Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
73	0.006758	0.3082	b0073	leuB	-14.41	0.035044	252 -- 295	42 -- 89	3-isopropylmalate dehydrogenase NAD(+)-dependent	_____________251_______________________________________________296\n_____________\|_________________________________________________\|\n5'-AAA...GUCCG_____G_UG____A__________A__________U__C_____C____CCGCU-3'\n______________GAAGU_A__ACCC_GGC__GCUGA__AGUGCUGGA_GC___GUG_GCAA\n______________:\|\|\|:_\|__\|\|\|\|_\|\|\|__\|\|\|:\|__\|:\|:\|\|\|\|\|_\|\|___\|\|\|_\|\|\|\|\n______________UUUCG_U__UGGG_CCG__CGAUU__UUAUGACCU_CG___CAC_CGUU\n__________3'-U_____G_CG________AC_____CA_________U__UUA___U____ACAGC...GCG-5'\n_____________\|_________________________________________________\|\n_____________90________________________________________________41\n	277 -- 283	56 -- 62	-44.364 kcal/mol	15.0484 kcal/mol	14.9103 kcal/mol	251 296@LB@ \| \|@LB@5'-AAA...GUCCG G UG A A U C C CCGCU-3'@LB@ GAAGU A ACCC GGC GCUGA AGUGCUGGA GC GUG GCAA@LB@ :\|\|\|: \| \|\|\|\| \|\|\| \|\|\|:\| \|:\|:\|\|\|\|\| \|\| \|\|\| \|\|\|\|@LB@ UUUCG U UGGG CCG CGAUU UUAUGACCU CG CAC CGUU@LB@ 3'-U G CG AC CA U UUA U ACAGC...GCG-5'@LB@ \| \|@LB@ 90 41@LB@@LB@@LB@Energy -14.41 kcal/mol@LB@Hybridization Energy -44.364 kcal/mol@LB@Unfolding Energy - mRNA 15.0484 kcal/mol@LB@Unfolding Energy - sRNA 14.9103 kcal/mol@LB@@LB@Position - mRNA 252 -- 295@LB@Position - sRNA 42 -- 89@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 56 -- 62@LB@
193	0.02468	0.4226	b0642	leuS	-10.30	0.169116	191 -- 213	41 -- 61	leucyl-tRNA synthetase	_____________190_____________________214\n_____________\|_______________________\|\n5'-AAU...GGACC_____CU__C___CAA_______ACCGC...AGA-3'\n______________ACUGG__GC_AUG___GAGCAAU\n______________\|\|\|\|\|__\|\|_\|\|\|___\|\|\|\|\|\|\|\n______________UGACC__CG_UAC___CUCGUUA\n3'-UUU...CAUUA_____UU__U___A_________CAGCA...GCG-5'\n_____________\|_______________________\|\n_____________62______________________40\n	207 -- 213	41 -- 47	-20.8037 kcal/mol	7.20782 kcal/mol	3.30062 kcal/mol	190 214@LB@ \| \|@LB@5'-AAU...GGACC CU C CAA ACCGC...AGA-3'@LB@ ACUGG GC AUG GAGCAAU@LB@ \|\|\|\|\| \|\| \|\|\| \|\|\|\|\|\|\|@LB@ UGACC CG UAC CUCGUUA@LB@3'-UUU...CAUUA UU U A CAGCA...GCG-5'@LB@ \| \|@LB@ 62 40@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -20.8037 kcal/mol@LB@Unfolding Energy - mRNA 7.20782 kcal/mol@LB@Unfolding Energy - sRNA 3.30062 kcal/mol@LB@@LB@Position - mRNA 191 -- 213@LB@Position - sRNA 41 -- 61@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 41 -- 47@LB@
