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
160	0.01787	0.3749	b3935	priA	-8.27	0.542824	222 -- 250	110 -- 140	Primosome factor n' (replication factor Y)	_____________221_________________________251\n_____________\|___________________________\|\n5'-GAA...UAACC______AU___A_____G_________UAUGC...GCG-3'\n______________CACCGA__UUC_AGUCA_G_AUGAUGC\n______________\|\|\|\|:\|__:\|\|_\|\|\|\|\|_:_\|\|\|\|\|\|\|\n______________GUGGUU__GAG_UCAGU_U_UACUACG\n3'-UUU...AAAAU______AU_________G_G_______UCCGU...UAG-5'\n_____________\|___________________________\|\n_____________141_________________________109\n	193 -- 199	161 -- 167	-24.457 kcal/mol	4.47787 kcal/mol	7.72013 kcal/mol	221 251@LB@ \| \|@LB@5'-GAA...UAACC AU A G UAUGC...GCG-3'@LB@ CACCGA UUC AGUCA G AUGAUGC@LB@ \|\|\|\|:\| :\|\| \|\|\|\|\| : \|\|\|\|\|\|\|@LB@ GUGGUU GAG UCAGU U UACUACG@LB@3'-UUU...AAAAU AU G G UCCGU...UAG-5'@LB@ \| \|@LB@ 141 109@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -24.457 kcal/mol@LB@Unfolding Energy - mRNA 4.47787 kcal/mol@LB@Unfolding Energy - sRNA 7.72013 kcal/mol@LB@@LB@Position - mRNA 222 -- 250@LB@Position - sRNA 110 -- 140@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 161 -- 167@LB@
7	0.0005448	0.1842	b1912	pgsA	-14.68	0.031521	247 -- 274	111 -- 134	phosphatidylglycerophosphate synthetase	_____________246__________________________275\n_____________\|____________________________\|\n5'-GUC...CAUCC_________UCUU_______________UCUGC...UUG-3'\n______________UUAUCCCAU____UGUAUUGGUCUUUUA\n______________\|:\|\|\|\|\|\|:____\|\|:\|\|::\|\|\|:\|\|:\|\n______________AGUAGGGUG____ACGUAGUCAGGAAGU\n3'-UUU...ACGCC____________________________UCGUA...UAG-5'\n_____________\|____________________________\|\n_____________135__________________________110\n	268 -- 274	111 -- 117	-27.9222 kcal/mol	1.79949 kcal/mol	14.1586 kcal/mol	246 275@LB@ \| \|@LB@5'-GUC...CAUCC UCUU UCUGC...UUG-3'@LB@ UUAUCCCAU UGUAUUGGUCUUUUA@LB@ \|:\|\|\|\|\|\|: \|\|:\|\|::\|\|\|:\|\|:\|@LB@ AGUAGGGUG ACGUAGUCAGGAAGU@LB@3'-UUU...ACGCC UCGUA...UAG-5'@LB@ \| \|@LB@ 135 110@LB@@LB@@LB@Energy -14.68 kcal/mol@LB@Hybridization Energy -27.9222 kcal/mol@LB@Unfolding Energy - mRNA 1.79949 kcal/mol@LB@Unfolding Energy - sRNA 14.1586 kcal/mol@LB@@LB@Position - mRNA 247 -- 274@LB@Position - sRNA 111 -- 134@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 111 -- 117@LB@
8	0.0005643	0.1842	b2557	purL	-10.01	0.273478	129 -- 143	111 -- 124	phosphoribosylformyl-glycineamide synthetase	_____________128______________144\n_____________\|________________\|\n5'-AGG...UUGGG________AA______AAGAC...UUU-3'\n______________UACACCGA__GCUUAG\n______________\|\|\|\|\|\|:\|__:\|\|:\|\|\n______________AUGUGGUU__UGAGUC\n3'-UUU...CUAAA________A_______AGUGU...UAG-5'\n_____________\|________________\|\n_____________125______________110\n	172 -- 178	181 -- 187	-14.8421 kcal/mol	1.97129 kcal/mol	3.669 kcal/mol	128 144@LB@ \| \|@LB@5'-AGG...UUGGG AA AAGAC...UUU-3'@LB@ UACACCGA GCUUAG@LB@ \|\|\|\|\|\|:\| :\|\|:\|\|@LB@ AUGUGGUU UGAGUC@LB@3'-UUU...CUAAA A AGUGU...UAG-5'@LB@ \| \|@LB@ 125 110@LB@@LB@@LB@Energy -10.01 kcal/mol@LB@Hybridization Energy -14.8421 kcal/mol@LB@Unfolding Energy - mRNA 1.97129 kcal/mol@LB@Unfolding Energy - sRNA 3.669 kcal/mol@LB@@LB@Position - mRNA 129 -- 143@LB@Position - sRNA 111 -- 124@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 181 -- 187@LB@
