Input and runtime details for job 6793193 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation	Additional homologs
190	0.009703	0.1776	b4125	dcuS	-9.98	0.246838	251 -- 265	60 -- 75	sensory histidine kinase in two-component regulatory system with DcuR regulator of anaerobic fumarate respiration		_____________250______________266\n_____________\|________________\|\n5'-UCC...AAAUU__G_____________CUUAA...UAU-3'\n______________GA_UAC_CACAGUGAU\n______________\|\|_\|\|\|_\|\|\|\|\|::\|\|\n______________CU_AUG_GUGUCGUUA\n3'-UUU...CGUUU__G___U_________AGCAA...GCA-5'\n_____________\|________________\|\n_____________76_______________59\n	259 -- 265	60 -- 66	-16.3548 kcal/mol	3.08747 kcal/mol	3.28851 kcal/mol	250 266@LB@ \| \|@LB@5'-UCC...AAAUU G CUUAA...UAU-3'@LB@ GA UAC CACAGUGAU@LB@ \|\| \|\|\| \|\|\|\|\|::\|\|@LB@ CU AUG GUGUCGUUA@LB@3'-UUU...CGUUU G U AGCAA...GCA-5'@LB@ \| \|@LB@ 76 59@LB@@LB@@LB@Energy -9.98 kcal/mol@LB@Hybridization Energy -16.3548 kcal/mol@LB@Unfolding Energy - mRNA 3.08747 kcal/mol@LB@Unfolding Energy - sRNA 3.28851 kcal/mol@LB@@LB@Position - mRNA 251 -- 265@LB@Position - sRNA 60 -- 75@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 60 -- 66@LB@
61	0.002486	0.1417	b1487	ddpA	-13.46	0.049908	168 -- 192	43 -- 71	D D-dipeptide ABC transporter periplasmic binding protein		_____________167___________________________193\n_____________\|_____________________________\|\n5'-UCA...CCCUG________________CAG____A_____AAACU...UGA-3'\n______________GCACACAGCA___CGU____UUA_UCAGG\n______________:\|\|\|\|\|\|\|\|\|___\|\|\|____\|:\|_\|\|\|\|\|\n______________UGUGUGUCGU___GCA____AGU_AGUCC\n3'-UUU...UCUGA__________UAA___ACAA___G_____CCUAA...GCA-5'\n_____________\|_____________________________\|\n_____________72____________________________42\n	171 -- 177	62 -- 68	-25.043 kcal/mol	7.26137 kcal/mol	4.32409 kcal/mol	167 193@LB@ \| \|@LB@5'-UCA...CCCUG CAG A AAACU...UGA-3'@LB@ GCACACAGCA CGU UUA UCAGG@LB@ :\|\|\|\|\|\|\|\|\| \|\|\| \|:\| \|\|\|\|\|@LB@ UGUGUGUCGU GCA AGU AGUCC@LB@3'-UUU...UCUGA UAA ACAA G CCUAA...GCA-5'@LB@ \| \|@LB@ 72 42@LB@@LB@@LB@Energy -13.46 kcal/mol@LB@Hybridization Energy -25.043 kcal/mol@LB@Unfolding Energy - mRNA 7.26137 kcal/mol@LB@Unfolding Energy - sRNA 4.32409 kcal/mol@LB@@LB@Position - mRNA 168 -- 192@LB@Position - sRNA 43 -- 71@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 62 -- 68@LB@
143	0.006558	0.1605	b0161	degP	-10.78	0.178564	159 -- 170	58 -- 69	serine endoprotease (protease Do) membrane-associated		_____________158__________171\n_____________\|____________\|\n5'-AUU...GAAGA____________UGCGU...CGA-3'\n______________ACACAGCAAUUU\n______________\|\|\|\|\|\|\|\|\|\|\|:\n______________UGUGUCGUUAAG\n3'-UUU...UGAUG____________CAACA...GCA-5'\n_____________\|____________\|\n_____________70___________57\n	164 -- 170	58 -- 64	-16.5275 kcal/mol	2.62124 kcal/mol	3.12494 kcal/mol	158 171@LB@ \| \|@LB@5'-AUU...GAAGA UGCGU...CGA-3'@LB@ ACACAGCAAUUU@LB@ \|\|\|\|\|\|\|\|\|\|\|:@LB@ UGUGUCGUUAAG@LB@3'-UUU...UGAUG CAACA...GCA-5'@LB@ \| \|@LB@ 70 57@LB@@LB@@LB@Energy -10.78 kcal/mol@LB@Hybridization Energy -16.5275 kcal/mol@LB@Unfolding Energy - mRNA 2.62124 kcal/mol@LB@Unfolding Energy - sRNA 3.12494 kcal/mol@LB@@LB@Position - mRNA 159 -- 170@LB@Position - sRNA 58 -- 69@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 58 -- 64@LB@
