Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
97	0.01056	0.3575	b2372	yfdV	-22.84	0.000764	17 -- 36	167 -- 186	putative transporter	_____________16___________________37\n_____________\|____________________\|\n5'-UUC...UUAAC____________________AACCG...CUC-3'\n______________CACCGGUAUUCAGUCGCGCA\n______________\|\|\|\|::\|\|:\|\|\|\|\|\|:\|:\|\|\n______________GUGGUUAUGAGUCAGUGUGU\n3'-UUU...AAAAU____________________ACUAC...UAG-5'\n_____________\|____________________\|\n_____________187__________________166\n	30 -- 36	167 -- 173	-32.2779 kcal/mol	2.6891 kcal/mol	5.05466 kcal/mol	16 37@LB@ \| \|@LB@5'-UUC...UUAAC AACCG...CUC-3'@LB@ CACCGGUAUUCAGUCGCGCA@LB@ \|\|\|\|::\|\|:\|\|\|\|\|\|:\|:\|\|@LB@ GUGGUUAUGAGUCAGUGUGU@LB@3'-UUU...AAAAU ACUAC...UAG-5'@LB@ \| \|@LB@ 187 166@LB@@LB@@LB@Energy -22.84 kcal/mol@LB@Hybridization Energy -32.2779 kcal/mol@LB@Unfolding Energy - mRNA 2.6891 kcal/mol@LB@Unfolding Energy - sRNA 5.05466 kcal/mol@LB@@LB@Position - mRNA 17 -- 36@LB@Position - sRNA 167 -- 186@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 167 -- 173@LB@
118	0.01293	0.3575	b1598	ydgD	-17.08	0.010207	53 -- 140	115 -- 186	putative peptidase	_____________52______________________________________________________________________141\n_____________\|_______________________________________________________________________\|\n5'-CUU...AUCCU_____UAUG__________UACC__CC___UUUAU_____CU______A____UCUGAUUUUAC_______UUCAU...AGG-3'\n______________UAUUU____CGCAC_UGAU____GC__GUU_____CUUUC__GAUUGU_GUUA___________UCCCACU\n______________\|\|:\|:____\|:\|\|\|_\|\|\|\|____\|\|__\|\|:_____\|\|\|\|\|__:\|\|\|\|:_\|\|:\|___________\|\|\|\|\|\|\|\n______________AUGAG____GUGUG_ACUA____CG__CAG_____GAAAG__UUAACG_CAGU___________AGGGUGA\n3'-UUU...UGGUU_____UCA______U____CGUC__UU___UU________UC______C______________________CGUAG...UAG-5'\n_____________\|_______________________________________________________________________\|\n_____________187_____________________________________________________________________114\n	122 -- 128	125 -- 131	-34.2678 kcal/mol	6.55961 kcal/mol	16.6417 kcal/mol	52 141@LB@ \| \|@LB@5'-CUU...AUCCU UAUG UACC CC UUUAU CU A UCUGAUUUUAC UUCAU...AGG-3'@LB@ UAUUU CGCAC UGAU GC GUU CUUUC GAUUGU GUUA UCCCACU@LB@ \|\|:\|: \|:\|\|\| \|\|\|\| \|\| \|\|: \|\|\|\|\| :\|\|\|\|: \|\|:\| \|\|\|\|\|\|\|@LB@ AUGAG GUGUG ACUA CG CAG GAAAG UUAACG CAGU AGGGUGA@LB@3'-UUU...UGGUU UCA U CGUC UU UU UC C CGUAG...UAG-5'@LB@ \| \|@LB@ 187 114@LB@@LB@@LB@Energy -17.08 kcal/mol@LB@Hybridization Energy -34.2678 kcal/mol@LB@Unfolding Energy - mRNA 6.55961 kcal/mol@LB@Unfolding Energy - sRNA 16.6417 kcal/mol@LB@@LB@Position - mRNA 53 -- 140@LB@Position - sRNA 115 -- 186@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 125 -- 131@LB@
137	0.01486	0.3575	b3967	murI	-16.98	0.010727	107 -- 167	42 -- 96	glutamate racemase	_____________106__________________________168\n_____________\|____________________________\|\n5'-GUU...GACUG________ACU_____________G___UCGCU...GGU-3'\n______________GGGU_AUU___UAUCAGUAUUUAG_CAC\n______________\|\|\|\|_\|\|\|___:\|:\|\|:\|\|:\|:\|\|_\|\|\|\n______________CCCA_UAA___GUGGUUAUGAGUC_GUG\n3'-UUU...GACCG____C___AAU_____________A___UGUAC...UAG-5'\n_____________\|____________________________\|\n_____________97___________________________41\n	35 -- 41	