AlignACE 3.0 10/20/99
AlignACE2 -i EC_operons064_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943442346
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	queA	92	synthesis of queuine in tRNA; probably S-adenosylmethionine:tRNA ribosyltransferase-isomerase
#1	tgt	55	tRNA-guanine transglycosylase
#2	yajC	22	orf, hypothetical protein
#3	secD	27	protein secretion; membrane protein, part of the channel
#4	ybaN	69	putative gene 58
#5	apt	152	adenine phosphoribosyltransferase
#6	relA	47	(p)ppGpp synthetase I (GTP pyrophosphokinase); regulation of RNA synthesis; stringent factor
#7	ygcA	56	putative enzyme
#8	dsbC	24	protein disulfide isomerase II
#9	xerD	111	site-specific recombinase
#10	gmk	251	guanylate kinase
#11	rpoZ	54	RNA polymerase, omega subunit
#12	yihV	161	putative kinase
#13	yihX	77	putative phosphatase

Motif 1
GCAACCTTTACCCCCTTTTGGATAGAATAT	0	15	0
TAGACTACCCGCCTCTTATTTTAGTCTGAG	0	64	1
TAAAACGTTGGACTGTTTTTCTGACGTAGT	1	26	1
     TAAATTTCCCTCATTATTAATA   	2	7	0
        CGTCCTCTCCTTTAGGGACCAG	6	35	0
      GGAGTTCCGTTATGGGACAATTAA	7	4	1
    AAATCTTCCCGTTCTTTTCAGACA  	8	8	0
GCCCCTTATGGTCACTCATTTGATCCATTA	9	87	0
      TTGCGCCCCTTATGGTCACTCATT	9	97	0
TCCTCGCAGACTCCGTTTTTGCCACTCGGC	10	56	0
TTCCGCATTTGCCTGTCATTCACTGCAATA	10	106	0
AGCCCTTGCTCACACTTTTTGCGCAAAGTT	10	156	0
CAGTATCATGCCCAGTCATTTCTTCACCTG	11	19	1
        AACCCTCTCCTGAATACAGTTA	12	2	1
ATACAGTTATGTCACTTTTTGTCATTTATG	12	23	1
TGCTTTGCTTGTCTGTTTTTGATCGTATTT	12	56	1
ATTGACAGCCGTCACTTTTTAAACAATTGG	12	104	1
          **********
MAP Score: 11.0624

Motif 2
CGATTATATTCTATCCAAAAGGGGGTAAAGGTT	0	10	1
CCAGTACATTCTGGCGTTTTCGAGCACAGGCGC	5	45	1
GGGACCAGACCTGCCGAAATCGGCAAATCGCAA	6	10	0
       TGTCTGAAAAGAACGGGAAGATTT  	8	3	1
CGATTCTGCTGTGGCTTTTGCGGCTAGTGTATC	9	23	1
TTATTGTGCCGTGACTAAAGCGATTCTGATACA	9	50	0
GATCAAATGAGTGACCATAAGGGGCGCAA    	9	92	1
ATCTGCCTGACTATCTACAGCGGAG        	10	2	0
GCAAAGCCGAGTGGCAAAAACGGAGTCTGCGAG	10	51	1
CAGTGAATGACAGGCAAATGCGGAAGCAGCTAC	10	111	1
          *** * * *****
MAP Score: 7.99104

Motif 3
AAAGCCGAGTGGCAAAAACGGAGTCTGCGAG	10	53	1
GAAGCAGCTACGCAAAACGCAACAACTTTGC	10	133	1
ATACACTAGCCGCAAAAGCCACAGCAGAATC	9	24	0
GGCACAATAAGGCATAATGGATCAAATGAGT	9	73	1
GTGAATGACAGGCAAATGCGGAAGCAGCTAC	10	113	1
CAAAAGCCACAGCAGAATCGAGAAGCTTACG	9	12	0
TGCCGAAATCGGCAAATCGCAA         	6	1	0
ACGTGATGAAAGCAAAGCCGAGTGGCAAAAA	10	40	1
AACAACTTTGCGCAAAAAGTGTGAGCAAGGG	10	153	1
CCTTAATTGTCCCATAACGGAACTCC     	7	5	0
CTTGCCACATAGCCAAACCCATCCTTTCCCG	13	40	1
CAAATGAGTGACCATAAGGGGCGCAA     	9	95	1
TTATATTCTATCCAAAAGGGGGTAAAGGTTG	0	13	1
GCTCGAAAACGCCAGAATGTACTGGCTGTAC	5	39	0
          ******* ***
MAP Score: 5.87712

Motif 4
TCAGACTAAAATAAGAGGCGGGTAGTCTAGTG	0	61	0
AACGTTTTAAACCAGCGCCGCGGAA       	1	3	0
       AGCACAACAATCGCAGTTGCAATTA	5	3	1
GGCGTTTTCGAGCACAGGCGCAGGCGGTCAAA	5	57	1
CAAAAGCCACAGCAGAATCGAGAAGCTTACGT	9	11	0
CGGCTAGTGTATCAGAATCGCTTTAGTCACGG	9	43	1
ACGTGATGAAAGCAAAGCCGAGTGGCAAAAAC	10	40	1
AAAGCCGAGTGGCAAAAACGGAGTCTGCGAGG	10	53	1
GTGAATGACAGGCAAATGCGGAAGCAGCTACG	10	113	1
CAAATGCGGAAGCAGCTACGCAAAACGCAACA	10	125	1
TATTTCGCTAATCACATACGAAAGATACTC  	10	231	1
TACAAATACGATCAAAAACAGACAAGCAAAGC	12	57	0
          ******  ****
MAP Score: 4.57405

