Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
54	0.0007167	0.04676	b0147	ligT	-15.11	0.004153	163 -- 244	1 -- 81	2'-5' RNA ligase	_____________162_________________________________________________________________________________________245\n_____________\|___________________________________________________________________________________________\|\n5'-CCA...GCCAC_____A__AUC___________UAACC_______CCU__C____CU__AC_____________CUUU___AUC__________________AGAAA...CGG-3'\n______________AUUGU_GC___GCGGUAAUUCA_______GAGUG___CA_AUGU__GA__CGCAACGUCUGUU____GCU___GAC_______UUACCUGC\n______________\|\|\|\|\|_\|\|___\|\|:\|\|\|\|\|\|\|\|_______:\|\|\|:___\|\|_\|\|:\|__\|\|__\|\|\|\|\|\|\|:\|::\|:____\|\|\|___\|\|\|_______\|:\|\|\|\|\|\|\n______________UAACA_CG___CGUCAUUAAGU_______UUCAU___GU_UAUA__CU__GCGUUGCGGGUAG____CGA___CUG_______AGUGGACG\n3'-UUU...UUAGU________AUA___________UUUUUCC_____UCU_______C___C_____________________A_____CAACGUA________-5'\n_____________\|__________________________________________________________________________________________\|\n_____________82_________________________________________________________________________________________1\n	238 -- 244	1 -- 7	-55.1488 kcal/mol	19.3452 kcal/mol	20.694 kcal/mol	162 245@LB@ \| \|@LB@5'-CCA...GCCAC A AUC UAACC CCU C CU AC CUUU AUC AGAAA...CGG-3'@LB@ AUUGU GC GCGGUAAUUCA GAGUG CA AUGU GA CGCAACGUCUGUU GCU GAC UUACCUGC@LB@ \|\|\|\|\| \|\| \|\|:\|\|\|\|\|\|\|\| :\|\|\|: \|\| \|\|:\| \|\| \|\|\|\|\|\|\|:\|::\|: \|\|\| \|\|\| \|:\|\|\|\|\|\|@LB@ UAACA CG CGUCAUUAAGU UUCAU GU UAUA CU GCGUUGCGGGUAG CGA CUG AGUGGACG@LB@3'-UUU...UUAGU AUA UUUUUCC UCU C C A CAACGUA -5'@LB@ \| \|@LB@ 82 1@LB@@LB@@LB@Energy -15.11 kcal/mol@LB@Hybridization Energy -55.1488 kcal/mol@LB@Unfolding Energy - mRNA 19.3452 kcal/mol@LB@Unfolding Energy - sRNA 20.694 kcal/mol@LB@@LB@Position - mRNA 163 -- 244@LB@Position - sRNA 1 -- 81@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 1 -- 7@LB@
58	0.0009751	0.05816	b3809	dapF	-9.70	0.129467	46 -- 52	1 -- 7	diaminopimelate epimerase	_____________45______53\n_____________\|_______\|\n5'-UCU...UUUCC_______AGAUA...UGG-3'\n______________CGCCUGC\n______________\|:\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	46 -- 52	1 -- 7	-13.4276 kcal/mol	1.39772 kcal/mol	2.34039 kcal/mol	45 53@LB@ \| \|@LB@5'-UCU...UUUCC AGAUA...UGG-3'@LB@ CGCCUGC@LB@ \|:\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -13.4276 kcal/mol@LB@Unfolding Energy - mRNA 1.39772 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 46 -- 52@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 1 -- 7@LB@
63	0.00104	0.05816	b1856	mepM	-14.49	0.006560	139 -- 249	1 -- 88	murein DD-endopeptidase space-maker hydrolase septation protein	_____________138________________________________________________________________________________________________________________250\n_____________\|__________________________________________________________________________________________________________________\|\n5'-CAA...AUUCC__________A___CAACCAG______AGCUGCCU_________AU___U__G__A___AUUAC_______AGAUA____GCUCU_____CC_______UAAUA__________GACCA...UCG-3'\n______________UGAGUCAAUU__GC_______UAUGCG_________GAAAGGAG__UAA_GA_GA_GUG_____GUGCAAC_____GCCC_____GUCGC__UGGCGUU_____AUUUACC_GC\n______________:\|\|:\|\|\|\|\|\|__\|\|_______\|\|\|\|\|:_________:\|\|\|\|\|\|:__\|\|\|_\|\|_:\|_:\|\|_____\|:\|\|\|\|\|_____\|\|\|\|_____:\|\|\|\|__\|\|:\|\|\|\|_____\|\|\|:\|\|\|_\|\|\n______________GCUUAGUUAA__CG_______AUACGU_________UUUUCCUU__AUU_CU_UU_UAC_____CGCGUUG_____CGGG_____UAGCG__ACUGCAA_____UAAGUGG_CG\n3'-UUU...AGCAU__________CA_______________CAUUAAGUU________C_______G__A___CU_____________________________A________CG__________A__-5'\n_____________\|_________________________________________________________________________________________________________________\|\n_____________89________________________________________________________________________________________________________________1\n	241 -- 247	4 -- 10	-60.5282 kcal/mol	25.2709 kcal/mol	20.7761 kcal/mol	138 250@LB@ \| \|@LB@5'-CAA...AUUCC A CAACCAG AGCUGCCU AU U G A AUUAC AGAUA GCUCU CC UAAUA GACCA...UCG-3'@LB@ UGAGUCAAUU GC UAUGCG GAAAGGAG UAA GA GA GUG GUGCAAC GCCC GUCGC UGGCGUU AUUUACC GC@LB@ :\|\|:\|\|\|\|\|\| \|\| \|\|\|\|\|: :\|\|\|\|\|\|: \|\|\| \|\| :\| :\|\| \|:\|\|\|\|\| \|\|\|\| :\|\|\|\| \|\|:\|\|\|\| \|\|\|:\|\|\| \|\|@LB@ GCUUAGUUAA CG AUACGU UUUUCCUU AUU CU UU UAC CGCGUUG CGGG UAGCG ACUGCAA UAAGUGG CG@LB@3'-UUU...AGCAU CA CAUUAAGUU C G A CU A CG A -5'@LB@ \| \|@LB@ 89 1@LB@@LB@@LB@Energy -14.49 kcal/mol@LB@Hybridization Energy -60.5282 kcal/mol@LB@Unfolding Energy - mRNA 25.2709 kcal/mol@LB@Unfolding Energy - sRNA 20.7761 kcal/mol@LB@@LB@Position - mRNA 139 -- 249@LB@Position - sRNA 1 -- 88@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 4 -- 10@LB@
71	0.001416	0.07026	b0880	cspD	-7.58	0.355655	51 -- 57	1 -- 7	inhibitor of DNA replication cold shock protein homolog	_____________50______58\n_____________\|_______\|\n5'-AUC...AUUCA_______CCCUU...CCA-3'\n______________UACCUGC\n______________:\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	51 -- 57	1 -- 7	-10.3464 kcal/mol	0.429757 kcal/mol	2.34039 kcal/mol	50 58@LB@ \| \|@LB@5'-AUC...AUUCA CCCUU...CCA-3'@LB@ UACCUGC@LB@ :\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -7.58 kcal/mol@LB@Hybridization Energy -10.3464 kcal/mol@LB@Unfolding Energy - mRNA 0.429757 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 51 -- 57@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 51 -- 57@LB@Position Seed - sRNA 1 -- 7@LB@
75	0.001837	0.08273	b1816	yoaE	-14.98	0.004573	118 -- 155	1 -- 35	putative membrane protein/conserved protein	_____________117____________________________________156\n_____________\|______________________________________\|\n5'-GAU...CUCUA___C__A___U_______C__U___U____A_______AUUAU...UUC-3'\n______________UGC_GC_CCU_UCGUUUG_AU_UUG_CGUU_CGCCUGC\n______________:\|\|_:\|_\|\|:_\|\|\|:\|\|\|_\|:_\|\|\|_\|:\|\|_\|:\|\|\|\|\|\n______________GCG_UG_GGG_AGCGAAC_UG_AAC_GUAA_GUGGACG\n3'-UUU...ACCUC___U__C___U__________C________________-5'\n_____________\|_____________________________________\|\n_____________36____________________________________1\n	149 -- 155	1 -- 7	-36.6264 kcal/mol	6.36146 kcal/mol	15.286 kcal/mol	117 156@LB@ \| \|@LB@5'-GAU...CUCUA C A U C U U A AUUAU...UUC-3'@LB@ UGC GC CCU UCGUUUG AU UUG CGUU CGCCUGC@LB@ :\|\| :\| \|\|: \|\|\|:\|\|\| \|: \|\|\| \|:\|\| \|:\|\|\|\|\|@LB@ GCG UG GGG AGCGAAC UG AAC GUAA GUGGACG@LB@3'-UUU...ACCUC U C U C -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -14.98 kcal/mol@LB@Hybridization Energy -36.6264 kcal/mol@LB@Unfolding Energy - mRNA 6.36146 kcal/mol@LB@Unfolding Energy - sRNA 15.286 kcal/mol@LB@@LB@Position - mRNA 118 -- 155@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 1 -- 7@LB@
