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	Additional homologs
163	0.006379	0.1377	b2210	mqo	-11.85	0.037664	161 -- 168	1 -- 8	malate dehydrogenase FAD/NAD(P)-binding domain		_____________160______169\n_____________\|________\|\n5'-GGC...AAAUC________AAUAA...AUG-3'\n______________UCACCUGC\n______________\|\|\|\|\|\|\|\|\n______________AGUGGACG\n3'-UUU...ACGUA________-5'\n_____________\|_______\|\n_____________9_______1\n	162 -- 168	1 -- 7	-15.6271 kcal/mol	1.41654 kcal/mol	2.36381 kcal/mol	160 169@LB@ \| \|@LB@5'-GGC...AAAUC AAUAA...AUG-3'@LB@ UCACCUGC@LB@ \|\|\|\|\|\|\|\|@LB@ AGUGGACG@LB@3'-UUU...ACGUA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -11.85 kcal/mol@LB@Hybridization Energy -15.6271 kcal/mol@LB@Unfolding Energy - mRNA 1.41654 kcal/mol@LB@Unfolding Energy - sRNA 2.36381 kcal/mol@LB@@LB@Position - mRNA 161 -- 168@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 1 -- 7@LB@
184	0.008005	0.1528	b3209	elbB	-11.15	0.057587	162 -- 192	53 -- 86	isoprenoid biosynthesis protein with amidotransferase-like domain		_____________161_________________________________193\n_____________\|___________________________________\|\n5'-GCG...AAAAA_____________U______C____GC________UGAUC...GUG-3'\n______________AAUUAA_UGUGUU___CAGU_AAUU___GAAAGGA\n______________\|\|\|:\|\|_\|\|\|\|:\|___\|\|\|\|_\|\|\|\|___:\|\|\|\|\|\|\n______________UUAGUU_ACACGA___GUCA_UUAA___UUUUCCU\n3'-UUU...CAUGC______A______UAC_________GUU_______UCAUU...ACG-5'\n_____________\|___________________________________\|\n_____________87__________________________________52\n	186 -- 192	53 -- 59	-19.5143 kcal/mol	4.60736 kcal/mol	3.76074 kcal/mol	161 193@LB@ \| \|@LB@5'-GCG...AAAAA U C GC UGAUC...GUG-3'@LB@ AAUUAA UGUGUU CAGU AAUU GAAAGGA@LB@ \|\|\|:\|\| \|\|\|\|:\| \|\|\|\| \|\|\|\| :\|\|\|\|\|\|@LB@ UUAGUU ACACGA GUCA UUAA UUUUCCU@LB@3'-UUU...CAUGC A UAC GUU UCAUU...ACG-5'@LB@ \| \|@LB@ 87 52@LB@@LB@@LB@Energy -11.15 kcal/mol@LB@Hybridization Energy -19.5143 kcal/mol@LB@Unfolding Energy - mRNA 4.60736 kcal/mol@LB@Unfolding Energy - sRNA 3.76074 kcal/mol@LB@@LB@Position - mRNA 162 -- 192@LB@Position - sRNA 53 -- 86@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 53 -- 59@LB@
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@
124	0.004441	0.1258	b1656	sodB	-12.34	0.027802	164 -- 220	1 -- 93	superoxide dismutase Fe		_____________163____________________________________________________________________________________________221\n_____________\|______________________________________________________________________________________________\|\n5'-UCU...GGCUA_________________________AAUUAA___U________________________A________AU___AA___________________ACUAC...AGA-3'\n______________UUGUACG____________UAUGCA______UAA_AAAGGA______________GAGU_GCAAUGUC__UCG_____________UUACCUGC\n______________\|:\|\|\|\|\|____________\|\|\|\|\|\|______:\|\|_\|\|\|\|\|\|______________\|\|\|:_\|\|\|\|:\|:\|__\|\|\|_____________\|:\|\|\|\|\|\|\n______________AGCAUGC____________AUACGU______GUU_UUUCCU______________CUCG_CGUUGCGG__AGC_____________AGUGGACG\n3'-UUU...GCCGC_______UUAGUUAACACG______CAUUAA___U______UCAUUCUGUUAUAC_____________GU___GAACUGCAACGUA________-5'\n_____________\|_____________________________________________________________________________________________\|\n_____________94____________________________________________________________________________________________1\n	214 -- 220	1 -- 7	-45.1977 kcal/mol	11.9384 kcal/mol	20.925 kcal/mol	163 221@LB@ \| \|@LB@5'-UCU...GGCUA AAUUAA U A AU AA ACUAC...AGA-3'@LB@ UUGUACG UAUGCA UAA AAAGGA GAGU GCAAUGUC UCG UUACCUGC@LB@ \|:\|\|\|\|\| \|\|\|\|\|\| :\|\| \|\|\|\|\|\| \|\|\|: \|\|\|\|:\|:\| \|\|\| \|:\|\|\|\|\|\|@LB@ AGCAUGC AUACGU GUU UUUCCU CUCG CGUUGCGG AGC AGUGGACG@LB@3'-UUU...GCCGC UUAGUUAACACG CAUUAA U UCAUUCUGUUAUAC GU GAACUGCAACGUA -5'@LB@ \| \|@LB@ 94 1@LB@@LB@@LB@Energy -12.34 kcal/mol@LB@Hybridization Energy -45.1977 kcal/mol@LB@Unfolding Energy - mRNA 11.9384 kcal/mol@LB@Unfolding Energy - sRNA 20.925 kcal/mol@LB@@LB@Position - mRNA 164 -- 220@LB@Position - sRNA 1 -- 93@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 1 -- 7@LB@
10	1.762e-05	0.005627	b1112	bhsA	-13.86	0.010205	165 -- 186	1 -- 22	biofilm cell surface and signaling protein	b0806 b0802	_____________164_____________________187\n_____________\|_______________________\|\n5'-UAA...UAAUU________AC_U___________AUAAG...AAC-3'\n______________GCUUG_CG__G_CAUUCAUCUGC\n______________\|\|\|\|\|_\|\|__\|_\|\|\|\|\|\|:\|\|\|\|\n______________CGAAC_GC__C_GUAAGUGGACG\n3'-UUU...GGUAG_____U__AA_____________-5'\n_____________\|______________________\|\n_____________23_____________________1\n	180 -- 186	1 -- 7	-25.8922 kcal/mol	3.94114 kcal/mol	8.09964 kcal/mol	164 187@LB@ \| \|@LB@5'-UAA...UAAUU AC U AUAAG...AAC-3'@LB@ GCUUG CG G CAUUCAUCUGC@LB@ \|\|\|\|\| \|\| \| \|\|\|\|\|\|:\|\|\|\|@LB@ CGAAC GC C GUAAGUGGACG@LB@3'-UUU...GGUAG U AA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -13.86 kcal/mol@LB@Hybridization Energy -25.8922 kcal/mol@LB@Unfolding Energy - mRNA 3.94114 kcal/mol@LB@Unfolding Energy - sRNA 8.09964 kcal/mol@LB@@LB@Position - mRNA 165 -- 186@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 1 -- 7@LB@
1	1.057e-08	3.724e-05	b0889	lrp	-13.58	0.012310	166 -- 227	21 -- 70	leucine-responsive global transcriptional regulator		_____________165_______________________________________________________________228\n_____________\|_________________________________________________________________\|\n5'-GUG...UCAGA___GAG____________AUAC__A_________AUAA___U__AUA___AGAA________G__AAAGA...AGC-3'\n______________CAG_____UAGGGAAGGA____AG_GAGACAAUA____UGG_AG___GCA____GCGCCC_U_GC\n______________\|\|\|_____:\|:::\|\|\|\|\|____\|\|_:\|\|\|\|\|\|\|\|____\|\|\|_\|\|___\|\|\|____:\|\|\|\|\|_\|_\|\|\n______________GUC_____GUUUUUUCCU____UC_UUCUGUUAU____ACC_UC___CGU____UGCGGG_A_CG\n3'-UUU...GAUAC___AUUAA________________A___________________G_______________U_G__AACUG...ACG-5'\n_____________\|_________________________________________________________________\|\n_____________71________________________________________________________________20\n	