125	0.0136	0.3627	b3647	ligB	-15.20	0.025592	210 -- 279	1 -- 59	DNA ligase NAD(+)-dependent	_____________209_____________________________________________________________________280\n_____________\|_______________________________________________________________________\|\n5'-GGC...AAGUA____U______AUUAAUA____UC________GG__AUCA___G______C_____GUCCGG_________CAGCC...AAA-3'\n______________UGGA_GGCGAU_______GGUA___UUGUGCU__CA____UCU_UGUGGG_GGUCU______CCUGGUCGC\n______________\|\|\|\|_:\|\|:\|\|_______:\|:\|___\|:\|\|\|\|\|__\|\|____\|\|\|_:\|:\|:\|_\|\|\|\|\|______\|\|\|\|:\|\|\|\|\n______________ACCU_UCGUUA_______UCGU___AGCACGA__GU____AGA_GCGCUC_CCAGA______GGACUAGCG\n3'-UUU...UUAUG___________CAC________UAC_______AA__CCA____G____________A______________-5'\n_____________\|______________________________________________________________________\|\n_____________60_____________________________________________________________________1\n	273 -- 279	1 -- 7	-52.2567 kcal/mol	22.9457 kcal/mol	14.1095 kcal/mol	209 280@LB@ \| \|@LB@5'-GGC...AAGUA U AUUAAUA UC GG AUCA G C GUCCGG CAGCC...AAA-3'@LB@ UGGA GGCGAU GGUA UUGUGCU CA UCU UGUGGG GGUCU CCUGGUCGC@LB@ \|\|\|\| :\|\|:\|\| :\|:\| \|:\|\|\|\|\| \|\| \|\|\| :\|:\|:\| \|\|\|\|\| \|\|\|\|:\|\|\|\|@LB@ ACCU UCGUUA UCGU AGCACGA GU AGA GCGCUC CCAGA GGACUAGCG@LB@3'-UUU...UUAUG CAC UAC AA CCA G A -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -15.20 kcal/mol@LB@Hybridization Energy -52.2567 kcal/mol@LB@Unfolding Energy - mRNA 22.9457 kcal/mol@LB@Unfolding Energy - sRNA 14.1095 kcal/mol@LB@@LB@Position - mRNA 210 -- 279@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 1 -- 7@LB@
44	0.003649	0.2787	b0147	ligT	-12.24	0.081601	33 -- 98	26 -- 85	2'-5' RNA ligase	_____________32____________________________________________________________________99\n_____________\|_____________________________________________________________________\|\n5'-CCA...AUUUC____________C___GCACUUAA_____C___C__C___CAAUCGA_______AA___AA________AAGAC...CGG-3'\n______________CCGGC_CCCGGU_GGC________UAAUA_CUG_GG_GCA_______GAGCGGU___GU___UUCAGGU\n______________\|\|:\|\|_\|\|\|\|\|:_\|\|\|________\|\|\|\|\|_\|\|\|_\|:_\|\|\|_______\|\|\|\|::\|___\|\|___\|\|\|\|\|\|\|\n______________GGUCG_GGGCCG_CCG________AUUAU_GAC_CU_CGU_______CUCGUUA___CA___AAGUCCA\n______3'-UUUUC_____U______A___AUUC________________U___UACA__________CAG__CGA_______AGAGG...GCG-5'\n_____________\|_____________________________________________________________________\|\n_____________86____________________________________________________________________25\n	92 -- 98	26 -- 32	-49.8324 kcal/mol	18.0057 kcal/mol	19.5911 kcal/mol	32 99@LB@ \| \|@LB@5'-CCA...AUUUC C GCACUUAA C C C CAAUCGA AA AA AAGAC...CGG-3'@LB@ CCGGC CCCGGU GGC UAAUA CUG GG GCA GAGCGGU GU UUCAGGU@LB@ \|\|:\|\| \|\|\|\|\|: \|\|\| \|\|\|\|\| \|\|\| \|: \|\|\| \|\|\|\|::\| \|\| \|\|\|\|\|\|\|@LB@ GGUCG GGGCCG CCG AUUAU GAC CU CGU CUCGUUA CA AAGUCCA@LB@ 3'-UUUUC U A AUUC U UACA CAG CGA AGAGG...GCG-5'@LB@ \| \|@LB@ 86 25@LB@@LB@@LB@Energy -12.24 kcal/mol@LB@Hybridization Energy -49.8324 kcal/mol@LB@Unfolding Energy - mRNA 18.0057 kcal/mol@LB@Unfolding Energy - sRNA 19.5911 kcal/mol@LB@@LB@Position - mRNA 33 -- 98@LB@Position - sRNA 26 -- 85@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 26 -- 32@LB@
