Input and runtime details for job 3202356 (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 3202356 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:02 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:03:47 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:03:55 CET 2018
	Job Completed		@ Sat Feb 17 02:04:28 CET 2018

DIRECT ACCESS: https://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

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_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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
44	0.001631	0.1267	stm1318	katE	-13.62	0.194137	191 -- 230	43 -- 82	catalase HPII	_____________190_________231\n_____________\|___________\|\n5'-GGC...UCUGC___________UCCCC...AUC-3'\n______________CGUUCCG_CUC\n______________\|\|\|\|\|\|\|_\|\|\|\n______________GCAAGGC_GAG\n3'-UUU...GAAAA_______C___UCCUUCA-5'\n_____________\|___________\|\n_____________83__________42\n	99 -- 105	12 -- 18	-14.968 kcal/mol	1.4568 kcal/mol	6.53351 kcal/mol	190 231@LB@ \| \|@LB@5'-GGC...UCUGC UCCCC...AUC-3'@LB@ CGUUCCG CUC@LB@ \|\|\|\|\|\|\| \|\|\|@LB@ GCAAGGC GAG@LB@3'-UUU...GAAAA C UCCUUCA-5'@LB@ \| \|@LB@ 83 42@LB@@LB@@LB@Energy -13.62 kcal/mol@LB@Hybridization Energy -14.968 kcal/mol@LB@Unfolding Energy - mRNA 1.4568 kcal/mol@LB@Unfolding Energy - sRNA 6.53351 kcal/mol@LB@@LB@Position - mRNA 191 -- 230@LB@Position - sRNA 43 -- 82@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 12 -- 18@LB@
113	0.005549	0.1728	stm2948	cysJ	-13.61	0.194760	269 -- 298	56 -- 85	sulfite reductase [NADPH] flavoprotein subunit alpha	_____________268_______________________299\n_____________\|_________________________\|\n5'-GUU...CCGCU____UUACUG_______________UGACG...UUG-3'\n______________UUGC______GAACAUAACGACGCA\n______________\|\|\|\|______:\|\|\|\|:\|\|\|:\|\|:\|\|\n______________AACG______UUUGUGUUGUUGUGU\n3'-UUU...UGGUU_________________________UGUAG...UCA-5'\n_____________\|_________________________\|\n_____________86________________________55\n	195 -- 201	74 -- 80	-20.7575 kcal/mol	3.67756 kcal/mol	3.73922 kcal/mol	268 299@LB@ \| \|@LB@5'-GUU...CCGCU UUACUG UGACG...UUG-3'@LB@ UUGC GAACAUAACGACGCA@LB@ \|\|\|\| :\|\|\|\|:\|\|\|:\|\|:\|\|@LB@ AACG UUUGUGUUGUUGUGU@LB@3'-UUU...UGGUU UGUAG...UCA-5'@LB@ \| \|@LB@ 86 55@LB@@LB@@LB@Energy -13.61 kcal/mol@LB@Hybridization Energy -20.7575 kcal/mol@LB@Unfolding Energy - mRNA 3.67756 kcal/mol@LB@Unfolding Energy - sRNA 3.73922 kcal/mol@LB@@LB@Position - mRNA 269 -- 298@LB@Position - sRNA 56 -- 85@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 74 -- 80@LB@
27	0.0006872	0.08814	stm1806	nhaB	-13.59	0.196266	64 -- 136	66 -- 135	Na+/H+ antiporter NhaB	_____________63___________________________________________________________________________137\n_____________\|____________________________________________________________________________\|\n5'-AGC...AUGAA_________GAUCAAG______AUU______U_____CU______AUC_U____G__UU__UU____U________CUCGC...CAU-3'\n______________GAAAAAGGG_______GC_ACC____UCUGA_AUCGC__GCCAAU___G_UAAG_AC__GC__GCAU__CGUCGCG\n______________\|\|\|\|\|\|\|\|\|_______\|\|_\|\|\|____\|\|\|\|\|_\|\|\|\|\|__:\|\|\|\|\|___\|_:\|\|:_\|\|__:\|__:\|\|:__\|:\|\|:\|:\n______________CUUUUUCCC_______CG_UGG____AGACU_UAGCG__UGGUUA___C_GUUU_UG__UG__UGUG__GUAGUGU\n3'-UUU...CUUCA_________AUCAGAG__A___CACC___________UC______A________G__U___U_____UU_______UGGCA...UCA-5'\n_____________\|____________________________________________________________________________\|\n_____________136__________________________________________________________________________65\n	