Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
60	0.005592	0.2905	b3577	yiaM	-14.71	0.031138	209 -- 232	41 -- 64	2 3-diketo-L-gulonate TRAP transporter small permease protein	_____________208______________________233\n_____________\|________________________\|\n5'-UUC...AAAAA______C________ACU______UAAUC...GCA-3'\n______________AAUACU_GAAGCAAU___GGCGAU\n______________\|\|\|\|\|\|_\|\|\|\|\|\|\|\|___:\|\|:\|\|\n______________UUAUGA_CUUCGUUA___UCGUUA\n3'-UUU...AUUCA______C________CAC______CAGCA...GCG-5'\n_____________\|________________________\|\n_____________65_______________________40\n	217 -- 223	50 -- 56	-21.6131 kcal/mol	3.60615 kcal/mol	3.30185 kcal/mol	208 233@LB@ \| \|@LB@5'-UUC...AAAAA C ACU UAAUC...GCA-3'@LB@ AAUACU GAAGCAAU GGCGAU@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|\| :\|\|:\|\|@LB@ UUAUGA CUUCGUUA UCGUUA@LB@3'-UUU...AUUCA C CAC CAGCA...GCG-5'@LB@ \| \|@LB@ 65 40@LB@@LB@@LB@Energy -14.71 kcal/mol@LB@Hybridization Energy -21.6131 kcal/mol@LB@Unfolding Energy - mRNA 3.60615 kcal/mol@LB@Unfolding Energy - sRNA 3.30185 kcal/mol@LB@@LB@Position - mRNA 209 -- 232@LB@Position - sRNA 41 -- 64@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 50 -- 56@LB@
96	0.01001	0.3393	b2714	ascG	-11.75	0.098239	209 -- 220	53 -- 64	asc operon transcriptional repressor; prpBC operon repressor	_____________208__________221\n_____________\|____________\|\n5'-AAA...ACGAC____________GGCGA...AAG-3'\n______________GAUGCUGGAAGU\n______________:\|\|:\|\|\|\|\|\|\|:\n______________UUAUGACCUUCG\n3'-UUU...AUUCA____________UUACA...GCG-5'\n_____________\|____________\|\n_____________65___________52\n	214 -- 220	53 -- 59	-16.9486 kcal/mol	2.31342 kcal/mol	2.88502 kcal/mol	208 221@LB@ \| \|@LB@5'-AAA...ACGAC GGCGA...AAG-3'@LB@ GAUGCUGGAAGU@LB@ :\|\|:\|\|\|\|\|\|\|:@LB@ UUAUGACCUUCG@LB@3'-UUU...AUUCA UUACA...GCG-5'@LB@ \| \|@LB@ 65 52@LB@@LB@@LB@Energy -11.75 kcal/mol@LB@Hybridization Energy -16.9486 kcal/mol@LB@Unfolding Energy - mRNA 2.31342 kcal/mol@LB@Unfolding Energy - sRNA 2.88502 kcal/mol@LB@@LB@Position - mRNA 209 -- 220@LB@Position - sRNA 53 -- 64@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 53 -- 59@LB@
125	0.0136	0.3627	b3647	ligB	-15.20	0.025592	210 -- 279	1 -- 59	DNA ligase NAD(+)-dependent	_____________209_____________________________________________________________________280\n_____________\|_______________________________________________________________________\|\n5'-GGC...AAGUA____U______AUUAAUA____UC________GG__AUCA___G______C_____GUCCGG_________CAGCC...AAA-3'\n______________UGGA_GGCGAU_______GGUA___UUGUGCU__CA____UCU_UGUGGG_GGUCU______CCUGGUCGC\n______________\|\|\|\|_:\|\|:\|\|_______:\|:\|___\|:\|\|\|\|\|__\|\|____\|\|\|_:\|:\|:\|_\|\|\|\|\|______\|\|\|\|:\|\|\|\|\n______________ACCU_UCGUUA_______UCGU___AGCACGA__GU____AGA_GCGCUC_CCAGA______GGACUAGCG\n3'-UUU...UUAUG___________CAC________UAC_______AA__CCA____G____________A______________-5'\n_____________\|______________________________________________________________________\|\n_____________60_____________________________________________________________________1\n	