191 -- 197	41 -- 47	-39.3483 kcal/mol	8.89245 kcal/mol	16.878 kcal/mol	165 228@LB@ \| \|@LB@5'-GUG...UCAGA GAG AUAC A AUAA U AUA AGAA G AAAGA...AGC-3'@LB@ CAG UAGGGAAGGA AG GAGACAAUA UGG AG GCA GCGCCC U GC@LB@ \|\|\| :\|:::\|\|\|\|\| \|\| :\|\|\|\|\|\|\|\| \|\|\| \|\| \|\|\| :\|\|\|\|\| \| \|\|@LB@ GUC GUUUUUUCCU UC UUCUGUUAU ACC UC CGU UGCGGG A CG@LB@3'-UUU...GAUAC AUUAA A G U G AACUG...ACG-5'@LB@ \| \|@LB@ 71 20@LB@@LB@@LB@Energy -13.58 kcal/mol@LB@Hybridization Energy -39.3483 kcal/mol@LB@Unfolding Energy - mRNA 8.89245 kcal/mol@LB@Unfolding Energy - sRNA 16.878 kcal/mol@LB@@LB@Position - mRNA 166 -- 227@LB@Position - sRNA 21 -- 70@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 41 -- 47@LB@
173	0.007186	0.145	b3554	yiaF	-10.99	0.063148	166 -- 198	46 -- 94	barrier effect co-colonization resistance factor; DUF3053 family lipoprotein		_____________165_______________________________________________199\n_____________\|_________________________________________________\|\n5'-AAU...GUGUC________CU__UU___G_______________________________AAAUG...AGC-3'\n______________GUUGUGCG__UU__UUG_GU_______________GAAAGG_AGUAAGA\n______________\|\|:\|\|:\|\|__\|:__\|\|\|_\|:_______________:\|\|\|\|\|_\|\|\|\|\|\|\|\n______________CAGCAUGC__AG__AAC_CG_______________UUUUCC_UCAUUCU\n3'-UUU...AGCCG________UU__UU___A__AUACGUCAUUAAGUU______U_______GUUAU...ACG-5'\n_____________\|_________________________________________________\|\n_____________95________________________________________________45\n	192 -- 198	46 -- 52	-24.2986 kcal/mol	7.73667 kcal/mol	5.5768 kcal/mol	165 199@LB@ \| \|@LB@5'-AAU...GUGUC CU UU G AAAUG...AGC-3'@LB@ GUUGUGCG UU UUG GU GAAAGG AGUAAGA@LB@ \|\|:\|\|:\|\| \|: \|\|\| \|: :\|\|\|\|\| \|\|\|\|\|\|\|@LB@ CAGCAUGC AG AAC CG UUUUCC UCAUUCU@LB@3'-UUU...AGCCG UU UU A AUACGUCAUUAAGUU U GUUAU...ACG-5'@LB@ \| \|@LB@ 95 45@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -24.2986 kcal/mol@LB@Unfolding Energy - mRNA 7.73667 kcal/mol@LB@Unfolding Energy - sRNA 5.5768 kcal/mol@LB@@LB@Position - mRNA 166 -- 198@LB@Position - sRNA 46 -- 94@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 46 -- 52@LB@
41	0.0003478	0.02948	b1478	adhP	-14.79	0.005262	167 -- 196	51 -- 77	ethanol-active dehydrogenase/acetaldehyde-active reductase		_____________166____________________________197\n_____________\|______________________________\|\n5'-GCA...UCACC__________AACA___UCC__________AACUA...GUU-3'\n______________UGCUAUGCAG____UCA___GAAAAGGAGG\n______________\|\|\|\|\|\|\|\|\|\|____\|\|\|___:\|\|\|\|\|\|\|:\|\n______________ACGAUACGUC____AGU___UUUUUCCUUC\n3'-UUU...UUAAC__________AUUA________________AUUCU...ACG-5'\n_____________\|______________________________\|\n_____________78_____________________________50\n	190 -- 196	51 -- 57	-28.1635 kcal/mol	8.82843 kcal/mol	4.54711 kcal/mol	166 197@LB@ \| \|@LB@5'-GCA...UCACC AACA UCC AACUA...GUU-3'@LB@ UGCUAUGCAG UCA GAAAAGGAGG@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\| :\|\|\|\|\|\|\|:\|@LB@ ACGAUACGUC AGU UUUUUCCUUC@LB@3'-UUU...UUAAC AUUA AUUCU...ACG-5'@LB@ \| \|@LB@ 78 50@LB@@LB@@LB@Energy -14.79 kcal/mol@LB@Hybridization Energy -28.1635 kcal/mol@LB@Unfolding Energy - mRNA 8.82843 kcal/mol@LB@Unfolding Energy - sRNA 4.54711 kcal/mol@LB@@LB@Position - mRNA 167 -- 196@LB@Position - sRNA 51 -- 77@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 51 -- 57@LB@
