AlignACE 3.0 10/20/99
AlignACE2 -i EC_sum_all075_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943443569
 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
AGAAAAACAGTCCAACGTTTTAAACCAGCGC	1	17	0
GCCAGTACATTCTGGCGTTTTCGAGCACAGG	5	44	1
GTTAAACAACTGTTACTTTTGATACGTTTAA	5	90	1
GTGGTACTCACGGCGCGTTTTAAACGTATCA	5	109	0
TCGATTCTGCTGTGGCTTTTGCGGCTAGTGT	9	22	1
TGCGCAAAGTTGTTGCGTTTTGCGTAGCTGC	10	136	0
TAGCCCTTGCTCACACTTTTTGCGCAAAGTT	10	156	0
TCTTCACCTGTGGAGCTTTTTAAGT      	11	39	1
AATACAGTTATGTCACTTTTTGTCATTTATG	12	22	1
AAGTGACGGCTGTCAATTTTTTGACGATAAA	12	90	0
AATTGACAGCCGTCACTTTTTAAACAATTGG	12	103	1
          *** *******
MAP Score: 10.7516

Motif 2
TTGCAGGGAGAGCGCCCCGGCACTAGACTACC	0	41	1
CACTAGACTACCCGCCTCTTATTTTAGTCTGA	0	61	1
       TTCCGCGGCGCTGGTTTAAAACGTT	1	3	1
TTTGACCGCCTGCGCCTGTGCTCGAAAACGCC	5	57	0
ACGTTTAAAACGCGCCGTGAGTACCACCGTAA	5	113	1
ATTTGCCGATTTCGGCAGGTCTGGTCCCTAAA	6	15	1
CTGTGGCTTTTGCGGCTAGTGTATCAGAATCG	9	31	1
TATGCCTTATTGTGCCGTGACTAAAGCGATTC	9	57	0
         TTGCGCCCCTTATGGTCACTCAT	9	98	0
GTTTTTGCCACTCGGCTTTGCTTTCATCACGT	10	40	0
GTCACATGGCCGCGCCGTGTATAATAAGCTCG	10	188	1
          ******  ****
MAP Score: 7.50395

Motif 3
         GGCAATTCCCTTAGGGAAAAATTTTAA   	3	7	0
TGCTAAAGTAGCCACTCTGTAAGCTGACAACACTCAAT 	4	41	1
CGCAATAATTGCAACTGCGATTGTTGTGCT         	5	1	0
GCGTTTTCGAGCACAGGCGCAGGCGGTCAAAGGTTAAAC	5	58	1
TTTAAAACGCGCCGTGAGTACCACCGTAACAAGCAGGCA	5	116	1
TCTCGATTCTGCTGTGGCTTTTGCGGCTAGTGTATCAGA	9	20	1
GCCTTATTGTGCCGTGACTAAAGCGATTCTGATACACTA	9	47	0
CGTGATGAAAGCAAAGCCGAGTGGCAAAAACGGAGTCTG	10	41	1
AACGGAGTCTGCGAGGACGCTTCCTGAAAATCGTCTTTA	10	69	1
TGAATGACAGGCAAATGCGGAAGCAGCTACGCAAAACGC	10	114	1
ACGTCACATGGCCGCGCCGTGTATAATAAGCTCGTATGT	10	186	1
GATGGGTTTGGCTATGTGGCAAGGTATGAAGCCAGGTTA	13	24	0
          ** * * **   ** *  *
MAP Score: 5.09888

Motif 4
TTCTCCACTACGTCAGAAAAACAGTCCAAC	1	32	0
TTTCTGACGTAGTGGAGAAAAA        	1	43	1
CTGATACACTAGCCGCAAAAGCCACAGCAG	9	28	0
CTTATTGTGCCGTGACTAAAGCGATTCTGA	9	54	0
AGATATACAACGTGATGAAAGCAAAGCCGA	10	31	1
AGCAAAGCCGAGTGGCAAAAACGGAGTCTG	10	50	1
GTATGTGATTAGCGAAATAAAGCCTACATA	10	220	0
AAGCTCCACAGGTGAAGAAATGACTGGGCA	11	27	0
AATGACAAAAAGTGACATAACTGTATTCAG	12	19	0
GCATGTCATAAATGACAAAAAGTGACATAA	12	29	0
TGTAATTTATCGTCAAAAAATTGACAGCCG	12	85	1
CCAGGTTAACGGTCACAAAAAT        	13	2	0
          **********
MAP Score: 3.35023

Motif 5
TTTTCGAGCACAGGCGCAGGCGGTCAAAGGTTAAACAA	5	61	1
GTGAGTACCACCGTAACAAGCAGGCATACACTT     	5	129	1
CCTCTCCTTTAGGGACCAGACCTGCCGAAATCGGCAAA	6	16	0
CGCTTTAGTCACGGCACAATAAGGCATAATGGATCAAA	9	61	1
GACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTT	10	66	0
CAGGCAAATGCGGAAGCAGCTACGCAAAACGCAACAAC	10	121	1
GCTACGCAAAACGCAACAACTTTGCGCAAAAAGTGTGA	10	139	1
CAAATACGATCAAAAACAGACAAGCAAAGCATGTCATA	12	49	0
          * * * **  *  *** *
MAP Score: 2.86817

Motif 6
GCAACTGCGATTGTTGTGCT          	5	0	0
TTGCGCAAAGTTGTTGCGTTTTGCGTAGCT	10	138	0
TTGCTCACACTTTTTGCGCAAAGTTGTTGC	10	151	0
CCATTATGCCTTATTGTGCCGTGACTAAAG	9	63	0
GTATGCCTGCTTGTTACGGTGGTACTCACG	5	128	0
AAAATGATAATTGTTATGCTAAAGTAGCCA	4	25	1
TATGTAGGCTTTATTTCGCTAATCACATAC	10	220	1
GCAGTTGCAATTATTGCGTACAGCCAGTAC	5	22	1
TCTGCTGTGGCTTTTGCGGCTAGTGTATCA	9	27	1
AAAATCGTCTTTATTGCAGTGAATGACAGG	10	95	1
          **********
MAP Score: 2.40841

Motif 7
GGCTACTTTAGCATAACAATTATCATTTTCATTGAGGTC	4	15	0
         AGCACAACAATCGCAGTTGCAATTATTGCG	5	1	1
CGTTTTAAACGTATCAAAAGTAACAGTTGTTTAACCTTT	5	86	0
CTTTTGATACGTTTAAAACGCGCCGTGAGTACCACCGTA	5	105	1
TGCGGCTAGTGTATCAGAATCGCTTTAGTCACGGCACAA	9	41	1
GCAAAGCCGAGTGGCAAAAACGGAGTCTGCGAGGACGCT	10	51	1
CAACAACTTTGCGCAAAAAGTGTGAGCAAGGGCTACGTC	10	152	1
ATGACAAAAAGTGACATAACTGTATTCAGGAGAGGGTT 	12	9	0
GTAATTTATCGTCAAAAAATTGACAGCCGTCACTTTTTA	12	86	1
TTCACCAATTGTTTAAAAAGTGACGGCTGTCAATTTTTT	12	99	0
          **  ** ** **   *  *
MAP Score: 0.352284