54	0.005402	0.3247	b3054	ygiF	-14.97	0.027422	5 -- 80	111 -- 177	inorganic triphosphatase	_____________4_______________________________________________________________________________81\n_____________\|_______________________________________________________________________________\|\n_______5'-GGCA_____GU___UAC_____AA___U______AUCAA_______CCUCUG___CA____U_G_______U___AA______CGCCC...CCG-3'\n______________UCAGU__CGC_____GCA__GCA__UCGAC_____UCGGAAU______UGU__GGUC_U_CCACUGC_UCA__CUUUUA\n______________\|\|\|\|\|__\|:\|_____\|\|\|__\|\|\|__\|\|:\|\|_____\|\|:\|\|\|\|______\|\|:__\|\|\|\|_\|_\|\|\|\|\|\|\|_\|\|\|__\|:\|\|:\|\n______________AGUCA__GUG_____CGU__CGU__AGUUG_____AGUCUUA______ACG__CCAG_A_GGUGACG_AGU__GGAAGU\n3'-UUU...UUAUG_____GU___UACUA___C____UC_____AA_________________________U_G_______U___CA______UCGUA...UAG-5'\n_____________\|_______________________________________________________________________________\|\n_____________178_____________________________________________________________________________110\n	62 -- 68	123 -- 129	-50.4846 kcal/mol	15.6316 kcal/mol	23.3828 kcal/mol	4 81@LB@ \| \|@LB@ 5'-GGCA GU UAC AA U AUCAA CCUCUG CA U G U AA CGCCC...CCG-3'@LB@ UCAGU CGC GCA GCA UCGAC UCGGAAU UGU GGUC U CCACUGC UCA CUUUUA@LB@ \|\|\|\|\| \|:\| \|\|\| \|\|\| \|\|:\|\| \|\|:\|\|\|\| \|\|: \|\|\|\| \| \|\|\|\|\|\|\| \|\|\| \|:\|\|:\|@LB@ AGUCA GUG CGU CGU AGUUG AGUCUUA ACG CCAG A GGUGACG AGU GGAAGU@LB@3'-UUU...UUAUG GU UACUA C UC AA U G U CA UCGUA...UAG-5'@LB@ \| \|@LB@ 178 110@LB@@LB@@LB@Energy -14.97 kcal/mol@LB@Hybridization Energy -50.4846 kcal/mol@LB@Unfolding Energy - mRNA 15.6316 kcal/mol@LB@Unfolding Energy - sRNA 23.3828 kcal/mol@LB@@LB@Position - mRNA 5 -- 80@LB@Position - sRNA 111 -- 177@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 123 -- 129@LB@
148	0.01584	0.3602	b1822	rlmA	-10.68	0.203557	148 -- 239	111 -- 186	23S rRNA m(1)G745 methyltransferase SAM-dependent	_____________147___________240\n_____________\|_____________\|\n5'-AAG...GCGUG_____C_______UUGCG...GGU-3'\n______________AUUCG_GUUACAC\n______________\|:\|\|:_\|\|:\|\|\|\|\n______________UGAGU_CAGUGUG\n3'-UUU...GGUUA_____________UACUA...UAG-5'\n_____________\|_____________\|\n_____________187___________110\n	163 -- 169	168 -- 174	-12.5288 kcal/mol	1.89227 kcal/mol	0.283892 kcal/mol	147 240@LB@ \| \|@LB@5'-AAG...GCGUG C UUGCG...GGU-3'@LB@ AUUCG GUUACAC@LB@ \|:\|\|: \|\|:\|\|\|\|@LB@ UGAGU CAGUGUG@LB@3'-UUU...GGUUA UACUA...UAG-5'@LB@ \| \|@LB@ 187 110@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -12.5288 kcal/mol@LB@Unfolding Energy - mRNA 1.89227 kcal/mol@LB@Unfolding Energy - sRNA 0.283892 kcal/mol@LB@@LB@Position - mRNA 148 -- 239@LB@Position - sRNA 111 -- 186@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 168 -- 174@LB@