66	0.001137	0.05992	b0076	leuO	-9.90	0.116504	167 -- 195	35 -- 60	global transcription factor		_____________166_____________________________196\n_____________\|_______________________________\|\n5'-UAU...AUAAG___________UAAGUGU_____________UAAGU...UGA-3'\n______________GGAAAGGGAGU_______GACA__GUGGAGU\n______________::\|\|\|\|\|:\|\|\|_______\|\|\|\|__:\|\|\|\|\|:\n______________UUUUUCCUUCA_______CUGU__UACCUCG\n3'-UUU...UAAGU___________UU_________UA_______CGUUG...ACG-5'\n_____________\|_______________________________\|\n_____________61______________________________34\n	189 -- 195	35 -- 41	-23.1584 kcal/mol	8.98888 kcal/mol	4.23745 kcal/mol	166 196@LB@ \| \|@LB@5'-UAU...AUAAG UAAGUGU UAAGU...UGA-3'@LB@ GGAAAGGGAGU GACA GUGGAGU@LB@ ::\|\|\|\|\|:\|\|\| \|\|\|\| :\|\|\|\|\|:@LB@ UUUUUCCUUCA CUGU UACCUCG@LB@3'-UUU...UAAGU UU UA CGUUG...ACG-5'@LB@ \| \|@LB@ 61 34@LB@@LB@@LB@Energy -9.90 kcal/mol@LB@Hybridization Energy -23.1584 kcal/mol@LB@Unfolding Energy - mRNA 8.98888 kcal/mol@LB@Unfolding Energy - sRNA 4.23745 kcal/mol@LB@@LB@Position - mRNA 167 -- 195@LB@Position - sRNA 35 -- 60@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 35 -- 41@LB@
195	0.008697	0.1548	b0192	nlpE	-11.98	0.034903	167 -- 206	41 -- 78	lipoprotein involved with copper homeostasis and adhesion		_____________166________________________________________207\n_____________\|__________________________________________\|\n5'-UCA...GCAAA____GCA_____CGGG___AA__________U__________AAAAA...CGC-3'\n______________GUGC___GCGGU____AAU__AAAGAAGGAA___GGAUGGUG\n______________\|\|\|\|___\|\|:\|\|____\|\|\|__\|\|\|:\|\|\|\|\|\|___:\|\|:::\|:\n______________CACG___CGUCA____UUA__UUUUUUCCUU___UCUGUUAU\n3'-UUU...GUUAA____AUA____________AG__________CAU________ACCUC...ACG-5'\n_____________\|__________________________________________\|\n_____________79_________________________________________40\n	200 -- 206	41 -- 47	-26.7874 kcal/mol	9.04038 kcal/mol	5.77415 kcal/mol	166 207@LB@ \| \|@LB@5'-UCA...GCAAA GCA CGGG AA U AAAAA...CGC-3'@LB@ GUGC GCGGU AAU AAAGAAGGAA GGAUGGUG@LB@ \|\|\|\| \|\|:\|\| \|\|\| \|\|\|:\|\|\|\|\|\| :\|\|:::\|:@LB@ CACG CGUCA UUA UUUUUUCCUU UCUGUUAU@LB@3'-UUU...GUUAA AUA AG CAU ACCUC...ACG-5'@LB@ \| \|@LB@ 79 40@LB@@LB@@LB@Energy -11.98 kcal/mol@LB@Hybridization Energy -26.7874 kcal/mol@LB@Unfolding Energy - mRNA 9.04038 kcal/mol@LB@Unfolding Energy - sRNA 5.77415 kcal/mol@LB@@LB@Position - mRNA 167 -- 206@LB@Position - sRNA 41 -- 78@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 41 -- 47@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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