273 -- 279	1 -- 7	-52.2567 kcal/mol	22.9457 kcal/mol	14.1095 kcal/mol	209 280@LB@ \| \|@LB@5'-GGC...AAGUA U AUUAAUA UC GG AUCA G C GUCCGG CAGCC...AAA-3'@LB@ UGGA GGCGAU GGUA UUGUGCU CA UCU UGUGGG GGUCU CCUGGUCGC@LB@ \|\|\|\| :\|\|:\|\| :\|:\| \|:\|\|\|\|\| \|\| \|\|\| :\|:\|:\| \|\|\|\|\| \|\|\|\|:\|\|\|\|@LB@ ACCU UCGUUA UCGU AGCACGA GU AGA GCGCUC CCAGA GGACUAGCG@LB@3'-UUU...UUAUG CAC UAC AA CCA G A -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -15.20 kcal/mol@LB@Hybridization Energy -52.2567 kcal/mol@LB@Unfolding Energy - mRNA 22.9457 kcal/mol@LB@Unfolding Energy - sRNA 14.1095 kcal/mol@LB@@LB@Position - mRNA 210 -- 279@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 1 -- 7@LB@
190	0.02395	0.4226	b1189	dadA	-13.37	0.052568	210 -- 233	43 -- 66	D-amino acid dehydrogenase	_____________209_______________________234\n_____________\|_________________________\|\n5'-CCG...GAGUU__C_____G________________GGCGU...CGG-3'\n______________GU_AUACU_GGAAGUGGUGUG_GUA\n______________\|\|_\|\|\|\|\|_\|\|\|\|\|:::\|\|\|\|_\|:\|\n______________CA_UAUGA_CCUUCGUUACAC_CGU\n3'-UUU...CGAUU__U__________________U___UACAG...GCG-5'\n_____________\|_________________________\|\n_____________67________________________42\n	219 -- 225	52 -- 58	-24.725 kcal/mol	8.04945 kcal/mol	3.30463 kcal/mol	209 234@LB@ \| \|@LB@5'-CCG...GAGUU C G GGCGU...CGG-3'@LB@ GU AUACU GGAAGUGGUGUG GUA@LB@ \|\| \|\|\|\|\| \|\|\|\|\|:::\|\|\|\| \|:\|@LB@ CA UAUGA CCUUCGUUACAC CGU@LB@3'-UUU...CGAUU U U UACAG...GCG-5'@LB@ \| \|@LB@ 67 42@LB@@LB@@LB@Energy -13.37 kcal/mol@LB@Hybridization Energy -24.725 kcal/mol@LB@Unfolding Energy - mRNA 8.04945 kcal/mol@LB@Unfolding Energy - sRNA 3.30463 kcal/mol@LB@@LB@Position - mRNA 210 -- 233@LB@Position - sRNA 43 -- 66@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 52 -- 58@LB@
173	0.02105	0.4072	b2840	ygeA	-11.88	0.093670	213 -- 233	44 -- 67	Asp/Glu_racemase family protein	_____________212______________________234\n_____________\|________________________\|\n5'-AAA...CAAUU___U__________G_________UGGGA...UUC-3'\n______________GGU__UGCUGGGAG_AA__UGAGC\n______________:\|\|__\|:\|\|\|\|:\|\|_\|\|__\|\|\|\|\|\n______________UCA__AUGACCUUC_UU__ACUCG\n3'-UUU...CCGAU___UU_________G__AC_____UUACA...GCG-5'\n_____________\|________________________\|\n_____________68_______________________43\n	219 -- 225	54 -- 60	-22.3324 kcal/mol	7.15309 kcal/mol	3.30407 kcal/mol	212 234@LB@ \| \|@LB@5'-AAA...CAAUU U G UGGGA...UUC-3'@LB@ GGU UGCUGGGAG AA UGAGC@LB@ :\|\| \|:\|\|\|\|:\|\| \|\| \|\|\|\|\|@LB@ UCA AUGACCUUC UU ACUCG@LB@3'-UUU...CCGAU UU G AC UUACA...GCG-5'@LB@ \| \|@LB@ 68 43@LB@@LB@@LB@Energy -11.88 kcal/mol@LB@Hybridization Energy -22.3324 kcal/mol@LB@Unfolding Energy - mRNA 7.15309 kcal/mol@LB@Unfolding Energy - sRNA 3.30407 kcal/mol@LB@@LB@Position - mRNA 213 -- 233@LB@Position - sRNA 44 -- 67@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 54 -- 60@LB@