Motif 5
TAGTGCCGGGGCGCTCTCCCTGCAACCTTTACCCCCTTT	0	27	0
     TTCCGCGGCGCTGGTTTAAAACGTTGGACTGTTT	1	5	1
TCGAGCACAGGCGCAGGCGGTCAAAGGTTAAACAACTGT	5	64	1
CGTTTAAAACGCGCCGTGAGTACCACCGTAACAAGCAGG	5	114	1
CTTCTCGATTCTGCTGTGGCTTTTGCGGCTAGTGTATCA	9	18	1
ATGCCTTATTGTGCCGTGACTAAAGCGATTCTGATACAC	9	49	0
        CTCCGCTGTAGATAGTCAGGCAGATATACAA	10	2	1
TCACATGGCCGCGCCGTGTATAATAAGCTCGTATGTAGG	10	189	1
TAAAAAGTGACGGCTGTCAATTTTTTGACGATAAATTAC	12	86	0
          **** ***  *     * *
MAP Score: 4.24239

Motif 6
CGTTGGACTGTTTTTCTGACGTAGTGGAGA	1	31	1
ACAACTGTTACTTTTGATACGTTTAAAACG	5	95	1
 CGTCCTCTCCTTTAGGGACCAGACCTGCC	6	28	0
  GGAGTTCCGTTATGGGACAATTAAGGTC	7	8	1
TCTTCCCGTTCTTTTCAGACA         	8	1	0
TCTGCTGTGGCTTTTGCGGCTAGTGTATCA	9	27	1
ATCAGAATCGCTTTAGTCACGGCACAATAA	9	53	1
GCAGACTCCGTTTTTGCCACTCGGCTTTGC	10	51	0
CCTGAATACAGTTATGTCACTTTTTGTCAT	12	18	1
         ATTTTTGTGACCGTTAACCTG	13	1	1
          **********
MAP Score: 2.88262

Motif 7
GCCCCGGCACTAGACTACCCGCCTCTTATTTT	0	54	1
CAACGTTTTAAACCAGCGCCGCGGAA      	1	4	0
          TAAATTTCCCTCATTATTAATA	2	10	0
ATTGTTATGCTAAAGTAGCCACTCTGTAAGCT	4	34	1
GCGATTCTGATACACTAGCCGCAAAAGCCACA	9	32	0
GATTTTCAGGAAGCGTCCTCGCAGACTCCGTT	10	69	0
TTGTTGCGTTTTGCGTAGCTGCTTCCGCATTT	10	126	0
AAGGGCTACGTCACATGGCCGCGCCGTGTATA	10	179	1
TTGTGACCGTTAACCTGGCTTCATACCTTGCC	13	14	1
ACCTGGCTTCATACCTTGCCACATAGCCAAAC	13	26	1
AGCCAAACCCATCCTTTCCCGCTACAGTTAAT	13	50	1
          **** * *****
MAP Score: 1.07039

Motif 8
       TTTTTCTCCACTACGTCAGAAAAACAGTCCAA	1	33	0
AAAGTAGCCACTCTGTAAGCTGACAACACTCAAT     	4	45	1
TGAGTACCACCGTAACAAGCAGGCATACACTT       	5	130	1
      GGAGTTCCGTTATGGGACAATTAAGGTCACACT	7	4	1
       TTGCGCCCCTTATGGTCACTCATTTGATCCAT	9	89	0
       CTCCGCTGTAGATAGTCAGGCAGATATACAAC	10	3	1
TAGCTGCTTCCGCATTTGCCTGTCATTCACTGCAATAAA	10	104	0
AATACAGTTATGTCACTTTTTGTCATTTATGACATGCTT	12	22	1
TGATCGTATTTGTAATTTATCGTCAAAAAATTGACAGCC	12	75	1
GTTAACCTGGCTTCATACCTTGCCACATAGCCAAACCCA	13	22	1
          ***  **    * **  **
MAP Score: 0.946635

Motif 9
GTTATGCTAAAGTAGCCACTCTGTAAGCTGACAACACTCA	4	37	1
TGTACGCAATAATTGCAACTGCGATTGTTGTGCT      	5	4	0
GCCAGTACATTCTGGCGTTTTCGAGCACAGGCGCAGGCGG	5	44	1
ATTTGCCGATTTCGGCAGGTCTGGTCCCTAAAGGAGAGGA	6	15	1
TCGATTCTGCTGTGGCTTTTGCGGCTAGTGTATCAGAATC	9	22	1
ATTTGATCCATTATGCCTTATTGTGCCGTGACTAAAGCGA	9	60	0
CTGTAGATAGTCAGGCAGATATACAACGTGATGAAAGCAA	10	15	1
AGCAAAGCCGAGTGGCAAAAACGGAGTCTGCGAGGACGCT	10	50	1
GCAGTGAATGACAGGCAAATGCGGAAGCAGCTACGCAAAA	10	110	1
AATGACAAAAAGTGACATAACTGTATTCAGGAGAGGGTT 	12	9	0
          *  ***   * **    ***
MAP Score: 0.496048