55	0.001955	0.1223	b0840	deoR	-10.34	0.214583	216 -- 260	60 -- 103	deoxyribose-5-phosphate-inducible deoxyribose operon transcriptional repressor; repressor of nupG and tsx		_____________215____________________________________________261\n_____________\|______________________________________________\|\n5'-GUG...GUCGC_______G________C__C__CU_____A____AA__________AAGUU...UUU-3'\n______________GAAGAGC_UAUCG_GG_AG_UG__GCAAG_AUUA__ACGCAGCGAU\n______________:\|\|:\|\|\|_:\|\|\|\|_\|\|_\|\|_\|\|__\|\|\|\|:_\|:\|\|__\|\|:\|\|\|\|:\|\|\n______________UUUUUCG_GUAGC_CC_UC_AC__CGUUU_UGAU__UGUGUCGUUA\n_________3'-UU_______G_____A__C__U__C______C____G___________AGCAA...GCA-5'\n_____________\|______________________________________________\|\n_____________104____________________________________________59\n	254 -- 260	60 -- 66	-39.4084 kcal/mol	12.9673 kcal/mol	16.1071 kcal/mol	215 261@LB@ \| \|@LB@5'-GUG...GUCGC G C C CU A AA AAGUU...UUU-3'@LB@ GAAGAGC UAUCG GG AG UG GCAAG AUUA ACGCAGCGAU@LB@ :\|\|:\|\|\| :\|\|\|\| \|\| \|\| \|\| \|\|\|\|: \|:\|\| \|\|:\|\|\|\|:\|\|@LB@ UUUUUCG GUAGC CC UC AC CGUUU UGAU UGUGUCGUUA@LB@ 3'-UU G A C U C C G AGCAA...GCA-5'@LB@ \| \|@LB@ 104 59@LB@@LB@@LB@Energy -10.34 kcal/mol@LB@Hybridization Energy -39.4084 kcal/mol@LB@Unfolding Energy - mRNA 12.9673 kcal/mol@LB@Unfolding Energy - sRNA 16.1071 kcal/mol@LB@@LB@Position - mRNA 216 -- 260@LB@Position - sRNA 60 -- 103@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 60 -- 66@LB@
146	0.006661	0.1605	b4479	dgoR	-11.67	0.120911	94 -- 106	61 -- 74	D-galactonate catabolism operon transcriptional repressor		_____________93_____________107\n_____________\|______________\|\n5'-UUU...ACAUU______________ACGCG...AAC-3'\n______________AC_ACGCACGGCAA\n______________\|\|_\|\|:\|\|\|:\|\|\|\|\n______________UG_UGUGUGUCGUU\n3'-UUU...GUUUC__A___________AAGCA...GCA-5'\n_____________\|______________\|\n_____________75_____________60\n	100 -- 106	61 -- 67	-16.8512 kcal/mol	1.93692 kcal/mol	3.24589 kcal/mol	93 107@LB@ \| \|@LB@5'-UUU...ACAUU ACGCG...AAC-3'@LB@ AC ACGCACGGCAA@LB@ \|\| \|\|:\|\|\|:\|\|\|\|@LB@ UG UGUGUGUCGUU@LB@3'-UUU...GUUUC A AAGCA...GCA-5'@LB@ \| \|@LB@ 75 60@LB@@LB@@LB@Energy -11.67 kcal/mol@LB@Hybridization Energy -16.8512 kcal/mol@LB@Unfolding Energy - mRNA 1.93692 kcal/mol@LB@Unfolding Energy - sRNA 3.24589 kcal/mol@LB@@LB@Position - mRNA 94 -- 106@LB@Position - sRNA 61 -- 74@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 61 -- 67@LB@
52	0.001789	0.121	b1799	dmlR	-11.56	0.127346	72 -- 108	34 -- 68	transcriptional activator of dmlA	b3060	_____________71_______________________________________109\n_____________\|________________________________________\|\n5'-CGC...GGGAU_________ACGCA_______________UU_____C___CUUCC...CGG-3'\n______________CGCAGCAAU_____UCGU__UUUCA_UCA__GGGUU_UCA\n______________\|:\|\|\|\|\|\|\|_____\|\|\|\|__\|\|\|\|\|_\|\|\|__\|\|:\|\|_:\|\|\n______________GUGUCGUUA_____AGCA__AAAGU_AGU__CCUAA_GGU\n3'-UUU...GAUGU__________________AC_____G___CC_____A___ACGAA...GCA-5'\n_____________\|________________________________________\|\n_____________69_______________________________________33\n	