80	0.001886	0.08273	b3205	yhbJ	-9.88	0.117656	21 -- 27	1 -- 7	adaptor protein for GlmZ/GlmY sRNA decay glucosamine-6-phosphate-regulated; NTPase	_____________20______28\n_____________\|_______\|\n5'-CGG...AAACG_______AUACU...CCG-3'\n______________CACCUGC\n______________\|\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	21 -- 27	1 -- 7	-13.6981 kcal/mol	1.48735 kcal/mol	2.34039 kcal/mol	20 28@LB@ \| \|@LB@5'-CGG...AAACG AUACU...CCG-3'@LB@ CACCUGC@LB@ \|\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -13.6981 kcal/mol@LB@Unfolding Energy - mRNA 1.48735 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 21 -- 27@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 1 -- 7@LB@
81	0.001932	0.08273	b2763	cysI	-12.36	0.027367	234 -- 285	1 -- 58	sulfite reductase beta subunit NAD(P)-binding heme-binding	_____________233_________________________________________________________286\n_____________\|___________________________________________________________\|\n5'-GAA...UGGUC_______AACU_____ACGCC__________AA______A___AA_____AC_______GCGGC...CGG-3'\n______________GAAGGAA____GACAG_____GAGCGC_AUG______GC_UGA____GCA__UACCUGC\n______________:\|\|\|\|\|\|____\|\|\|\|:_____\|\|\|\|\|\|_\|:\|______\|\|_\|\|\|____\|\|\|__:\|\|\|\|\|\|\n______________UUUCCUU____CUGUU_____CUCGCG_UGC______CG_ACU____CGU__GUGGACG\n3'-UUU...AGUUU_______CAUU_____AUAC_______U___GGGUAG__A___GCAA___AA_______-5'\n_____________\|__________________________________________________________\|\n_____________59_________________________________________________________1\n	279 -- 285	1 -- 7	-40.3147 kcal/mol	11.0832 kcal/mol	16.8724 kcal/mol	233 286@LB@ \| \|@LB@5'-GAA...UGGUC AACU ACGCC AA A AA AC GCGGC...CGG-3'@LB@ GAAGGAA GACAG GAGCGC AUG GC UGA GCA UACCUGC@LB@ :\|\|\|\|\|\| \|\|\|\|: \|\|\|\|\|\| \|:\| \|\| \|\|\| \|\|\| :\|\|\|\|\|\|@LB@ UUUCCUU CUGUU CUCGCG UGC CG ACU CGU GUGGACG@LB@3'-UUU...AGUUU CAUU AUAC U GGGUAG A GCAA AA -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -12.36 kcal/mol@LB@Hybridization Energy -40.3147 kcal/mol@LB@Unfolding Energy - mRNA 11.0832 kcal/mol@LB@Unfolding Energy - sRNA 16.8724 kcal/mol@LB@@LB@Position - mRNA 234 -- 285@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 1 -- 7@LB@
82	0.001946	0.08273	b2661	gabD	-10.13	0.102437	19 -- 25	1 -- 7	succinate-semialdehyde dehydrogenase I NADP-dependent	_____________18______26\n_____________\|_______\|\n5'-CAC...AUCCA_______AAUGC...CGG-3'\n______________CACCUGC\n______________\|\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	19 -- 25	1 -- 7	-13.7555 kcal/mol	1.28845 kcal/mol	2.34039 kcal/mol	18 26@LB@ \| \|@LB@5'-CAC...AUCCA AAUGC...CGG-3'@LB@ CACCUGC@LB@ \|\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -10.13 kcal/mol@LB@Hybridization Energy -13.7555 kcal/mol@LB@Unfolding Energy - mRNA 1.28845 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 19 -- 25@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 1 -- 7@LB@