148	0.01761	0.3998	b4262	lptG	-10.98	0.131149	190 -- 206	42 -- 57	lipopolysaccharide export ABC permease	_____________189_______________207\n_____________\|_________________\|\n5'-CCA...GUAAA____________U____CCUUU...UCA-3'\n______________GGAGCGGUGUGA_GCAA\n______________\|:\|\|\|::\|\|\|\|\|_\|\|\|\|\n______________CUUCGUUACACU_CGUU\n3'-UUU...AUGAC_________________ACAGC...GCG-5'\n_____________\|_________________\|\n_____________58________________41\n	195 -- 201	46 -- 52	-21.8951 kcal/mol	7.70229 kcal/mol	3.20882 kcal/mol	189 207@LB@ \| \|@LB@5'-CCA...GUAAA U CCUUU...UCA-3'@LB@ GGAGCGGUGUGA GCAA@LB@ \|:\|\|\|::\|\|\|\|\| \|\|\|\|@LB@ CUUCGUUACACU CGUU@LB@3'-UUU...AUGAC ACAGC...GCG-5'@LB@ \| \|@LB@ 58 41@LB@@LB@@LB@Energy -10.98 kcal/mol@LB@Hybridization Energy -21.8951 kcal/mol@LB@Unfolding Energy - mRNA 7.70229 kcal/mol@LB@Unfolding Energy - sRNA 3.20882 kcal/mol@LB@@LB@Position - mRNA 190 -- 206@LB@Position - sRNA 42 -- 57@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 46 -- 52@LB@
14	0.0009144	0.2195	b0181	lpxA	-19.56	0.004514	124 -- 202	1 -- 90	UDP-N-acetylglucosamine acetyltransferase	_____________123_____________________________________________________________________________________________203\n_____________\|_______________________________________________________________________________________________\|\n5'-CGG...UUUUA_____G_U_________CGA____A___________C_______C_________________CG___________G_______________A___GAUUG...GAC-3'\n______________AAGGG_U_GC_UCUGGU___UGGU_AAGUAGU_UUG_GAAGCAA___GA_UGAUGU_GUGCU__UAG_____CCG_GAGG_____CCUGAU_CGU\n______________\|\|::\|_:_\|\|_:\|:\|\|:___\|\|\|:_\|\|\|\|\|:\|_:\|\|_\|\|\|\|\|\|\|___\|\|_::\|\|\|\|_\|\|\|\|\|__:\|\|_____\|\|\|_\|\|\|\|_____\|\|\|\|\|\|_\|\|:\n______________UUUUC_G_CG_GGGCCG___ACCG_UUCAUUA_GAC_CUUCGUU___CU_GUUACA_CACGA__GUC_____GGC_CUCC_____GGACUA_GCG\n___________3'-_____G_U__U_____________A_______U___________ACA__C______G_____AA___CAAGA___G____CAGAA__________-5'\n______________\|_____________________________________________________________________________________________\|\n______________90____________________________________________________________________________________________1\n	159 -- 165	51 -- 57	-68.8911 kcal/mol	23.6052 kcal/mol	25.7298 kcal/mol	123 203@LB@ \| \|@LB@5'-CGG...UUUUA G U CGA A C C CG G A GAUUG...GAC-3'@LB@ AAGGG U GC UCUGGU UGGU AAGUAGU UUG GAAGCAA GA UGAUGU GUGCU UAG CCG GAGG CCUGAU CGU@LB@ \|\|::\| : \|\| :\|:\|\|: \|\|\|: \|\|\|\|\|:\| :\|\| \|\|\|\|\|\|\| \|\| ::\|\|\|\| \|\|\|\|\| :\|\| \|\|\| \|\|\|\| \|\|\|\|\|\| \|\|:@LB@ UUUUC G CG GGGCCG ACCG UUCAUUA GAC CUUCGUU CU GUUACA CACGA GUC GGC CUCC GGACUA GCG@LB@ 3'- G U U A U ACA C G AA CAAGA G CAGAA -5'@LB@ \| \|@LB@ 90 1@LB@@LB@@LB@Energy -19.56 kcal/mol@LB@Hybridization Energy -68.8911 kcal/mol@LB@Unfolding Energy - mRNA 23.6052 kcal/mol@LB@Unfolding Energy - sRNA 25.7298 kcal/mol@LB@@LB@Position - mRNA 124 -- 202@LB@Position - sRNA 1 -- 90@LB@Position Seed - mRNA 159 -- 165@LB@Position Seed - sRNA 51 -- 57@LB@
86	0.008505	0.3323	b0879	macB	-10.85	0.137944	147 -- 181	15 -- 61	macrolide ABC transporter peremase/ATPase	_____________146_____________________________________________182\n_____________\|_______________________________________________\|\n5'-AAU...AAAGG___U__________________AA____________GA__G______CCAAA...CGG-3'\n______________GCU_GAAGC_____GGGCGAUG__GU_______GGU__UU_GUGAGG\n______________:\|\|_\|\|\|\|\|_____\|:\|\|:\|\|\|__\|\|_______\|\|\|__\|:_\|:\|\|\|\|\n______________UGA_CUUCG_____CUCGUUAC__CA_______CCA__AG_CGCUCC\n3'-UUU...CAUUA___C_____UUACA________AG__CGAAAGU___AG__G______CAGAA...GCG-5'\n_____________\|_______________________________________________\|\n_____________62______________________________________________14\n	157 -- 163	40 -- 46	-34.4359 kcal/mol	9.61218 kcal/mol	13.9754 kcal/mol	146 182@LB@ \| \|@LB@5'-AAU...AAAGG U AA GA G CCAAA...CGG-3'@LB@ GCU GAAGC GGGCGAUG GU GGU UU GUGAGG@LB@ :\|\| \|\|\|\|\| \|:\|\|:\|\|\| \|\| \|\|\| \|: \|:\|\|\|\|@LB@ UGA CUUCG CUCGUUAC CA CCA AG CGCUCC@LB@3'-UUU...CAUUA C UUACA AG CGAAAGU AG G CAGAA...GCG-5'@LB@ \| \|@LB@ 62 14@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -34.4359 kcal/mol@LB@Unfolding Energy - mRNA 9.61218 kcal/mol@LB@Unfolding Energy - sRNA 13.9754 kcal/mol@LB@@LB@Position - mRNA 147 -- 181@LB@Position - sRNA 15 -- 61@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 40 -- 46@LB@
69	0.006014	0.2917	b3416	malQ	-15.44	0.023264	163 -- 216	38 -- 88	4-alpha-glucanotransferase (amylomaltase)	_____________162_____________________________________________________217\n_____________\|_______________________________________________________\|\n5'-GCG...UUAUC_____C_________A___AAAACGCUAA_______UC____GAA_____AC___UGGAU...CCA-3'\n______________AGGCU_GUAUCUGGC_GGC___________GGAAGC__GAUG___AGCAA__GUC\n______________\|:\|\|:_\|:\|:\|:\|\|\|_\|\|\|___________\|\|\|\|\|\|__:\|\|\|___\|\|\|\|\|__\|\|\|\n______________UUCGG_CGUGGGCCG_CCG___________CCUUCG__UUAC___UCGUU__CAG\n_________3'-UU_____U_________A___AUUCAUUAUGA____________AC______A____CACGA...GCG-5'\n_____________\|_______________________________________________________\|\n_____________89______________________________________________________37\n	171 -- 177	74 -- 80	-43.8565 kcal/mol	13.5036 kcal/mol	14.9106 kcal/mol	162 217@LB@ \| \|@LB@5'-GCG...UUAUC