74 -- 80	60 -- 66	-24.8584 kcal/mol	8.52016 kcal/mol	4.78423 kcal/mol	71 109@LB@ \| \|@LB@5'-CGC...GGGAU ACGCA UU C CUUCC...CGG-3'@LB@ CGCAGCAAU UCGU UUUCA UCA GGGUU UCA@LB@ \|:\|\|\|\|\|\|\| \|\|\|\| \|\|\|\|\| \|\|\| \|\|:\|\| :\|\|@LB@ GUGUCGUUA AGCA AAAGU AGU CCUAA GGU@LB@3'-UUU...GAUGU AC G CC A ACGAA...GCA-5'@LB@ \| \|@LB@ 69 33@LB@@LB@@LB@Energy -11.56 kcal/mol@LB@Hybridization Energy -24.8584 kcal/mol@LB@Unfolding Energy - mRNA 8.52016 kcal/mol@LB@Unfolding Energy - sRNA 4.78423 kcal/mol@LB@@LB@Position - mRNA 72 -- 108@LB@Position - sRNA 34 -- 68@LB@Position Seed - mRNA 74 -- 80@LB@Position Seed - sRNA 60 -- 66@LB@
96	0.004462	0.1538	b3260	dusB	-10.19	0.227205	72 -- 117	38 -- 74	tRNA-dihydrouridine synthase B		_____________71_____________________________________________118\n_____________\|______________________________________________\|\n5'-ACU...AUCGC__C____U__UUUUAAAU_______U___AUC__U_____A_____GGUCA...GAG-3'\n______________AC_ACGC_CA________GCAAUUC_UUG___CA_CUCAG_GGAUU\n______________\|\|_\|\|:\|_\|\|________\|\|\|\|\|\|\|_\|\|\|___\|\|_\|\|\|\|\|_\|\|\|\|\|\n______________UG_UGUG_GU________CGUUAAG_AAC___GU_GAGUC_CCUAA\n3'-UUU...GUUUC__A____U_________________C___AAA________C_____AGGUA...GCA-5'\n_____________\|______________________________________________\|\n_____________75_____________________________________________37\n	90 -- 96	58 -- 64	-26.7161 kcal/mol	11.7467 kcal/mol	4.77867 kcal/mol	71 118@LB@ \| \|@LB@5'-ACU...AUCGC C U UUUUAAAU U AUC U A GGUCA...GAG-3'@LB@ AC ACGC CA GCAAUUC UUG CA CUCAG GGAUU@LB@ \|\| \|\|:\| \|\| \|\|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\| \|\|\|\|\|@LB@ UG UGUG GU CGUUAAG AAC GU GAGUC CCUAA@LB@3'-UUU...GUUUC A U C AAA C AGGUA...GCA-5'@LB@ \| \|@LB@ 75 37@LB@@LB@@LB@Energy -10.19 kcal/mol@LB@Hybridization Energy -26.7161 kcal/mol@LB@Unfolding Energy - mRNA 11.7467 kcal/mol@LB@Unfolding Energy - sRNA 4.77867 kcal/mol@LB@@LB@Position - mRNA 72 -- 117@LB@Position - sRNA 38 -- 74@LB@Position Seed - mRNA 90 -- 96@LB@Position Seed - sRNA 58 -- 64@LB@
152	0.007399	0.1668	b0591	entS	-13.87	0.039944	258 -- 287	45 -- 70	enterobactin exporter iron-regulated		_____________257____________________________288\n_____________\|______________________________\|\n5'-AAU...CGUUU_________UUCC___CUC______U____AUUGU...UGG-3'\n______________CGCGCAGUA____UCG___GUUUCA_CUCA\n______________\|:\|:\|\|\|:\|____\|\|\|___\|\|\|\|\|\|_\|\|\|\|\n______________GUGUGUCGU____AGC___CAAAGU_GAGU\n3'-UUU...CUGAU_________UA_____AA____________CCCCU...GCA-5'\n_____________\|______________________________\|\n_____________71_____________________________44\n	260 -- 266	62 -- 68	-23.1768 kcal/mol	5.59312 kcal/mol	3.71317 kcal/mol	257 288@LB@ \| \|@LB@5'-AAU...CGUUU UUCC CUC U AUUGU...UGG-3'@LB@ CGCGCAGUA UCG GUUUCA CUCA@LB@ \|:\|:\|\|\|:\| \|\|\| \|\|\|\|\|\| \|\|\|\|@LB@ GUGUGUCGU AGC CAAAGU GAGU@LB@3'-UUU...CUGAU UA AA CCCCU...GCA-5'@LB@ \| \|@LB@ 71 44@LB@@LB@@LB@Energy -13.87 kcal/mol@LB@Hybridization Energy -23.1768 kcal/mol@LB@Unfolding Energy - mRNA 5.59312 kcal/mol@LB@Unfolding Energy - sRNA 3.71317 kcal/mol@LB@@LB@Position - mRNA 258 -- 287@LB@Position - sRNA 45 -- 70@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 62 -- 68@LB@