130 -- 136	66 -- 72	-51.3167 kcal/mol	14.8404 kcal/mol	22.5826 kcal/mol	63 137@LB@ \| \|@LB@5'-AGC...AUGAA GAUCAAG AUU U CU AUC U G UU UU U CUCGC...CAU-3'@LB@ GAAAAAGGG GC ACC UCUGA AUCGC GCCAAU G UAAG AC GC GCAU CGUCGCG@LB@ \|\|\|\|\|\|\|\|\| \|\| \|\|\| \|\|\|\|\| \|\|\|\|\| :\|\|\|\|\| \| :\|\|: \|\| :\| :\|\|: \|:\|\|:\|:@LB@ CUUUUUCCC CG UGG AGACU UAGCG UGGUUA C GUUU UG UG UGUG GUAGUGU@LB@3'-UUU...CUUCA AUCAGAG A CACC UC A G U U UU UGGCA...UCA-5'@LB@ \| \|@LB@ 136 65@LB@@LB@@LB@Energy -13.59 kcal/mol@LB@Hybridization Energy -51.3167 kcal/mol@LB@Unfolding Energy - mRNA 14.8404 kcal/mol@LB@Unfolding Energy - sRNA 22.5826 kcal/mol@LB@@LB@Position - mRNA 64 -- 136@LB@Position - sRNA 66 -- 135@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 66 -- 72@LB@
189	0.01049	0.1967	stm0871	ybjM	-13.57	0.197684	34 -- 53	71 -- 89	similar to E. coli orf hypothetical protein (AAC73935.1); Blastp hit to AAC73935.1 (125 aa) 72% identity in aa 1 - 125	_____________33___________________54\n_____________\|____________________\|\n5'-AAU...GCAUC______AA____________AUAUA...GCG-3'\n______________CAAAUA__AACAACACAACA\n______________\|\|\|\|:\|__\|\|\|\|\|\|\|\|\|\|\|\|\n______________GUUUGU__UUGUUGUGUUGU\n3'-UUU...UUAAC______G_____________AGUGU...UCA-5'\n_____________\|____________________\|\n_____________90___________________70\n	47 -- 53	71 -- 77	-19.7565 kcal/mol	2.01075 kcal/mol	3.79866 kcal/mol	33 54@LB@ \| \|@LB@5'-AAU...GCAUC AA AUAUA...GCG-3'@LB@ CAAAUA AACAACACAACA@LB@ \|\|\|\|:\| \|\|\|\|\|\|\|\|\|\|\|\|@LB@ GUUUGU UUGUUGUGUUGU@LB@3'-UUU...UUAAC G AGUGU...UCA-5'@LB@ \| \|@LB@ 90 70@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -19.7565 kcal/mol@LB@Unfolding Energy - mRNA 2.01075 kcal/mol@LB@Unfolding Energy - sRNA 3.79866 kcal/mol@LB@@LB@Position - mRNA 34 -- 53@LB@Position - sRNA 71 -- 89@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 71 -- 77@LB@
164	0.008796	0.191	stm2932	ygbE	-13.54	0.199482	240 -- 279	44 -- 82	putative inner membrane protein	_____________239________________280\n_____________\|__________________\|\n5'-CGC...GCGUA__________________UUUCA...CCA-3'\n______________AUAGC__CAUAACAUUAC\n______________\|:\|:\|__\|\|:\|\|\|\|\|:\|\|\n______________UGUUG__GUGUUGUAGUG\n3'-UUU...GUUUG_____UU___________UUGGC...UCA-5'\n_____________\|__________________\|\n_____________83_________________43\n	250 -- 256	67 -- 73	-14.8194 kcal/mol	1.59581 kcal/mol	5.25507 kcal/mol	239 280@LB@ \| \|@LB@5'-CGC...GCGUA UUUCA...CCA-3'@LB@ AUAGC CAUAACAUUAC@LB@ \|:\|:\| \|\|:\|\|\|\|\|:\|\|@LB@ UGUUG GUGUUGUAGUG@LB@3'-UUU...GUUUG UU UUGGC...UCA-5'@LB@ \| \|@LB@ 83 43@LB@@LB@@LB@Energy -13.54 kcal/mol@LB@Hybridization Energy -14.8194 kcal/mol@LB@Unfolding Energy - mRNA 1.59581 kcal/mol@LB@Unfolding Energy - sRNA 5.25507 kcal/mol@LB@@LB@Position - mRNA 240 -- 279@LB@Position - sRNA 44 -- 82@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 67 -- 73@LB@