145	0.01736	0.3998	b1607	ydgC	-14.56	0.032924	216 -- 264	42 -- 89	GlpM family inner membrane protein	_____________215__________________________________________________265\n_____________\|____________________________________________________\|\n5'-AUG...UAAUC________________GC______________UU__U_______UUU_____AAACG...CAC-3'\n______________AAAGCC_GCGCUCGGU__GCU_GGUAGUGCUG__GA__UGGUGU___AGCAA\n______________\|\|\|\|\|\|_\|\|:\|:\|\|\|:__\|\|\|_:\|\|\|:\|:\|\|\|__\|\|__:::\|\|\|___\|\|\|\|\|\n______________UUUCGG_CGUGGGCCG__CGA_UCAUUAUGAC__CU__GUUACA___UCGUU\n__________3'-U______U_________AC___U______________UC______C_______ACAGC...GCG-5'\n_____________\|____________________________________________________\|\n_____________90___________________________________________________41\n	239 -- 245	58 -- 64	-48.2837 kcal/mol	18.8097 kcal/mol	14.9103 kcal/mol	215 265@LB@ \| \|@LB@5'-AUG...UAAUC GC UU U UUU AAACG...CAC-3'@LB@ AAAGCC GCGCUCGGU GCU GGUAGUGCUG GA UGGUGU AGCAA@LB@ \|\|\|\|\|\| \|\|:\|:\|\|\|: \|\|\| :\|\|\|:\|:\|\|\| \|\| :::\|\|\| \|\|\|\|\|@LB@ UUUCGG CGUGGGCCG CGA UCAUUAUGAC CU GUUACA UCGUU@LB@ 3'-U U AC U UC C ACAGC...GCG-5'@LB@ \| \|@LB@ 90 41@LB@@LB@@LB@Energy -14.56 kcal/mol@LB@Hybridization Energy -48.2837 kcal/mol@LB@Unfolding Energy - mRNA 18.8097 kcal/mol@LB@Unfolding Energy - sRNA 14.9103 kcal/mol@LB@@LB@Position - mRNA 216 -- 264@LB@Position - sRNA 42 -- 89@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 58 -- 64@LB@
178	0.02201	0.4113	b4176	yjeT	-16.79	0.013635	217 -- 249	54 -- 87	DUF2065 family protein	_____________216_________________________________250\n_____________\|___________________________________\|\n5'-UCA...AAUCU____________CC______U______________GUUUA...CGA-3'\n______________GGCUGGCGCUUG__CUGGUU___UGGUACUGGAAG\n______________:\|\|::\|\|:\|::\|__\|\|\|\|:\|___\|::\|\|\|\|\|\|\|\|\|\n______________UCGGUCGUGGGC__GACCGA___AUUAUGACCUUC\n________3'-UUU____________C_______UUC____________GUUAC...GCG-5'\n_____________\|___________________________________\|\n_____________88__________________________________53\n	243 -- 249	54 -- 60	-41.1583 kcal/mol	10.0538 kcal/mol	14.3172 kcal/mol	216 250@LB@ \| \|@LB@5'-UCA...AAUCU CC U GUUUA...CGA-3'@LB@ GGCUGGCGCUUG CUGGUU UGGUACUGGAAG@LB@ :\|\|::\|\|:\|::\| \|\|\|\|:\| \|::\|\|\|\|\|\|\|\|\|@LB@ UCGGUCGUGGGC GACCGA AUUAUGACCUUC@LB@ 3'-UUU C UUC GUUAC...GCG-5'@LB@ \| \|@LB@ 88 53@LB@@LB@@LB@Energy -16.79 kcal/mol@LB@Hybridization Energy -41.1583 kcal/mol@LB@Unfolding Energy - mRNA 10.0538 kcal/mol@LB@Unfolding Energy - sRNA 14.3172 kcal/mol@LB@@LB@Position - mRNA 217 -- 249@LB@Position - sRNA 54 -- 87@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 54 -- 60@LB@