C A AAAACGCUAA UC GAA AC UGGAU...CCA-3'@LB@ AGGCU GUAUCUGGC GGC GGAAGC GAUG AGCAA GUC@LB@ \|:\|\|: \|:\|:\|:\|\|\| \|\|\| \|\|\|\|\|\| :\|\|\| \|\|\|\|\| \|\|\|@LB@ UUCGG CGUGGGCCG CCG CCUUCG UUAC UCGUU CAG@LB@ 3'-UU U A AUUCAUUAUGA AC A CACGA...GCG-5'@LB@ \| \|@LB@ 89 37@LB@@LB@@LB@Energy -15.44 kcal/mol@LB@Hybridization Energy -43.8565 kcal/mol@LB@Unfolding Energy - mRNA 13.5036 kcal/mol@LB@Unfolding Energy - sRNA 14.9106 kcal/mol@LB@@LB@Position - mRNA 163 -- 216@LB@Position - sRNA 38 -- 88@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 74 -- 80@LB@
13	0.000833	0.2153	b1531	marA	-8.74	0.292618	190 -- 205	38 -- 57	multiple antibiotic resistance transcriptional regulator	_____________189__________________206\n_____________\|____________________\|\n5'-AAG...AAAAA____________________CAGAC...AGC-3'\n______________GAGGUA___UGA_CGAUGUC\n______________\|\|:\|:\|___\|\|\|_\|:\|\|\|\|\|\n______________CUUCGU___ACU_GUUACAG\n3'-UUU...AUGAC______UAC___C_______CACGA...GCG-5'\n_____________\|____________________\|\n_____________58___________________37\n	199 -- 205	38 -- 44	-15.3925 kcal/mol	3.44101 kcal/mol	3.2161 kcal/mol	189 206@LB@ \| \|@LB@5'-AAG...AAAAA CAGAC...AGC-3'@LB@ GAGGUA UGA CGAUGUC@LB@ \|\|:\|:\| \|\|\| \|:\|\|\|\|\|@LB@ CUUCGU ACU GUUACAG@LB@3'-UUU...AUGAC UAC C CACGA...GCG-5'@LB@ \| \|@LB@ 58 37@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -15.3925 kcal/mol@LB@Unfolding Energy - mRNA 3.44101 kcal/mol@LB@Unfolding Energy - sRNA 3.2161 kcal/mol@LB@@LB@Position - mRNA 190 -- 205@LB@Position - sRNA 38 -- 57@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 38 -- 44@LB@
18	0.001289	0.2406	b3930	menA	-10.08	0.182848	73 -- 82	42 -- 51	1 4-dihydroxy-2-naphthoate octaprenyltransferase	_____________72_________83\n_____________\|__________\|\n5'-AGC...AGAUU__________ACAUC...CGC-3'\n______________AUGUGAGCAA\n______________\|\|\|\|\|\|\|\|\|\|\n______________UACACUCGUU\n3'-UUU...UUCGU__________ACAGC...GCG-5'\n_____________\|__________\|\n_____________52_________41\n	76 -- 82	42 -- 48	-14.1762 kcal/mol	2.92742 kcal/mol	1.16834 kcal/mol	72 83@LB@ \| \|@LB@5'-AGC...AGAUU ACAUC...CGC-3'@LB@ AUGUGAGCAA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UACACUCGUU@LB@3'-UUU...UUCGU ACAGC...GCG-5'@LB@ \| \|@LB@ 52 41@LB@@LB@@LB@Energy -10.08 kcal/mol@LB@Hybridization Energy -14.1762 kcal/mol@LB@Unfolding Energy - mRNA 2.92742 kcal/mol@LB@Unfolding Energy - sRNA 1.16834 kcal/mol@LB@@LB@Position - mRNA 73 -- 82@LB@Position - sRNA 42 -- 51@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 42 -- 48@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)

Job resubmission

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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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