64	0.003108	0.1596	stm4162	thiF	-13.53	0.200092	247 -- 294	34 -- 76	molybdopterin/thiamine biosynthesis adenylyltransferase	_____________246___________________295\n_____________\|_____________________\|\n5'-GCA...GCUCG_______________A_____AGCAA...UUG-3'\n______________GCGAUAUCGCGAUUG_AGGCC\n______________:\|:\|:\|\|\|:\|:\|::\|_\|:\|\|\|\n______________UGUUGUAGUGUUGGC_UUCGG\n3'-UUU...UGUUG_______________A_____UUUUC...UCA-5'\n_____________\|_____________________\|\n_____________77____________________33\n	248 -- 254	69 -- 75	-25.2172 kcal/mol	7.66984 kcal/mol	8.92374 kcal/mol	246 295@LB@ \| \|@LB@5'-GCA...GCUCG A AGCAA...UUG-3'@LB@ GCGAUAUCGCGAUUG AGGCC@LB@ :\|:\|:\|\|\|:\|:\|::\| \|:\|\|\|@LB@ UGUUGUAGUGUUGGC UUCGG@LB@3'-UUU...UGUUG A UUUUC...UCA-5'@LB@ \| \|@LB@ 77 33@LB@@LB@@LB@Energy -13.53 kcal/mol@LB@Hybridization Energy -25.2172 kcal/mol@LB@Unfolding Energy - mRNA 7.66984 kcal/mol@LB@Unfolding Energy - sRNA 8.92374 kcal/mol@LB@@LB@Position - mRNA 247 -- 294@LB@Position - sRNA 34 -- 76@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 69 -- 75@LB@
188	0.01049	0.1967	stm0290	N/A	-13.50	0.202376	129 -- 157	48 -- 69		_____________128____________________________________________________158\n_____________\|______________________________________________________\|\n5'-UGC...UUCUC______C___CAUACCGCA____________________________UC_____UGAAA...GAA-3'\n______________AUGGAU_GAC__________UACAGGA________AGGGU_GUUUUG__CUGCC\n______________\|\|\|\|\|:_\|\|\|__________\|\|\|\|\|\|\|________\|\|\|\|\|_\|\|:\|:\|__\|\|:\|\|\n______________UACCUG_CUG__________AUGUCCU________UCCCA_CAGAGC__GAUGG\n3'-UUU...AGUGA______U___UCCCAUUUAC_______UCACUUUU_____U_____________CACCA...UCA-5'\n_____________\|______________________________________________________\|\n_____________70_____________________________________________________47\n	220 -- 226	139 -- 145	-35.7606 kcal/mol	12.8035 kcal/mol	12.8046 kcal/mol	128 158@LB@ \| \|@LB@5'-UGC...UUCUC C CAUACCGCA UC UGAAA...GAA-3'@LB@ AUGGAU GAC UACAGGA AGGGU GUUUUG CUGCC@LB@ \|\|\|\|\|: \|\|\| \|\|\|\|\|\|\| \|\|\|\|\| \|\|:\|:\| \|\|:\|\|@LB@ UACCUG CUG AUGUCCU UCCCA CAGAGC GAUGG@LB@3'-UUU...AGUGA U UCCCAUUUAC UCACUUUU U CACCA...UCA-5'@LB@ \| \|@LB@ 70 47@LB@@LB@@LB@Energy -13.50 kcal/mol@LB@Hybridization Energy -35.7606 kcal/mol@LB@Unfolding Energy - mRNA 12.8035 kcal/mol@LB@Unfolding Energy - sRNA 12.8046 kcal/mol@LB@@LB@Position - mRNA 129 -- 157@LB@Position - sRNA 48 -- 69@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 139 -- 145@LB@