130	0.0142	0.3575	b0885	aat	-14.04	0.042507	189 -- 220	112 -- 144	leucyl/phenylalanyl-tRNA-protein transferase	_____________188_______________________________221\n_____________\|_________________________________\|\n5'-CGU...UUUUG________________CU_______________UCGCC...UUA-3'\n______________CGGUCAUGC_____GC__GGU___UCAGCUUUC\n______________\|:\|\|\|\|::\|_____\|\|__\|\|:___\|\|\|:\|\|\|\|\|\n______________GUCAGUGUG_____CG__CCG___AGUUGAAAG\n3'-UUU...UAUGA_________UACUA__U____UUC_________UCUUA...UAG-5'\n_____________\|_________________________________\|\n_____________145_______________________________111\n	214 -- 220	145 -- 151	-24.916 kcal/mol	8.31603 kcal/mol	8.21863 kcal/mol	188 221@LB@ \| \|@LB@5'-CGU...UUUUG CU UCGCC...UUA-3'@LB@ CGGUCAUGC GC GGU UCAGCUUUC@LB@ \|:\|\|\|\|::\| \|\| \|\|: \|\|\|:\|\|\|\|\|@LB@ GUCAGUGUG CG CCG AGUUGAAAG@LB@3'-UUU...UAUGA UACUA U UUC UCUUA...UAG-5'@LB@ \| \|@LB@ 145 111@LB@@LB@@LB@Energy -14.04 kcal/mol@LB@Hybridization Energy -24.916 kcal/mol@LB@Unfolding Energy - mRNA 8.31603 kcal/mol@LB@Unfolding Energy - sRNA 8.21863 kcal/mol@LB@@LB@Position - mRNA 189 -- 220@LB@Position - sRNA 112 -- 144@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 145 -- 151@LB@
194	0.02283	0.3833	b3823	rhtC	-9.67	0.316154	216 -- 300	113 -- 178	threonine efflux pump	_____________215___________________301\n_____________\|_____________________\|\n5'-AGA...UAUUU____CC_______________CAUUG...GUU-3'\n______________CUCA__GUCGC_CAUGGUGCA\n______________\|\|\|\|__\|\|\|:\|_\|\|\|\|:\|\|\|\|\n______________GAGU__CAGUG_GUACUACGU\n3'-UUU...GUUAU___________U_________CCGUU...UAG-5'\n_____________\|_____________________\|\n_____________179___________________112\n	228 -- 234	161 -- 167	-23.3741 kcal/mol	7.13181 kcal/mol	4.79874 kcal/mol	215 301@LB@ \| \|@LB@5'-AGA...UAUUU CC CAUUG...GUU-3'@LB@ CUCA GUCGC CAUGGUGCA@LB@ \|\|\|\| \|\|\|:\| \|\|\|\|:\|\|\|\|@LB@ GAGU CAGUG GUACUACGU@LB@3'-UUU...GUUAU U CCGUU...UAG-5'@LB@ \| \|@LB@ 179 112@LB@@LB@@LB@Energy -9.67 kcal/mol@LB@Hybridization Energy -23.3741 kcal/mol@LB@Unfolding Energy - mRNA 7.13181 kcal/mol@LB@Unfolding Energy - sRNA 4.79874 kcal/mol@LB@@LB@Position - mRNA 216 -- 300@LB@Position - sRNA 113 -- 178@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 161 -- 167@LB@
184	0.02128	0.3833	b2831	mutH	-12.07	0.107608	142 -- 230	114 -- 189	methyl-directed mismatch repair protein	_____________141______________231\n_____________\|________________\|\n5'-UUC...CUGCG________________AUUGC...CGG-3'\n______________AAUAUUCGG_CACAUA\n______________\|\|\|\|:\|\|:\|_\|\|\|\|:\|\n______________UUAUGAGUC_GUGUGU\n3'-UUU...UGUGG_________A______ACUAC...UAG-5'\n_____________\|________________\|\n_____________190______________113\n	154 -- 160	174 -- 180	-15.1193 kcal/mol	2.199 kcal/mol	0.596263 kcal/mol	141 231@LB@ \| \|@LB@5'-UUC...CUGCG AUUGC...CGG-3'@LB@ AAUAUUCGG CACAUA@LB@ \|\|\|\|:\|\|:\| \|\|\|\|:\|@LB@ UUAUGAGUC GUGUGU@LB@3'-UUU...UGUGG A ACUAC...UAG-5'@LB@ \| \|@LB@ 190 113@LB@@LB@@LB@Energy -12.07 kcal/mol@LB@Hybridization Energy -15.1193 kcal/mol@LB@Unfolding Energy - mRNA 2.199 kcal/mol@LB@Unfolding Energy - sRNA 0.596263 kcal/mol@LB@@LB@Position - mRNA 142 -- 230@LB@Position - sRNA 114 -- 189@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 174 -- 180@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@
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@

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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