85	0.002164	0.08969	b0910	cmk	-11.54	0.045559	249 -- 300	1 -- 56	cytidylate kinase	_____________248________________________________________________________300\n_____________\|__________________________________________________________\|\n5'-CCG...GUGCA_____________CCUU_________G______G__GGAA________AUGG_______-3'\n______________GGGA___AAGGCA_______GUGUAA_G_CUAU_GC____GCGUUGCA____CAUCUGC\n______________:\|\|\|___\|\|\|:\|\|_______\|:\|:\|\|_\|_\|:\|\|_\|\|____:\|\|\|\|\|\|\|____\|\|:\|\|\|\|\n______________UCCU___UUCUGU_______CGCGUU_C_GGUA_CG____UGCAACGU____GUGGACG\n3'-UUU...UUUUU____UCA______UAUACCU______G_G____G__AAC_________AA_________-5'\n_____________\|__________________________________________________________\|\n_____________57_________________________________________________________1\n	294 -- 300	1 -- 7	-44.7718 kcal/mol	16.3932 kcal/mol	16.8439 kcal/mol	248 300@LB@ \| \|@LB@5'-CCG...GUGCA CCUU G G GGAA AUGG -3'@LB@ GGGA AAGGCA GUGUAA G CUAU GC GCGUUGCA CAUCUGC@LB@ :\|\|\| \|\|\|:\|\| \|:\|:\|\| \| \|:\|\| \|\| :\|\|\|\|\|\|\| \|\|:\|\|\|\|@LB@ UCCU UUCUGU CGCGUU C GGUA CG UGCAACGU GUGGACG@LB@3'-UUU...UUUUU UCA UAUACCU G G G AAC AA -5'@LB@ \| \|@LB@ 57 1@LB@@LB@@LB@Energy -11.54 kcal/mol@LB@Hybridization Energy -44.7718 kcal/mol@LB@Unfolding Energy - mRNA 16.3932 kcal/mol@LB@Unfolding Energy - sRNA 16.8439 kcal/mol@LB@@LB@Position - mRNA 249 -- 300@LB@Position - sRNA 1 -- 56@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 1 -- 7@LB@
90	0.002477	0.09689	b4020	yjbB	-17.01	0.000941	168 -- 222	1 -- 56	putative Na+/Pi-cotransporter	_____________167________________________________________________________223\n_____________\|__________________________________________________________\|\n5'-UCC...GCUUC_____CA__UA______A____AACC___AA______GUUA___C_____________UUUCU...UGC-3'\n______________AGGAA__UA__ACGAUA_GGAG_____UG__C_UCGU____ACG_UGC_UUCACCUGC\n______________\|\|\|\|\|__\|\|__\|\|:\|\|\|_\|\|\|\|_____:\|__\|_\|\|\|:____\|\|\|_\|\|\|_\|\|\|\|\|\|\|\|\|\n______________UCCUU__AU__UGUUAU_CCUC_____GC__G_AGCG____UGC_ACG_AAGUGGACG\n3'-UUU...UUUUU_____C___UC______A____GCGUU__GG_U____AAC____A___U_________-5'\n_____________\|_________________________________________________________\|\n_____________57________________________________________________________1\n	216 -- 222	1 -- 7	-44.3986 kcal/mol	10.5518 kcal/mol	16.8439 kcal/mol	167 223@LB@ \| \|@LB@5'-UCC...GCUUC CA UA A AACC AA GUUA C UUUCU...UGC-3'@LB@ AGGAA UA ACGAUA GGAG UG C UCGU ACG UGC UUCACCUGC@LB@ \|\|\|\|\| \|\| \|\|:\|\|\| \|\|\|\| :\| \| \|\|\|: \|\|\| \|\|\| \|\|\|\|\|\|\|\|\|@LB@ UCCUU AU UGUUAU CCUC GC G AGCG UGC ACG AAGUGGACG@LB@3'-UUU...UUUUU C UC A GCGUU GG U AAC A U -5'@LB@ \| \|@LB@ 57 1@LB@@LB@@LB@Energy -17.01 kcal/mol@LB@Hybridization Energy -44.3986 kcal/mol@LB@Unfolding Energy - mRNA 10.5518 kcal/mol@LB@Unfolding Energy - sRNA 16.8439 kcal/mol@LB@@LB@Position - mRNA 168 -- 222@LB@Position - sRNA 1 -- 56@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 1 -- 7@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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usability assessment

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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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