185	0.009421	0.1776	b3094	exuR	-10.10	0.235203	51 -- 95	35 -- 75	hexuronate regulon transcriptional repressor; autorepressor		_____________50____________________________________________96\n_____________\|_____________________________________________\|\n5'-CCG...AUAAC___CC_____C____CAUUAAC_______GUA__UUUUA______CUUCA...CUG-3'\n______________GAU__CGCAC_GCAA_______GUUUCGU___AG_____GUUUCC\n______________\|\|:__\|:\|\|\|_\|\|\|\|_______\|\|\|\|\|::___\|\|_____:\|\|\|\|\|\n______________CUG__GUGUG_CGUU_______CAAAGUG___UC_____UAAAGG\n3'-UUU...CGUUU___AU_____U____AAGCAA________AG___CCC________UACGA...GCA-5'\n_____________\|_____________________________________________\|\n_____________76____________________________________________34\n	73 -- 79	48 -- 54	-21.0703 kcal/mol	6.16224 kcal/mol	4.80541 kcal/mol	50 96@LB@ \| \|@LB@5'-CCG...AUAAC CC C CAUUAAC GUA UUUUA CUUCA...CUG-3'@LB@ GAU CGCAC GCAA GUUUCGU AG GUUUCC@LB@ \|\|: \|:\|\|\| \|\|\|\| \|\|\|\|\|:: \|\| :\|\|\|\|\|@LB@ CUG GUGUG CGUU CAAAGUG UC UAAAGG@LB@3'-UUU...CGUUU AU U AAGCAA AG CCC UACGA...GCA-5'@LB@ \| \|@LB@ 76 34@LB@@LB@@LB@Energy -10.10 kcal/mol@LB@Hybridization Energy -21.0703 kcal/mol@LB@Unfolding Energy - mRNA 6.16224 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 51 -- 95@LB@Position - sRNA 35 -- 75@LB@Position Seed - mRNA 73 -- 79@LB@Position Seed - sRNA 48 -- 54@LB@
23	0.0001955	0.02926	b3846	fadB	-13.56	0.047358	39 -- 83	35 -- 77	fused 3-hydroxybutyryl-CoA epimerase/delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase/enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase		_____________38________________________________________________84\n_____________\|_________________________________________________\|\n5'-AGU...ACCUU___U__C_____CUU____CA____________C___A_C_U_______GCCGA...CUG-3'\n______________AAG_CU_CGCAU___AGCA__UCGU____UCAU_CAG_G_G_GAUUUCU\n______________\|\|\|_\|\|_\|:\|\|:___\|\|\|\|__\|\|\|\|____\|\|\|:_\|\|\|_\|_\|_\|\|\|\|\|\|:\n______________UUC_GA_GUGUG___UCGU__AGCA____AGUG_GUC_C_C_CUAAAGG\n3'-UUU...CCCGU___U__U____________UA____ACAA____A_______________UACGA...GCA-5'\n_____________\|_________________________________________________\|\n_____________78________________________________________________34\n	77 -- 83	35 -- 41	-27.7125 kcal/mol	9.35112 kcal/mol	4.80542 kcal/mol	38 84@LB@ \| \|@LB@5'-AGU...ACCUU U C CUU CA C A C U GCCGA...CUG-3'@LB@ AAG CU CGCAU AGCA UCGU UCAU CAG G G GAUUUCU@LB@ \|\|\| \|\| \|:\|\|: \|\|\|\| \|\|\|\| \|\|\|: \|\|\| \| \| \|\|\|\|\|\|:@LB@ UUC GA GUGUG UCGU AGCA AGUG GUC C C CUAAAGG@LB@3'-UUU...CCCGU U U UA ACAA A UACGA...GCA-5'@LB@ \| \|@LB@ 78 34@LB@@LB@@LB@Energy -13.56 kcal/mol@LB@Hybridization Energy -27.7125 kcal/mol@LB@Unfolding Energy - mRNA 9.35112 kcal/mol@LB@Unfolding Energy - sRNA 4.80542 kcal/mol@LB@@LB@Position - mRNA 39 -- 83@LB@Position - sRNA 35 -- 77@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 35 -- 41@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

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service.

When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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