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
3	3.356e-06	0.003937	b3724	phoU	-15.84	0.012477	157 -- 192	43 -- 78	negative regulator of PhoR/PhoB two-component regulator	_____________156____________________________________193\n_____________\|______________________________________\|\n5'-ACC...AAACA______________C_________ACGG__G_______AGUGC...AGC-3'\n______________GAAGACUACAU_CA_CGG_UCGUU____UU_AUUCAGG\n______________:\|\|\|\|\|\|\|\|\|:_\|\|_\|::_\|\|\|\|\|____\|\|_\|:\|\|\|\|\|\n______________UUUCUGAUGUG_GU_GUU_AGCAA____AA_UGAGUCC\n3'-UUU...ACCCG___________U__C___A_____CA____G_______CCUAA...GCA-5'\n_____________\|______________________________________\|\n_____________79_____________________________________42\n	186 -- 192	43 -- 49	-29.823 kcal/mol	9.63349 kcal/mol	4.35315 kcal/mol	156 193@LB@ \| \|@LB@5'-ACC...AAACA C ACGG G AGUGC...AGC-3'@LB@ GAAGACUACAU CA CGG UCGUU UU AUUCAGG@LB@ :\|\|\|\|\|\|\|\|\|: \|\| \|:: \|\|\|\|\| \|\| \|:\|\|\|\|\|@LB@ UUUCUGAUGUG GU GUU AGCAA AA UGAGUCC@LB@3'-UUU...ACCCG U C A CA G CCUAA...GCA-5'@LB@ \| \|@LB@ 79 42@LB@@LB@@LB@Energy -15.84 kcal/mol@LB@Hybridization Energy -29.823 kcal/mol@LB@Unfolding Energy - mRNA 9.63349 kcal/mol@LB@Unfolding Energy - sRNA 4.35315 kcal/mol@LB@@LB@Position - mRNA 157 -- 192@LB@Position - sRNA 43 -- 78@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 43 -- 49@LB@
106	0.004704	0.1538	b0995	torR	-15.76	0.013096	243 -- 292	33 -- 70	response regulator in two-component regulatory system with TorS	_____________242_________________________________________________293\n_____________\|___________________________________________________\|\n5'-CCA...UUACC__G_________ACAAUCCUAC__________A__GGUAUACC________UACGGCGA-3'\n______________CA_GC_GCGAUU__________UUCACUCAGG_GG________GUUUCCGU\n______________\|\|_:\|_\|\|:\|\|\|__________\|\|\|\|\|\|\|\|\|\|_\|\|________:\|\|\|\|\|:\|\n______________GU_UG_CGUUAA__________AAGUGAGUCC_CC________UAAAGGUA\n3'-UUU...CUGAU__G__U______GCAACA_________________________________CGAAU...GCA-5'\n_____________\|___________________________________________________\|\n_____________71__________________________________________________32\n	286 -- 292	33 -- 39	-31.2367 kcal/mol	10.6838 kcal/mol	4.7924 kcal/mol	242 293@LB@ \| \|@LB@5'-CCA...UUACC G ACAAUCCUAC A GGUAUACC UACGGCGA-3'@LB@ CA GC GCGAUU UUCACUCAGG GG GUUUCCGU@LB@ \|\| :\| \|\|:\|\|\| \|\|\|\|\|\|\|\|\|\| \|\| :\|\|\|\|\|:\|@LB@ GU UG CGUUAA AAGUGAGUCC CC UAAAGGUA@LB@3'-UUU...CUGAU G U GCAACA CGAAU...GCA-5'@LB@ \| \|@LB@ 71 32@LB@@LB@@LB@Energy -15.76 kcal/mol@LB@Hybridization Energy -31.2367 kcal/mol@LB@Unfolding Energy - mRNA 10.6838 kcal/mol@LB@Unfolding Energy - sRNA 4.7924 kcal/mol@LB@@LB@Position - mRNA 243 -- 292@LB@Position - sRNA 33 -- 70@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 33 -- 39@LB@
