AlignACE 3.0 10/20/99
AlignACE2 -i EC_operons064_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943440989
 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	apt	152	adenine phosphoribosyltransferase
#5	relA	47	(p)ppGpp synthetase I (GTP pyrophosphokinase); regulation of RNA synthesis; stringent factor
#6	ygcA	56	putative enzyme
#7	dsbC	24	protein disulfide isomerase II
#8	xerD	111	site-specific recombinase
#9	gmk	251	guanylate kinase
#10	rpoZ	54	RNA polymerase, omega subunit
#11	yihV	161	putative kinase
#12	yihX	77	putative phosphatase

Motif 1
AGAAAAACAGTCCAACGTTTTAAACCAGCGC	1	17	0
GCCAGTACATTCTGGCGTTTTCGAGCACAGG	4	44	1
GTTAAACAACTGTTACTTTTGATACGTTTAA	4	90	1
GTGGTACTCACGGCGCGTTTTAAACGTATCA	4	109	0
TCGATTCTGCTGTGGCTTTTGCGGCTAGTGT	8	22	1
TGCGCAAAGTTGTTGCGTTTTGCGTAGCTGC	9	136	0
TAGCCCTTGCTCACACTTTTTGCGCAAAGTT	9	156	0
TCTTCACCTGTGGAGCTTTTTAAGT      	10	39	1
AATACAGTTATGTCACTTTTTGTCATTTATG	11	22	1
AAGTGACGGCTGTCAATTTTTTGACGATAAA	11	90	0
AATTGACAGCCGTCACTTTTTAAACAATTGG	11	103	1
          *** *******
MAP Score: 11.3885

Motif 2
TATATTCTATCCAAAAGGGGGTAAAGGTTG	0	14	1
TAAAATTTTTCCCTAAGGGAATTGCC    	3	11	1
GGTCTGGTCCCTAAAGGAGAGGACG     	5	32	1
CTTAATTGTCCCATAACGGAACTCC     	6	5	0
GCCGCAAAAGCCACAGCAGAATCGAGAAGC	8	17	0
AGTCACGGCACAATAAGGCATAATGGATCA	8	67	1
AAATGAGTGACCATAAGGGGCGCAA     	8	96	1
GCCTGACTATCTACAGCGGAG         	9	1	0
AGCCGAGTGGCAAAAACGGAGTCTGCGAGG	9	55	1
GAATGACAGGCAAATGCGGAAGCAGCTACG	9	115	1
TTAAAAAGCTCCACAGGTGAAGAAATGACT	10	32	0
TCATAAATGACAAAAAGTGACATAACTGTA	11	24	0
CAAATACGATCAAAAACAGACAAGCAAAGC	11	57	0
ACTTTTTAAACAATTGGTGAAATTAAAATG	11	117	1
          **********
MAP Score: 11.2927

Motif 3
ATCAAAAGTAACAGTTGTTTAACCTTTGACCGCCTG	4	77	0
TAAACAACTGTTACTTTTGATACGTTTAAAACGCGC	4	92	1
     GGAGTTCCGTTATGGGACAATTAAGGTCACA	6	5	1
CGTGACTAAAGCGATTCTGATACACTAGCCGCAAAA	8	38	0
ACTCATTTGATCCATTATGCCTTATTGTGCCGTGAC	8	68	0
TCATGCCCAGTCATTTCTTCACCTGTGGAGCTTTTT	10	24	1
TCTCCTGAATACAGTTATGTCACTTTTTGTCATTTA	11	15	1
TCACTTTTTGTCATTTATGACATGCTTTGCTTGTCT	11	34	1
GTGACGGCTGTCAATTTTTTGACGATAAATTACAAA	11	83	0
TTGACAGCCGTCACTTTTTAAACAATTGGTGAAATT	11	105	1
          *** ** **  **  *
MAP Score: 6.22055

