCAGTAAAGAAAATGGCTTGCTGGA	13	43	1
TTTATACTAAGAAAAAGAAAAAAAGTTGGAGGCAC	15	95	1
CTTTTGTACGGCAAAATAAAAAAGGGCCTGTCCAG	16	20	0
          * * ** * **** *
MAP Score: 18.5597

Motif 4
GCTCGATTCCCATATACTCTTTTCCGAAGTTTT	0	39	0
      CCGTCATGCACCTCTCTTCTAAAAAAA	0	283	0
       TGTCATTCCCTCTTTCTCCGCTTATG	1	89	0
CCCTCCATTTCATAATCCTTTTTATTTTTTCCA	4	123	0
     CTTGAAAGCCTCCTTTTTTTCTATACGT	5	142	0
CCGGTCGAACCATCCGCCTTTTTCATCCTGATC	6	240	0
  TCTTGATCTACTCCCCGTTTTGGTAAAAAAA	6	279	0
AACAGAAAAACATGCCCTTTTTCAAAAAGAAAC	8	24	0
CCTGTCGTAGCAGGTGCTGTTTTTTTCTTATCA	9	26	1
     GTGATCACTCCCTTTTTTATTTTCATAG	9	81	0
        ACCATGCACCTCTTCACTGTATCTA	12	166	0
AGACAGCTGCCATTTTCTTTTTCATACATGTGA	13	79	1
         AAAATCTCCTTTCCTGCAATAACT	14	101	0
ACAATACAATTATCCCCCGTTTTTCATACATAA	15	45	0
AGGGCCTGTCCAGGCCCTTTTCT          	16	0	0
AGGGCCTGGACAGGCCCTTTTTTATTTTGCCGT	16	15	1
          **  * *******
MAP Score: 13.9129

Motif 5
CCATTTTATTTATCAGTTTATAATAATTATAGTTGG	7	29	1
TGAGAAATAATATGTTACGATAATAAATTTTGAATC	17	173	1
GTTGACAATGTATTTGGAAATAATGAGAAACTTCAA	5	53	0
TCCTCCTTGATATGATCGGATAATGAGTGTTTCGAT	3	63	0
ACTCTGCGCGTATTTTGTTATAATGAGTCATGGAAT	7	66	1
ATAAAATGGTTTTCTTTTAATAATGATT        	7	2	0
CAGATAAAATTATACCCATAAAATGAATAAAAGTAA	13	18	0
GATTCACCCATATCATAGCATAATAGAACAAAGCGG	6	140	0
CGTTCCACTTTTTTAATTGATAAAGAAGGCCGGCTC	0	71	1
TAATAGCTTTTATACTAAGAAAAAGAAAAAAAGTTG	15	87	1
TGTGTCAGTGTTTAATGGTAAAATAGATTTATAATG	14	55	1
TGTTTCGAATTTTGGGCATAAAAAAAGACAGCTGTG	4	54	0
CTACTCCCCGTTTTGGTAAAAAAAGATCAACCGGTC	6	267	0
TATCCCCCGTTTTTCATACATAAAAGCTCCTTGCAC	15	32	0
TTATCATTACTATGAAAATAAAAAAGGGAGTGATCA	9	72	1
AATGCAATTATAGACACGGAAAATAAAATACGCAAG	12	89	0
TTTAGTTCTTTTGTACGGCAAAATAAAAAAGGGCCT	16	26	0
AAATATCTTTTATACGATAACAATAATATTTTTTGA	16	76	0
ACCATCACGCTTGGAAAAAATAAAAAGGATTATGAA	4	112	1
CCCTCAAAGATATGTCTGAAAAGTAAATCTCTATGA	0	162	1
          ***      *******
MAP Score: 7.97878

Motif 6
CCGGTTGATCTTTTTTTACCAAAACGGGGAGTAGATC	6	269	1
ATCTCTATTGTTTCTTTTTGAAAAAGGGCATGTTTTT	8	15	1
CTTTTTTTCTTTTTCTTAGTATAAAAGCTATTATAAG	15	83	0
CAGCTGCCATTTTCTTTTTCATACATGTGATACGTTC	13	82	1
GCAGGCTAGCTTTTTTGTGCAAAAGCGTGGTAATTTA	2	18	1
TGTTTTTCTGTTTCTTTCATACAATCTATTAAATCAA	8	45	1
CCTCTTAAATTTTATTTAAAAAAATATCTTTTATACG	16	96	0
ATGTAAGAATTTTTTTTAGAAGAGAGGTGCATGACGG	0	273	1
CATAATCCTTTTTATTTTTTCCAAGCGTGATGGTTTT	4	109	0
GCAGGTGCTGTTTTTTTCTTATCATTGTTCAATTTTG	9	35	1
GCAAGGAGCTTTTATGTATGAAAAACGGGGGATAATT	15	34	1
AATAAAATGGTTTTCTTTTAATAATGATT        	7	2	0
AGCCATTTTCTTTACTGCAGATAAAATTATACCCATA	13	34	0
CTCATAGAGATTTACTTTTCAGACATATCTTTGAGGG	0	162	0
TGGCTGCGGCTTTTTTGTTTAGAGCGACAGAAAATAT	5	17	1
GTTCCACTTTTTTAATTGATAAAGAAGGCCGGCTCAT	0	72	1
          *** ***   * **  *
MAP Score: 5.81249

Motif 7
GGAAGCTGAAGAAAAACTTCGGAAAAGAGT	0	27	1
TCGACGGAATGAATTCCTTCACCGTGACAA	3	32	0
CAGTGGCGTATAAAACCATCACGCTTGGAA	4	98	1
          TAAAACCTTTCTGATTTGGC	6	0	1
TAAACAGGATGAAAACTTTCAATGCATCGA	6	101	0
TCAAGAGTATGAAAACTATCATCGGTATGA	6	174	1
ATTATTAAAAGAAAACCATTTTATTTATCA	7	14	1
TGCGAAAAGCGAATACCTTCTCGCAACCCA	12	132	1
          **********
MAP Score: 1.75823