200	0.01028	0.1776	b2803	fucK	-15.72	0.013449	16 -- 30	62 -- 76	L-fuculokinase	_____________15______________31\n_____________\|_______________\|\n5'-AUC...UGCCU_______________UGGAU...CGC-3'\n______________GGGCUGCGCACGGCA\n______________:\|:\|\|:\|:\|\|\|:\|\|\|\n______________UCUGAUGUGUGUCGU\n3'-UUU...CCGUU_______________UAAGC...GCA-5'\n_____________\|_______________\|\n_____________77______________61\n	24 -- 30	62 -- 68	-24.6836 kcal/mol	5.71098 kcal/mol	3.25371 kcal/mol	15 31@LB@ \| \|@LB@5'-AUC...UGCCU UGGAU...CGC-3'@LB@ GGGCUGCGCACGGCA@LB@ :\|:\|\|:\|:\|\|\|:\|\|\|@LB@ UCUGAUGUGUGUCGU@LB@3'-UUU...CCGUU UAAGC...GCA-5'@LB@ \| \|@LB@ 77 61@LB@@LB@@LB@Energy -15.72 kcal/mol@LB@Hybridization Energy -24.6836 kcal/mol@LB@Unfolding Energy - mRNA 5.71098 kcal/mol@LB@Unfolding Energy - sRNA 3.25371 kcal/mol@LB@@LB@Position - mRNA 16 -- 30@LB@Position - sRNA 62 -- 76@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 62 -- 68@LB@
131	0.005914	0.1577	b2360	yfdQ	-15.68	0.013816	114 -- 143	46 -- 74	CPS-53 (KpLE1) prophage; uncharacterized protein	_____________113____________________________144\n_____________\|______________________________\|\n5'-UCC...GGAAA___C__________G__AUUAAUA______UUAAU...CUG-3'\n______________ACU_CGCGCAGCAG_UC_______UCAUUC\n______________\|\|\|_\|:\|:\|\|\|\|\|:_\|\|_______\|\|\|:\|\|\n______________UGA_GUGUGUCGUU_AG_______AGUGAG\n3'-UUU...GUUUC___U__________A__CAACAA_______UCCCC...GCA-5'\n_____________\|______________________________\|\n_____________75_____________________________45\n	121 -- 127	61 -- 67	-23.4619 kcal/mol	4.06011 kcal/mol	3.72594 kcal/mol	113 144@LB@ \| \|@LB@5'-UCC...GGAAA C G AUUAAUA UUAAU...CUG-3'@LB@ ACU CGCGCAGCAG UC UCAUUC@LB@ \|\|\| \|:\|:\|\|\|\|\|: \|\| \|\|\|:\|\|@LB@ UGA GUGUGUCGUU AG AGUGAG@LB@3'-UUU...GUUUC U A CAACAA UCCCC...GCA-5'@LB@ \| \|@LB@ 75 45@LB@@LB@@LB@Energy -15.68 kcal/mol@LB@Hybridization Energy -23.4619 kcal/mol@LB@Unfolding Energy - mRNA 4.06011 kcal/mol@LB@Unfolding Energy - sRNA 3.72594 kcal/mol@LB@@LB@Position - mRNA 114 -- 143@LB@Position - sRNA 46 -- 74@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 61 -- 67@LB@
20	0.0001757	0.02926	b4175	hflC	-15.67	0.013919	175 -- 193	40 -- 75	HflB protease modulator specific for phage lambda cII repressor	_____________174__________________________________194\n_____________\|____________________________________\|\n5'-UUA...GUAAC____________________________________AAUAA...GUU-3'\n______________GACUAC___CAGCG______________UCAGGGGG\n______________\|\|\|\|\|\|___\|\|\|\|:______________\|\|\|\|\|\|\|:\n______________CUGAUG___GUCGU______________AGUCCCCU\n3'-UUU...CGUUU______UGU_____UAAGCAACAAAGUG________AAAGG...GCA-5'\n_____________\|____________________________________\|\n_____________76___________________________________39\n	187 -- 193	40 -- 46	-24.7611 kcal/mol	4.31935 kcal/mol	4.77786 kcal/mol	174 194@LB@ \| \|@LB@5'-UUA...GUAAC AAUAA...GUU-3'@LB@ GACUAC CAGCG UCAGGGGG@LB@ \|\|\|\|\|\| \|\|\|\|: \|\|\|\|\|\|\|:@LB@ CUGAUG GUCGU AGUCCCCU@LB@3'-UUU...CGUUU UGU UAAGCAACAAAGUG AAAGG...GCA-5'@LB@ \| \|@LB@ 76 39@LB@@LB@@LB@Energy -15.67 kcal/mol@LB@Hybridization Energy -24.7611 kcal/mol@LB@Unfolding Energy - mRNA 4.31935 kcal/mol@LB@Unfolding Energy - sRNA 4.77786 kcal/mol@LB@@LB@Position - mRNA 175 -- 193@LB@Position - sRNA 40 -- 75@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 40 -- 46@LB@