174 -- 180	-22.1424 kcal/mol	5.45848 kcal/mol	5.03792 kcal/mol	106 168@LB@ \| \|@LB@5'-GUU...GACUG ACU G UCGCU...GGU-3'@LB@ GGGU AUU UAUCAGUAUUUAG CAC@LB@ \|\|\|\| \|\|\| :\|:\|\|:\|\|:\|:\|\| \|\|\|@LB@ CCCA UAA GUGGUUAUGAGUC GUG@LB@3'-UUU...GACCG C AAU A UGUAC...UAG-5'@LB@ \| \|@LB@ 97 41@LB@@LB@@LB@Energy -16.98 kcal/mol@LB@Hybridization Energy -22.1424 kcal/mol@LB@Unfolding Energy - mRNA 5.45848 kcal/mol@LB@Unfolding Energy - sRNA 5.03792 kcal/mol@LB@@LB@Position - mRNA 107 -- 167@LB@Position - sRNA 42 -- 96@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 174 -- 180@LB@
119	0.013	0.3575	b0801	ybiC	-16.26	0.015008	158 -- 253	108 -- 187	putative dehydrogenase	_____________157____________________________________________________________________________________________254\n_____________\|______________________________________________________________________________________________\|\n5'-GCU...AUAAA_____AA__AA______ACAUAAA_____________CAU_____A__________G_UUUGAUGCUCAGAC_____________UA_______UGUAU...UUG-3'\n______________AAUAC__CA__CACAUA_______CAGG__AGUUAAC____GGAA__GUGGUCAUC_C______________GCUGCA_CAGUUU__UUCAGGC\n______________\|\|\|\|\|__\|\|__\|\|\|\|:\|_______\|\|\|\|__\|\|\|:\|\|\|____:\|\|\|__\|:\|\|\|\|\|\|\|_\|______________:\|\|\|\|\|_\|\|\|\|::__\|\|\|\|:\|\|\n______________UUAUG__GU__GUGUGU_______GUCC__UCAGUUG____UCUU__CGCCAGUAG_G______________UGACGU_GUCAGG__AAGUUCG\n3'-UUU...UGUGG_____A___CA______ACUAC______GU_______AAAG____AA_________G_____________________A_______________UACCA...UAG-5'\n_____________\|______________________________________________________________________________________________\|\n_____________188____________________________________________________________________________________________107\n	247 -- 253	108 -- 114	-56.5044 kcal/mol	18.8914 kcal/mol	26.5178 kcal/mol	157 254@LB@ \| \|@LB@5'-GCU...AUAAA AA AA ACAUAAA CAU A G UUUGAUGCUCAGAC UA UGUAU...UUG-3'@LB@ AAUAC CA CACAUA CAGG AGUUAAC GGAA GUGGUCAUC C GCUGCA CAGUUU UUCAGGC@LB@ \|\|\|\|\| \|\| \|\|\|\|:\| \|\|\|\| \|\|\|:\|\|\| :\|\|\| \|:\|\|\|\|\|\|\| \| :\|\|\|\|\| \|\|\|\|:: \|\|\|\|:\|\|@LB@ UUAUG GU GUGUGU GUCC UCAGUUG UCUU CGCCAGUAG G UGACGU GUCAGG AAGUUCG@LB@3'-UUU...UGUGG A CA ACUAC GU AAAG AA G A UACCA...UAG-5'@LB@ \| \|@LB@ 188 107@LB@@LB@@LB@Energy -16.26 kcal/mol@LB@Hybridization Energy -56.5044 kcal/mol@LB@Unfolding Energy - mRNA 18.8914 kcal/mol@LB@Unfolding Energy - sRNA 26.5178 kcal/mol@LB@@LB@Position - mRNA 158 -- 253@LB@Position - sRNA 108 -- 187@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 108 -- 114@LB@
91	0.01018	0.3575	b1660	ydhC	-16.12	0.016020	223 -- 255	172 -- 209	putative arabinose efflux transporter	_____________222_____________________________________256\n_____________\|_______________________________________\|\n5'-GAA...AUUUU______G_________________A______________UUCUG...AGG-3'\n______________UAGUCU_GCUGGCGGGU____UUG_GC__GUACUCGGUU\n______________\|\|:\|\|\|_\|\|\|\|\|\|\|\|\|\|____\|\|:_:\|__:\|\|\|\|\|:\|\|:\n______________AUUAGA_CGACCGCCCA____AAU_UG__UAUGAGUCAG\n3'-UUU...UCCAU_________________CUAA___G__GU__________UGUGU...UAG-5'\n_____________\|_______________________________________\|\n_____________210_____________________________________171\n	249 -- 255	172 -- 178	-38.0361 kcal/mol	10.2504 kcal/mol	15.0669 kcal/mol	