165	0.008886	0.1918	stm0281	N/A	-13.47	0.204933	267 -- 289	36 -- 56	type VI secretion system-associated protein	_____________266______________________________________________290\n_____________\|________________________________________________\|\n5'-UGA...UAAUU____A_____A______A__UAU___C_____UGACC_C_______G_AGUGA...ACC-3'\n______________ACGG_ACGGG_UAAAUG_AU___GAG_UGGAA_____G_GUAGUCU_G\n______________\|\|:\|_\|\|:\|\|_\|\|\|\|\|\|_\|:___:\|\|_\|\|:\|\|_____\|_\|\|\|\|\|\|\|_\|\n______________UGUC_UGUCC_AUUUAC_UG___UUC_ACUUU_____C_CAUCAGA_C\n3'-UUU...AUACC__________C______A__UCC_________UUC___________G_GAUGG...UCA-5'\n_____________\|________________________________________________\|\n_____________57_______________________________________________35\n	219 -- 225	121 -- 127	-29.4304 kcal/mol	8.43831 kcal/mol	11.9516 kcal/mol	266 290@LB@ \| \|@LB@5'-UGA...UAAUU A A A UAU C UGACC C G AGUGA...ACC-3'@LB@ ACGG ACGGG UAAAUG AU GAG UGGAA G GUAGUCU G@LB@ \|\|:\| \|\|:\|\| \|\|\|\|\|\| \|: :\|\| \|\|:\|\| \| \|\|\|\|\|\|\| \|@LB@ UGUC UGUCC AUUUAC UG UUC ACUUU C CAUCAGA C@LB@3'-UUU...AUACC C A UCC UUC G GAUGG...UCA-5'@LB@ \| \|@LB@ 57 35@LB@@LB@@LB@Energy -13.47 kcal/mol@LB@Hybridization Energy -29.4304 kcal/mol@LB@Unfolding Energy - mRNA 8.43831 kcal/mol@LB@Unfolding Energy - sRNA 11.9516 kcal/mol@LB@@LB@Position - mRNA 267 -- 289@LB@Position - sRNA 36 -- 56@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 121 -- 127@LB@
121	0.006021	0.1758	stm3903	ilvE	-13.34	0.214101	130 -- 170	39 -- 78	branched chain amino acid aminotransferase	_____________129__________________171\n_____________\|____________________\|\n5'-GGU...CCAGA___CU___C___U_______AAUCC...GUA-3'\n______________GCG___GC_ACA_CACAACA\n______________\|\|:___:\|_\|\|\|_\|\|\|\|\|\|\|\n______________CGU___UG_UGU_GUGUUGU\n3'-UUU...GUUAA___UUG__U___U_______AGUGU...UCA-5'\n_____________\|____________________\|\n_____________79___________________38\n	164 -- 170	71 -- 77	-14.4922 kcal/mol	2.12049 kcal/mol	3.80671 kcal/mol	129 171@LB@ \| \|@LB@5'-GGU...CCAGA CU C U AAUCC...GUA-3'@LB@ GCG GC ACA CACAACA@LB@ \|\|: :\| \|\|\| \|\|\|\|\|\|\|@LB@ CGU UG UGU GUGUUGU@LB@3'-UUU...GUUAA UUG U U AGUGU...UCA-5'@LB@ \| \|@LB@ 79 38@LB@@LB@@LB@Energy -13.34 kcal/mol@LB@Hybridization Energy -14.4922 kcal/mol@LB@Unfolding Energy - mRNA 2.12049 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 130 -- 170@LB@Position - sRNA 39 -- 78@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 71 -- 77@LB@
192	0.01067	0.197	stm2650	yfiP	-13.22	0.223534	188 -- 232	36 -- 90	DTW domain-containing protein	_____________187_________________________233\n_____________\|___________________________\|\n5'-UCA...UCUCC________UUUCUAUGACC________UGUCC...GCU-3'\n______________GCAAACGC___________AAUAACGC\n______________\|\|\|\|\|\|:\|___________\|\|:\|\|\|:\|\n______________CGUUUGUG___________UUGUUGUG\n3'-UUU...GUUAA___________________________UUGUA...UCA-5'\n_____________\|___________________________\|\n_____________91__________________________35\n	208 -- 214	75 -- 81	-16.7007 kcal/mol	3.95203 kcal/mol	3.72363 kcal/mol	187 233@LB@ \| \|@LB@5'-UCA...UCUCC UUUCUAUGACC UGUCC...GCU-3'@LB@ GCAAACGC AAUAACGC@LB@ \|\|\|\|\|\|:\| \|\|:\|\|\|:\|@LB@ CGUUUGUG UUGUUGUG@LB@3'-UUU...GUUAA UUGUA...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -16.7007 kcal/mol@LB@Unfolding Energy - mRNA 3.95203 kcal/mol@LB@Unfolding Energy - sRNA 3.72363 kcal/mol@LB@@LB@Position - mRNA 188 -- 232@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 75 -- 81@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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