33	0.0005309	0.05552	b2905	gcvT	-15.66	0.013961	227 -- 265	34 -- 74	aminomethyltransferase tetrahydrofolate-dependent subunit (T protein) of glycine cleavage complex	_____________226___________________________________________266\n_____________\|_____________________________________________\|\n5'-CUG...UACGA__A_______________CG__________CAU__U_________CGGCU...AAA-3'\n______________AC_ACACAC_GC__UUUG__G___CGCUCG___GG_GGAUUUCCA\n______________\|\|_\|\|\|\|\|\|_\|\|__\|\|:\|__\|___\|:\|\|\|:___\|\|_\|\|\|\|\|\|\|\|\|\n______________UG_UGUGUG_CG__AAGC__C___GUGAGU___CC_CCUAAAGGU\n3'-UUU...GUUUC__A______U__UU____AA_AAA_____________________ACGAA...GCA-5'\n_____________\|_____________________________________________\|\n_____________75____________________________________________33\n	259 -- 265	34 -- 40	-32.8395 kcal/mol	12.3643 kcal/mol	4.81599 kcal/mol	226 266@LB@ \| \|@LB@5'-CUG...UACGA A CG CAU U CGGCU...AAA-3'@LB@ AC ACACAC GC UUUG G CGCUCG GG GGAUUUCCA@LB@ \|\| \|\|\|\|\|\| \|\| \|\|:\| \| \|:\|\|\|: \|\| \|\|\|\|\|\|\|\|\|@LB@ UG UGUGUG CG AAGC C GUGAGU CC CCUAAAGGU@LB@3'-UUU...GUUUC A U UU AA AAA ACGAA...GCA-5'@LB@ \| \|@LB@ 75 33@LB@@LB@@LB@Energy -15.66 kcal/mol@LB@Hybridization Energy -32.8395 kcal/mol@LB@Unfolding Energy - mRNA 12.3643 kcal/mol@LB@Unfolding Energy - sRNA 4.81599 kcal/mol@LB@@LB@Position - mRNA 227 -- 265@LB@Position - sRNA 34 -- 74@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 34 -- 40@LB@
195	0.009901	0.1776	b1098	tmk	-15.44	0.015998	201 -- 230	41 -- 71	thymidylate kinase	_____________200_____________________________231\n_____________\|_______________________________\|\n5'-UAA...AAAAA___________GUAUAUCG______G_____CUGGA...GCG-3'\n______________AUGCGCAGUAA_________UCAUU_AGGGG\n______________\|::\|:\|\|\|:\|\|_________\|\|\|:\|_\|\|\|\|\|\n______________UGUGUGUCGUU_________AGUGA_UCCCC\n3'-UUU...UCUGA___________AAGCAACAA_____G_____UAAAG...GCA-5'\n_____________\|_______________________________\|\n_____________72______________________________40\n	205 -- 211	61 -- 67	-28.5877 kcal/mol	8.40445 kcal/mol	4.74226 kcal/mol	200 231@LB@ \| \|@LB@5'-UAA...AAAAA GUAUAUCG G CUGGA...GCG-3'@LB@ AUGCGCAGUAA UCAUU AGGGG@LB@ \|::\|:\|\|\|:\|\| \|\|\|:\| \|\|\|\|\|@LB@ UGUGUGUCGUU AGUGA UCCCC@LB@3'-UUU...UCUGA AAGCAACAA G UAAAG...GCA-5'@LB@ \| \|@LB@ 72 40@LB@@LB@@LB@Energy -15.44 kcal/mol@LB@Hybridization Energy -28.5877 kcal/mol@LB@Unfolding Energy - mRNA 8.40445 kcal/mol@LB@Unfolding Energy - sRNA 4.74226 kcal/mol@LB@@LB@Position - mRNA 201 -- 230@LB@Position - sRNA 41 -- 71@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 61 -- 67@LB@
68	0.002787	0.1417	b3001	gpr	-15.31	0.017381	36 -- 59	44 -- 69	L-glyceraldehyde 3-phosphate reductase	_____________35__________________________60\n_____________\|___________________________\|\n5'-UCC...GUUAA________________CAC________UUGGU...GGC-3'\n______________ACGCGGCA__UCGUUG___UC_CUCAG\n______________\|\|:\|:\|\|\|__\|\|\|\|\|\|___\|\|_\|\|\|\|\|\n______________UGUGUCGU__AGCAAC___AG_GAGUC\n3'-UUU...UGAUG________UA______AA___U_____CCCUA...GCA-5'\n_____________\|___________________________\|\n_____________70__________________________43\n	37 -- 43	62 -- 68	-25.5933 kcal/mol	6.1914 kcal/mol	4.09554 kcal/mol	35 60@LB@ \| \|@LB@5'-UCC...GUUAA CAC UUGGU...GGC-3'@LB@ ACGCGGCA UCGUUG UC CUCAG@LB@ \|\|:\|:\|\|\| \|\|\|\|\|\| \|\| \|\|\|\|\|@LB@ UGUGUCGU AGCAAC AG GAGUC@LB@3'-UUU...UGAUG UA AA U CCCUA...GCA-5'@LB@ \| \|@LB@ 70 43@LB@@LB@@LB@Energy -15.31 kcal/mol@LB@Hybridization Energy -25.5933 kcal/mol@LB@Unfolding Energy - mRNA 6.1914 kcal/mol@LB@Unfolding Energy - sRNA 4.09554 kcal/mol@LB@@LB@Position - mRNA 36 -- 59@LB@Position - sRNA 44 -- 69@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 62 -- 68@LB@