222 256@LB@ \| \|@LB@5'-GAA...AUUUU G A UUCUG...AGG-3'@LB@ UAGUCU GCUGGCGGGU UUG GC GUACUCGGUU@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|: :\| :\|\|\|\|\|:\|\|:@LB@ AUUAGA CGACCGCCCA AAU UG UAUGAGUCAG@LB@3'-UUU...UCCAU CUAA G GU UGUGU...UAG-5'@LB@ \| \|@LB@ 210 171@LB@@LB@@LB@Energy -16.12 kcal/mol@LB@Hybridization Energy -38.0361 kcal/mol@LB@Unfolding Energy - mRNA 10.2504 kcal/mol@LB@Unfolding Energy - sRNA 15.0669 kcal/mol@LB@@LB@Position - mRNA 223 -- 255@LB@Position - sRNA 172 -- 209@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 172 -- 178@LB@
135	0.01453	0.3575	b2934	cmtB	-15.85	0.018111	229 -- 275	145 -- 186	putative mannitol-specific enzyme IIA component of PTS	_____________228___________________276\n_____________\|_____________________\|\n5'-AUA...AGAAU_____________________UCAGC...UGG-3'\n______________CAUCAAU_CUCAGUUAUACAU\n______________\|\|:\|\|\|\|_\|\|\|\|\|\|:\|:\|\|\|\|\n______________GUGGUUA_GAGUCAGUGUGUA\n3'-UUU...AAAAU_______U_____________CUACG...UAG-5'\n_____________\|_____________________\|\n_____________187___________________144\n	242 -- 248	166 -- 172	-24.8158 kcal/mol	1.5387 kcal/mol	5.06797 kcal/mol	228 276@LB@ \| \|@LB@5'-AUA...AGAAU UCAGC...UGG-3'@LB@ CAUCAAU CUCAGUUAUACAU@LB@ \|\|:\|\|\|\| \|\|\|\|\|\|:\|:\|\|\|\|@LB@ GUGGUUA GAGUCAGUGUGUA@LB@3'-UUU...AAAAU U CUACG...UAG-5'@LB@ \| \|@LB@ 187 144@LB@@LB@@LB@Energy -15.85 kcal/mol@LB@Hybridization Energy -24.8158 kcal/mol@LB@Unfolding Energy - mRNA 1.5387 kcal/mol@LB@Unfolding Energy - sRNA 5.06797 kcal/mol@LB@@LB@Position - mRNA 229 -- 275@LB@Position - sRNA 145 -- 186@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 166 -- 172@LB@
138	0.01487	0.3575	b3771	ilvD	-15.83	0.018324	35 -- 66	67 -- 98	dihydroxyacid dehydratase	_____________34______67\n_____________\|_______\|\n5'-GCG...AAAAA_______GCACG...GUA-3'\n______________UGGGACG\n______________\|\|\|\|\|\|\|\n______________ACCCUGC\n3'-UUU...GCAAC_______GAAUU...UAG-5'\n_____________\|_______\|\n_____________99______66\n	147 -- 153	87 -- 93	-12.7493 kcal/mol	2.26202 kcal/mol	4.21173 kcal/mol	34 67@LB@ \| \|@LB@5'-GCG...AAAAA GCACG...GUA-3'@LB@ UGGGACG@LB@ \|\|\|\|\|\|\|@LB@ ACCCUGC@LB@3'-UUU...GCAAC GAAUU...UAG-5'@LB@ \| \|@LB@ 99 66@LB@@LB@@LB@Energy -15.83 kcal/mol@LB@Hybridization Energy -12.7493 kcal/mol@LB@Unfolding Energy - mRNA 2.26202 kcal/mol@LB@Unfolding Energy - sRNA 4.21173 kcal/mol@LB@@LB@Position - mRNA 35 -- 66@LB@Position - sRNA 67 -- 98@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 87 -- 93@LB@
112	0.01232	0.3575	b1540	rspR	-15.19	0.024761	13 -- 44	171 -- 202	transcriptional repressor for rspAB	_____________12_________________________________________________________45\n_____________\|__________________________________________________________\|\n5'-CAG...GCCGU__________UCA_______GCC______C___A____CAAUACCCUGGAA_______CGGUU...GCA-3'\n______________CUGGUGGGUG_____ACGCU___UGCUCA_GUC_AUAU_____________AUGAUGC\n______________\|\|\|\|:\|\|\|\|\|_____\|\|:\|:___\|:\|\|\|\|_\|\|\|_\|:\|:_____________\|\|\|\|\|\|\|\n______________GACCGCCCAC_____UGUGG___AUGAGU_CAG_UGUG_____________UACUACG\n3'-UUU...UAGAC__________UAAAA_____UU____________________________________UCCGU...UAG-5'\n_____________\|__________________________________________________________\|\n_____________203________________________________________________________170\n	