Motif 4
TAAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCC	0	35	1
TTAACCTTTGACCGCCTGCGCCTGTGCTCGAAAACGCCA	4	56	0
CCTGCTTGTTACGGTGGTACTCACGGCGCGTTTTAAACG	4	114	0
GTGTATCAGAATCGCTTTAGTCACGGCACAATAAGGCAT	8	49	1
AGTGGCAAAAACGGAGTCTGCGAGGACGCTTCCTGAAAA	9	60	1
ATGACAGGCAAATGCGGAAGCAGCTACGCAAAACGCAAC	9	117	1
CTTTGCGCAAAAAGTGTGAGCAAGGGCTACGTCACATGG	9	158	1
          *  * *   **  **** *
MAP Score: 3.9481

Motif 5
AGCACAACAATCGCAGTTGCAATTATTGCGTACAGCCAGT	4	10	1
AAAGGTTAAACAACTGTTACTTTTGATACGTTTAAAACGC	4	86	1
TGCCTGCTTGTTACGGTGGTACTCACGGCGCGTTTTAAAC	4	115	0
CTTCTCGATTCTGCTGTGGCTTTTGCGGCTAGTGTATCAG	8	18	1
        CTCCGCTGTAGATAGTCAGGCAGATATACAAC	9	2	1
GTAGCTGCTTCCGCATTTGCCTGTCATTCACTGCAATAAA	9	104	0
ATAATAAGCTCGTATGTAGGCTTTATTTCGCTAATCACAT	9	208	1
       GAGTATCTTTCGTATGTGATTAGCGAAATAAAG	9	228	0
GTCATTTCTTCACCTGTGGAGCTTTTTAAGT         	10	33	1
TAAAAAGTGACGGCTGTCAATTTTTTGACGATAAATTACA	11	85	0
          *  * ** *   **  * **
MAP Score: 3.69287

Motif 6
GTAGTCTAGTGCCGGGGCGCTCTCCCTGCAACCTTTACCCCC	0	30	0
         TTCCGCGGCGCTGGTTTAAAACGTTGGACTGTT	1	1	1
GCGTTTTCGAGCACAGGCGCAGGCGGTCAAAGGTTAAACAAC	4	58	1
TTAGGGACCAGACCTGCCGAAATCGGCAAATCGCAA      	5	4	0
CGTGATGAAAGCAAAGCCGAGTGGCAAAAACGGAGTCTGCGA	9	41	1
AACGGAGTCTGCGAGGACGCTTCCTGAAAATCGTCTTTATTG	9	69	1
GAGCTTATTATACACGGCGCGGCCATGTGACGTAGCCCTTGC	9	177	0
GATGGGTTTGGCTATGTGGCAAGGTATGAAGCCAGGTTAACG	12	21	0
          **   * ***   *    ** *
MAP Score: 3.60176

Motif 7
GTAGTCTAGTGCCGGGGCGCTCTCCCTGCAACCTTTA	0	35	0
CGCAATAATTGCAACTGCGATTGTTGTGCT       	4	3	0
GCGTTTTCGAGCACAGGCGCAGGCGGTCAAAGGTTAA	4	58	1
TCTCGATTCTGCTGTGGCTTTTGCGGCTAGTGTATCA	8	20	1
GCCTTATTGTGCCGTGACTAAAGCGATTCTGATACAC	8	49	0
AAGCCGAGTGGCAAAAACGGAGTCTGCGAGGACGCTT	9	54	1
TGAATGACAGGCAAATGCGGAAGCAGCTACGCAAAAC	9	114	1
ATGTGACGTAGCCCTTGCTCACACTTTTTGCGCAAAG	9	158	0
TGTATAATAAGCTCGTATGTAGGCTTTATTTCGCTAA	9	205	1
          **   **** * **  *
MAP Score: 3.49972

Motif 8
CAGGCGCAGGCGGTCAAAGGTTAAACAACTGTTACT	4	71	1
GGTTAAACAACTGTTACTTTTGATACGTTTAAAACG	4	89	1
TGTAGATAGTCAGGCAGATATACAACGTGATGAAAG	9	16	1
CAGTGAATGACAGGCAAATGCGGAAGCAGCTACGCA	9	111	1
GTATCATGCCCAGTCATTTCTTCACCTGTGGAGCTT	10	21	1
AAAGTGACGGCTGTCAATTTTTTGACGATAAATTAC	11	86	0
AAATTGACAGCCGTCACTTTTTAAACAATTGGTGAA	11	102	1
          * **** ** *   **
MAP Score: 2.68488