171	0.008374	0.1723	b4485	ytfR	-15.31	0.017344	177 -- 203	32 -- 71	putative sugar ABC transporter ATPase	_____________176_______________________________________204\n_____________\|_________________________________________\|\n5'-CCU...UGGGA_____________________A___________AA______ACGAC...GCC-3'\n______________GCACGC____________UUU_CAC_CGGGGGA___CCAUG\n______________:\|\|\|:\|____________\|\|\|_\|\|\|_\|:\|\|\|\|\|___\|\|\|\|\|\n______________UGUGUG____________AAA_GUG_GUCCCCU___GGUAC\n3'-UUU...UCUGA______UCGUUAAGCAAC_______A_______AAA_____GAAUA...GCA-5'\n_____________\|_________________________________________\|\n_____________72________________________________________31\n	190 -- 196	40 -- 46	-27.8319 kcal/mol	5.2959 kcal/mol	7.22604 kcal/mol	176 204@LB@ \| \|@LB@5'-CCU...UGGGA A AA ACGAC...GCC-3'@LB@ GCACGC UUU CAC CGGGGGA CCAUG@LB@ :\|\|\|:\| \|\|\| \|\|\| \|:\|\|\|\|\| \|\|\|\|\|@LB@ UGUGUG AAA GUG GUCCCCU GGUAC@LB@3'-UUU...UCUGA UCGUUAAGCAAC A AAA GAAUA...GCA-5'@LB@ \| \|@LB@ 72 31@LB@@LB@@LB@Energy -15.31 kcal/mol@LB@Hybridization Energy -27.8319 kcal/mol@LB@Unfolding Energy - mRNA 5.2959 kcal/mol@LB@Unfolding Energy - sRNA 7.22604 kcal/mol@LB@@LB@Position - mRNA 177 -- 203@LB@Position - sRNA 32 -- 71@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 40 -- 46@LB@
126	0.00562	0.157	b3017	ftsP	-15.30	0.017476	190 -- 242	38 -- 84	septal ring component that protects the divisome from stress; multicopy suppressor of ftsI(Ts)	_____________189____________________________________________________243\n_____________\|______________________________________________________\|\n5'-GAC...UUUAC____A_____U__GU___U____CGG____CAG________GGCAUC_______GCACU...CGC-3'\n______________AUGG_GCAAA_AU__CAC_CAGU____CGU___UUCAUUCA______GGGGAUU\n______________\|\|\|\|_\|\|\|\|\|_\|:__\|\|\|_\|\|\|:____\|\|\|___\|\|\|\|:\|\|\|______\|\|\|\|\|\|\|\n______________UACC_CGUUU_UG__GUG_GUCG____GCA___AAGUGAGU______CCCCUAA\n3'-UUU...CCCUC__________C__AU___U____UUAA___ACA_____________________AGGUA...GCA-5'\n_____________\|______________________________________________________\|\n_____________85_____________________________________________________37\n	236 -- 242	38 -- 44	-40.4092 kcal/mol	11.1124 kcal/mol	13.9994 kcal/mol	189 243@LB@ \| \|@LB@5'-GAC...UUUAC A U GU U CGG CAG GGCAUC GCACU...CGC-3'@LB@ AUGG GCAAA AU CAC CAGU CGU UUCAUUCA GGGGAUU@LB@ \|\|\|\| \|\|\|\|\| \|: \|\|\| \|\|\|: \|\|\| \|\|\|\|:\|\|\| \|\|\|\|\|\|\|@LB@ UACC CGUUU UG GUG GUCG GCA AAGUGAGU CCCCUAA@LB@3'-UUU...CCCUC C AU U UUAA ACA AGGUA...GCA-5'@LB@ \| \|@LB@ 85 37@LB@@LB@@LB@Energy -15.30 kcal/mol@LB@Hybridization Energy -40.4092 kcal/mol@LB@Unfolding Energy - mRNA 11.1124 kcal/mol@LB@Unfolding Energy - sRNA 13.9994 kcal/mol@LB@@LB@Position - mRNA 190 -- 242@LB@Position - sRNA 38 -- 84@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 38 -- 44@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching