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
71	0.002886	0.1417	b2431	yfeX	-11.26	0.145044	235 -- 277	40 -- 74	porphyrinogen oxidase cytoplasmic	_____________234_________________________________________278\n_____________\|___________________________________________\|\n5'-AUU...AGAAC____C______________GAUCGAA__CAACGUGAA______AGUUG...CCA-3'\n______________AUUG_CGCGCGGCGAUUUG_______GC_________AGGGGA\n______________\|:\|:_\|:\|:\|:\|\|:\|\|\|:\|_______:\|_________\|\|\|\|\|\|\n______________UGAU_GUGUGUCGUUAAGC_______UG_________UCCCCU\n3'-UUU...GUUUC___________________AACAAAG__AG_____________AAAGG...GCA-5'\n_____________\|___________________________________________\|\n_____________75__________________________________________39\n	246 -- 252	58 -- 64	-30.0675 kcal/mol	14.0273 kcal/mol	4.77707 kcal/mol	234 278@LB@ \| \|@LB@5'-AUU...AGAAC C GAUCGAA CAACGUGAA AGUUG...CCA-3'@LB@ AUUG CGCGCGGCGAUUUG GC AGGGGA@LB@ \|:\|: \|:\|:\|:\|\|:\|\|\|:\| :\| \|\|\|\|\|\|@LB@ UGAU GUGUGUCGUUAAGC UG UCCCCU@LB@3'-UUU...GUUUC AACAAAG AG AAAGG...GCA-5'@LB@ \| \|@LB@ 75 39@LB@@LB@@LB@Energy -11.26 kcal/mol@LB@Hybridization Energy -30.0675 kcal/mol@LB@Unfolding Energy - mRNA 14.0273 kcal/mol@LB@Unfolding Energy - sRNA 4.77707 kcal/mol@LB@@LB@Position - mRNA 235 -- 277@LB@Position - sRNA 40 -- 74@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 58 -- 64@LB@
72	0.002899	0.1417	b3688	yidQ	-12.98	0.064171	231 -- 261	39 -- 71	DUF1375 family outer membrane protein	_____________230_______________________________262\n_____________\|_________________________________\|\n5'-AUG...UCAUG___________AAUGACA__________A____GCUCC...GAA-3'\n______________AUAUGCAGCGG_________UUACUCGG_GGAU\n______________\|:\|::\|\|\|\|::_________\|:\|\|\|\|:\|_\|\|\|\|\n______________UGUGUGUCGUU_________AGUGAGUC_CCUA\n3'-UUU...UCUGA___________AAGCAACAA________C____AAGGU...GCA-5'\n_____________\|_________________________________\|\n_____________72________________________________38\n	250 -- 256	44 -- 50	-25.1937 kcal/mol	7.46905 kcal/mol	4.74947 kcal/mol	230 262@LB@ \| \|@LB@5'-AUG...UCAUG AAUGACA A GCUCC...GAA-3'@LB@ AUAUGCAGCGG UUACUCGG GGAU@LB@ \|:\|::\|\|\|\|:: \|:\|\|\|\|:\| \|\|\|\|@LB@ UGUGUGUCGUU AGUGAGUC CCUA@LB@3'-UUU...UCUGA AAGCAACAA C AAGGU...GCA-5'@LB@ \| \|@LB@ 72 38@LB@@LB@@LB@Energy -12.98 kcal/mol@LB@Hybridization Energy -25.1937 kcal/mol@LB@Unfolding Energy - mRNA 7.46905 kcal/mol@LB@Unfolding Energy - sRNA 4.74947 kcal/mol@LB@@LB@Position - mRNA 231 -- 261@LB@Position - sRNA 39 -- 71@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 44 -- 50@LB@
73	0.00298	0.1437	b0474	adk	-13.48	0.049381	180 -- 198	34 -- 50	adenylate kinase	_____________179_________________199\n_____________\|___________________\|\n5'-ACC...CGACA_____UA____________CAAUG...AUA-3'\n______________CAUUU__AGGGGAUUUUCG\n______________\|\|:\|:__\|\|\|\|\|\|\|\|\|:\|:\n______________GUGAG__UCCCCUAAAGGU\n3'-UUU...ACAAA___________________ACGAA...GCA-5'\n_____________\|___________________\|\n_____________51__________________33\n	191 -- 197	35 -- 41	-19.9961 kcal/mol	4.64453 kcal/mol	1.87382 kcal/mol	179 199@LB@ \| \|@LB@5'-ACC...CGACA UA CAAUG...AUA-3'@LB@ CAUUU AGGGGAUUUUCG@LB@ \|\|:\|: \|\|\|\|\|\|\|\|\|:\|:@LB@ GUGAG UCCCCUAAAGGU@LB@3'-UUU...ACAAA ACGAA...GCA-5'@LB@ \| \|@LB@ 51 33@LB@@LB@@LB@Energy -13.48 kcal/mol@LB@Hybridization Energy -19.9961 kcal/mol@LB@Unfolding Energy - mRNA 4.64453 kcal/mol@LB@Unfolding Energy - sRNA 1.87382 kcal/mol@LB@@LB@Position - mRNA 180 -- 198@LB@Position - sRNA 34 -- 50@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 35 -- 41@LB@
74	0.003066	0.1452	b0467	priC	-11.71	0.118543	157 -- 193	43 -- 75	primosomal replication protein N''	_____________156___________________________________194\n_____________\|_____________________________________\|\n5'-GGG...AGAGU______UUUA_____A_____AUCAU_______G___UCUUA...GUU-3'\n______________GGCUAC____GCAUA_CAAUU_____UUUCAUU_AGG\n______________\|:\|\|\|\|____:\|\|:\|_\|\|\|\|\|_____\|\|\|\|\|:\|_\|\|\|\n______________CUGAUG____UGUGU_GUUAA_____AAAGUGA_UCC\n3'-UUU...CGUUU_______________C_____GCAAC_______G___CCUAA...GCA-5'\n_____________\|_____________________________________\|\n_____________76____________________________________42\n	183 -- 189	47 -- 53	-24.815 kcal/mol	8.75149 kcal/mol	4.35266 kcal/mol	156 194@LB@ \| \|@LB@5'-GGG...AGAGU UUUA A AUCAU G UCUUA...GUU-3'@LB@ GGCUAC GCAUA CAAUU UUUCAUU AGG@LB@ \|:\|\|\|\| :\|\|:\| \|\|\|\|\| \|\|\|\|\|:\| \|\|\|@LB@ CUGAUG UGUGU GUUAA AAAGUGA UCC@LB@3'-UUU...CGUUU C GCAAC G CCUAA...GCA-5'@LB@ \| \|@LB@ 76 42@LB@@LB@@LB@Energy -11.71 kcal/mol@LB@Hybridization Energy -24.815 kcal/mol@LB@Unfolding Energy - mRNA 8.75149 kcal/mol@LB@Unfolding Energy - sRNA 4.35266 kcal/mol@LB@@LB@Position - mRNA 157 -- 193@LB@Position - sRNA 43 -- 75@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 47 -- 53@LB@
75	0.003119	0.1452	b0871	poxB	-11.12	0.154817	181 -- 203	32 -- 50	pyruvate dehydrogenase thiamine triphosphate-binding FAD-binding	_____________180_____________________204\n_____________\|_______________________\|\n5'-CCG...UAUCA________AGAU___GAA_____AAACA...GUG-3'\n______________CAUUCAGG____GGA___CCAUG\n______________\|\|:\|\|\|\|\|____\|\|\|___\|\|\|\|\|\n______________GUGAGUCC____CCU___GGUAC\n3'-UUU...ACAAA_______________AAA_____GAAUA...GCA-5'\n_____________\|_______________________\|\n_____________51______________________31\n	182 -- 188	43 -- 49	-21.2585 kcal/mol	5.84423 kcal/mol	4.29868 kcal/mol	180 204@LB@ \| \|@LB@5'-CCG...UAUCA AGAU GAA AAACA...GUG-3'@LB@ CAUUCAGG GGA CCAUG@LB@ \|\|:\|\|\|\|\| \|\|\| \|\|\|\|\|@LB@ GUGAGUCC CCU GGUAC@LB@3'-UUU...ACAAA AAA GAAUA...GCA-5'@LB@ \| \|@LB@ 51 31@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -21.2585 kcal/mol@LB@Unfolding Energy - mRNA 5.84423 kcal/mol@LB@Unfolding Energy - sRNA 4.29868 kcal/mol@LB@@LB@Position - mRNA 181 -- 203@LB@Position - sRNA 32 -- 50@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 43 -- 49@LB@
76	0.003141	0.1452	b0187	yaeR	-8.98	0.354982	261 -- 292	48 -- 78	putative lyase	_____________260_______________________________293\n_____________\|_________________________________\|\n5'-AAA...UGAGC_______UUC___U_____AU__UUG_______GCUGCAAA-3'\n______________AAAG_CU___UAC_GCGAU__UC___GUUUCAC\n______________\|\|\|\|_\|\|___:\|\|_\|\|:\|\|__\|\|___\|\|\|\|\|\|\|\n______________UUUC_GA___GUG_CGUUA__AG___CAAAGUG\n3'-UUU...ACCCG____U__UGU___U_________CAA_______AGUCC...GCA-5'\n_____________\|_________________________________\|\n_____________79________________________________47\n	286 -- 292	48 -- 54	-17.4111 kcal/mol	4.74942 kcal/mol	3.68736 kcal/mol	260 293@LB@ \| \|@LB@5'-AAA...UGAGC UUC U AU UUG GCUGCAAA-3'@LB@ AAAG CU UAC GCGAU UC GUUUCAC@LB@ \|\|\|\| \|\| :\|\| \|\|:\|\| \|\| \|\|\|\|\|\|\|@LB@ UUUC GA GUG CGUUA AG CAAAGUG@LB@3'-UUU...ACCCG U UGU U CAA AGUCC...GCA-5'@LB@ \| \|@LB@ 79 47@LB@@LB@@LB@Energy -8.98 kcal/mol@LB@Hybridization Energy -17.4111 kcal/mol@LB@Unfolding Energy - mRNA 4.74942 kcal/mol@LB@Unfolding Energy - sRNA 3.68736 kcal/mol@LB@@LB@Position - mRNA 261 -- 292@LB@Position - sRNA 48 -- 78@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 48 -- 54@LB@
77	0.003184	0.1452	b4406	yaeP	-9.70	0.274250	222 -- 254	40 -- 71	UPF0253 family protein	_____________221________________________________255\n_____________\|__________________________________\|\n5'-ACC...AGUUA_______A_____A__CG_AAA________C___GACUU...UGC-3'\n______________AUACGCA_GCGGU_CG__G___UCGC_CAG_GGA\n______________\|:\|\|:\|\|_\|\|::\|_\|\|__\|___\|\|:\|_\|\|\|_\|\|\|\n______________UGUGUGU_CGUUA_GC__C___AGUG_GUC_CCU\n3'-UUU...UCUGA_____________A__AA_AA_____A___C___AAAGG...GCA-5'\n_____________\|__________________________________\|\n_____________72_________________________________39\n	222 -- 228	65 -- 71	-25.8836 kcal/mol	11.435 kcal/mol	4.74818 kcal/mol	221 255@LB@ \| \|@LB@5'-ACC...AGUUA A A CG AAA C GACUU...UGC-3'@LB@ AUACGCA GCGGU CG G UCGC CAG GGA@LB@ \|:\|\|:\|\| \|\|::\| \|\| \| \|\|:\| \|\|\| \|\|\|@LB@ UGUGUGU CGUUA GC C AGUG GUC CCU@LB@3'-UUU...UCUGA A AA AA A C AAAGG...GCA-5'@LB@ \| \|@LB@ 72 39@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -25.8836 kcal/mol@LB@Unfolding Energy - mRNA 11.435 kcal/mol@LB@Unfolding Energy - sRNA 4.74818 kcal/mol@LB@@LB@Position - mRNA 222 -- 254@LB@Position - sRNA 40 -- 71@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 65 -- 71@LB@
78	0.003218	0.1452	b1641	slyB	-13.21	0.056987	203 -- 235	43 -- 75	outer membrane lipoprotein	_____________202_________________________________236\n_____________\|___________________________________\|\n5'-CCG...UCAAU_____A___________G_________AUGG____UCUGU...AAG-3'\n______________GAUUA_ACGC_GU_AUU_GUUGUUUCA____UAGG\n______________\|\|:\|\|_\|\|:\|_\|:_\|\|\|_\|\|\|\|\|\|\|\|\|____:\|\|\|\n______________CUGAU_UGUG_CG_UAA_CAACAAAGU____GUCC\n3'-UUU...CGUUU_____G____U__U___G_________GA______CCUAA...GCA-5'\n_____________\|___________________________________\|\n_____________76__________________________________42\n	221 -- 227	49 -- 55	-26.1882 kcal/mol	8.63028 kcal/mol	4.35266 kcal/mol	202 236@LB@ \| \|@LB@5'-CCG...UCAAU A G AUGG UCUGU...AAG-3'@LB@ GAUUA ACGC GU AUU GUUGUUUCA UAGG@LB@ \|\|:\|\| \|\|:\| \|: \|\|\| \|\|\|\|\|\|\|\|\| :\|\|\|@LB@ CUGAU UGUG CG UAA CAACAAAGU GUCC@LB@3'-UUU...CGUUU G U U G GA CCUAA...GCA-5'@LB@ \| \|@LB@ 76 42@LB@@LB@@LB@Energy -13.21 kcal/mol@LB@Hybridization Energy -26.1882 kcal/mol@LB@Unfolding Energy - mRNA 8.63028 kcal/mol@LB@Unfolding Energy - sRNA 4.35266 kcal/mol@LB@@LB@Position - mRNA 203 -- 235@LB@Position - sRNA 43 -- 75@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 49 -- 55@LB@
79	0.00332	0.1462	b1845	ptrB	-10.90	0.169644	42 -- 70	35 -- 70	protease II	_____________41____________________________________71\n_____________\|_____________________________________\|\n5'-UCU...AGAAU________C_____AA____________CU_______UCUGU...AGC-3'\n______________CGCACAGC_AUUUG__________CAGG__GAUUUUC\n______________\|:\|\|\|\|\|\|_\|\|\|:\|__________\|\|\|\|__\|\|\|\|\|:\|\n______________GUGUGUCG_UAAGC__________GUCC__CUAAAGG\n3'-UUU...CUGAU________U_____AACAAAGUGA____C________UACGA...GCA-5'\n_____________\|_____________________________________\|\n_____________71____________________________________34\n	64 -- 70	35 -- 41	-24.5069 kcal/mol	8.82337 kcal/mol	4.7817 kcal/mol	41 71@LB@ \| \|@LB@5'-UCU...AGAAU C AA CU UCUGU...AGC-3'@LB@ CGCACAGC AUUUG CAGG GAUUUUC@LB@ \|:\|\|\|\|\|\| \|\|\|:\| \|\|\|\| \|\|\|\|\|:\|@LB@ GUGUGUCG UAAGC GUCC CUAAAGG@LB@3'-UUU...CUGAU U AACAAAGUGA C UACGA...GCA-5'@LB@ \| \|@LB@ 71 34@LB@@LB@@LB@Energy -10.90 kcal/mol@LB@Hybridization Energy -24.5069 kcal/mol@LB@Unfolding Energy - mRNA 8.82337 kcal/mol@LB@Unfolding Energy - sRNA 4.7817 kcal/mol@LB@@LB@Position - mRNA 42 -- 70@LB@Position - sRNA 35 -- 70@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 35 -- 41@LB@
80	0.003376	0.1462	b3098	yqjD	-10.12	0.233597	155 -- 204	31 -- 75	membrane-anchored ribosome-binding protein	_____________154_________________________________________________205\n_____________\|___________________________________________________\|\n5'-UCA...CGCGC______UA__UCA____A___CACUAC_______CCU__A__AAA______CGAAA...AAG-3'\n______________GACUAC__AC___CAAU__GU______UUACUCA___GG_GA___CUAUGU\n______________\|\|\|\|\|\|__\|\|___\|\|\|\|__\|\|______\|:\|\|\|\|\|___\|\|_\|\|___\|:\|\|\|:\n______________CUGAUG__UG___GUUA__CA______AGUGAGU___CC_CU___GGUACG\n3'-UUU...CGUUU______UG__UC_____AG__ACAA_________C_______AAA______AAUAU...GCA-5'\n_____________\|___________________________________________________\|\n_____________76__________________________________________________30\n	181 -- 187	45 -- 51	-24.4421 kcal/mol	7.05998 kcal/mol	7.26183 kcal/mol	154 205@LB@ \| \|@LB@5'-UCA...CGCGC UA UCA A CACUAC CCU A AAA CGAAA...AAG-3'@LB@ GACUAC AC CAAU GU UUACUCA GG GA CUAUGU@LB@ \|\|\|\|\|\| \|\| \|\|\|\| \|\| \|:\|\|\|\|\| \|\| \|\| \|:\|\|\|:@LB@ CUGAUG UG GUUA CA AGUGAGU CC CU GGUACG@LB@3'-UUU...CGUUU UG UC AG ACAA C AAA AAUAU...GCA-5'@LB@ \| \|@LB@ 76 30@LB@@LB@@LB@Energy -10.12 kcal/mol@LB@Hybridization Energy -24.4421 kcal/mol@LB@Unfolding Energy - mRNA 7.05998 kcal/mol@LB@Unfolding Energy - sRNA 7.26183 kcal/mol@LB@@LB@Position - mRNA 155 -- 204@LB@Position - sRNA 31 -- 75@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 45 -- 51@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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