62 -- 68	161 -- 167	-40.6001 kcal/mol	15.8189 kcal/mol	17.3482 kcal/mol	12 45@LB@ \| \|@LB@5'-CAG...GCCGU UCA GCC C A CAAUACCCUGGAA CGGUU...GCA-3'@LB@ CUGGUGGGUG ACGCU UGCUCA GUC AUAU AUGAUGC@LB@ \|\|\|\|:\|\|\|\|\| \|\|:\|: \|:\|\|\|\| \|\|\| \|:\|: \|\|\|\|\|\|\|@LB@ GACCGCCCAC UGUGG AUGAGU CAG UGUG UACUACG@LB@3'-UUU...UAGAC UAAAA UU UCCGU...UAG-5'@LB@ \| \|@LB@ 203 170@LB@@LB@@LB@Energy -15.19 kcal/mol@LB@Hybridization Energy -40.6001 kcal/mol@LB@Unfolding Energy - mRNA 15.8189 kcal/mol@LB@Unfolding Energy - sRNA 17.3482 kcal/mol@LB@@LB@Position - mRNA 13 -- 44@LB@Position - sRNA 171 -- 202@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 161 -- 167@LB@
102	0.01106	0.3575	b0647	ybeT	-15.01	0.026876	192 -- 264	115 -- 176	Sel1 family TPR-like repeat protein	_____________191___________265\n_____________\|_____________\|\n5'-AUA...CGAAG__U__________AUAAA...UGG-3'\n______________CA_UCACACAUGA\n______________\|\|_\|\|\|\|\|\|\|\|\|\|\n______________GU_AGUGUGUACU\n3'-UUU...UAUGA__C__________ACGUC...UAG-5'\n_____________\|_____________\|\n_____________177___________114\n	198 -- 204	164 -- 170	-15.9732 kcal/mol	2.87622 kcal/mol	4.17773 kcal/mol	191 265@LB@ \| \|@LB@5'-AUA...CGAAG U AUAAA...UGG-3'@LB@ CA UCACACAUGA@LB@ \|\| \|\|\|\|\|\|\|\|\|\|@LB@ GU AGUGUGUACU@LB@3'-UUU...UAUGA C ACGUC...UAG-5'@LB@ \| \|@LB@ 177 114@LB@@LB@@LB@Energy -15.01 kcal/mol@LB@Hybridization Energy -15.9732 kcal/mol@LB@Unfolding Energy - mRNA 2.87622 kcal/mol@LB@Unfolding Energy - sRNA 4.17773 kcal/mol@LB@@LB@Position - mRNA 192 -- 264@LB@Position - sRNA 115 -- 176@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 164 -- 170@LB@
95	0.01047	0.3575	b4232	fbp	-15.00	0.027086	59 -- 98	140 -- 173	fructose-1 6-bisphosphatase I	_____________58_______________________________________________99\n_____________\|________________________________________________\|\n5'-AAA...CUGCC_____UU____________U_________G_GAAAC__A_________AAUCC...CCA-3'\n______________GCUCA__UUACGCAU_AUG_CGGGCAAGU_A_____GC_UUUCAGGAU\n______________:\|\|\|\|__\|:\|\|:\|\|\|_\|\|\|_\|:\|\|\|\|\|\|\|_\|_____:\|_\|\|\|\|\|\|:\|\|\n______________UGAGU__AGUGUGUA_UAC_GUCCGUUCA_U_____UG_AAAGUCUUA\n3'-UUU...GGUUA_____C_________C_____________G__________________ACGCC...UAG-5'\n_____________\|________________________________________________\|\n_____________174______________________________________________139\n	92 -- 98	140 -- 146	-39.7088 kcal/mol	14.0477 kcal/mol	8.83532 kcal/mol	58 99@LB@ \| \|@LB@5'-AAA...CUGCC UU U G GAAAC A AAUCC...CCA-3'@LB@ GCUCA UUACGCAU AUG CGGGCAAGU A GC UUUCAGGAU@LB@ :\|\|\|\| \|:\|\|:\|\|\| \|\|\| \|:\|\|\|\|\|\|\| \| :\| \|\|\|\|\|\|:\|\|@LB@ UGAGU AGUGUGUA UAC GUCCGUUCA U UG AAAGUCUUA@LB@3'-UUU...GGUUA C C G ACGCC...UAG-5'@LB@ \| \|@LB@ 174 139@LB@@LB@@LB@Energy -15.00 kcal/mol@LB@Hybridization Energy -39.7088 kcal/mol@LB@Unfolding Energy - mRNA 14.0477 kcal/mol@LB@Unfolding Energy - sRNA 8.83532 kcal/mol@LB@@LB@Position - mRNA 59 -- 98@LB@Position - sRNA 140 -- 173@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 140 -- 146@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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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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