26	0.002118	0.2692	b1181	ycgN	-20.05	0.003709	218 -- 269	37 -- 88	UPF0153 family cysteine cluster protein	_____________217_____________________________________________________270\n_____________\|_______________________________________________________\|\n5'-UUU...CUGAU____G_U______UU_____A______AACC__________AA____________GAAUG...GUC-3'\n______________GAGC_A_GUACCU__CUGGC_AAGUAA____CUGGA__CGA__UGAGCGAUG_CG\n______________:\|\|\|_\|_\|:\|\|\|:__\|\|\|\|\|_\|\|\|\|\|\|____\|\|\|\|\|__\|:\|__\|\|\|\|\|:\|\|\|_\|\|\n______________UUCG_U_CGUGGG__GACCG_UUCAUU____GACCU__GUU__ACUCGUUAC_GC\n_________3'-UU____G________CC_____A______AU_______UC___AC_________A__ACGAA...GCG-5'\n_____________\|_______________________________________________________\|\n_____________89______________________________________________________36\n	261 -- 267	40 -- 46	-50.5987 kcal/mol	15.641 kcal/mol	14.9108 kcal/mol	217 270@LB@ \| \|@LB@5'-UUU...CUGAU G U UU A AACC AA GAAUG...GUC-3'@LB@ GAGC A GUACCU CUGGC AAGUAA CUGGA CGA UGAGCGAUG CG@LB@ :\|\|\| \| \|:\|\|\|: \|\|\|\|\| \|\|\|\|\|\| \|\|\|\|\| \|:\| \|\|\|\|\|:\|\|\| \|\|@LB@ UUCG U CGUGGG GACCG UUCAUU GACCU GUU ACUCGUUAC GC@LB@ 3'-UU G CC A AU UC AC A ACGAA...GCG-5'@LB@ \| \|@LB@ 89 36@LB@@LB@@LB@Energy -20.05 kcal/mol@LB@Hybridization Energy -50.5987 kcal/mol@LB@Unfolding Energy - mRNA 15.641 kcal/mol@LB@Unfolding Energy - sRNA 14.9108 kcal/mol@LB@@LB@Position - mRNA 218 -- 269@LB@Position - sRNA 37 -- 88@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 40 -- 46@LB@
189	0.02313	0.4113	b2438	eutK	-12.08	0.086588	220 -- 243	37 -- 62	putative ethanol utilization carboxysome structural protein	_____________219________________________244\n_____________\|__________________________\|\n5'-CGA...GGGAU____________AC______UG____CCGCG...GUC-3'\n______________UGCUGGAAGUGG____GGCA__GUCG\n______________\|:\|\|\|\|\|\|\|:::____:\|\|\|__\|\|\|\|\n______________AUGACCUUCGUU____UCGU__CAGC\n3'-UUU...UCAUU____________ACAC____UA____ACGAA...GCG-5'\n_____________\|__________________________\|\n_____________63_________________________36\n	224 -- 230	52 -- 58	-25.7957 kcal/mol	10.4122 kcal/mol	3.3026 kcal/mol	219 244@LB@ \| \|@LB@5'-CGA...GGGAU AC UG CCGCG...GUC-3'@LB@ UGCUGGAAGUGG GGCA GUCG@LB@ \|:\|\|\|\|\|\|\|::: :\|\|\| \|\|\|\|@LB@ AUGACCUUCGUU UCGU CAGC@LB@3'-UUU...UCAUU ACAC UA ACGAA...GCG-5'@LB@ \| \|@LB@ 63 36@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -25.7957 kcal/mol@LB@Unfolding Energy - mRNA 10.4122 kcal/mol@LB@Unfolding Energy - sRNA 3.3026 kcal/mol@LB@@LB@Position - mRNA 220 -- 243@LB@Position - sRNA 37 -- 62@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 52 -- 58@LB@
59	0.005518	0.2905	b3663	yicN	-20.80	0.002740	224 -- 256	26 -- 61	DUF1198 family protein	_____________223__________________________________257\n_____________\|____________________________________\|\n5'-CUU...GCCAC_____C________UU__G_________________GCUGA...AUC-3'\n______________GCUGG_GGUAGUGU__GU___GUUG_GUUUUCGGGU\n______________:\|\|\|\|_:\|:\|:\|\|\|__\|:___\|\|:\|_\|:\|\|\|\|:\|\|\|\n______________UGACC_UCGUUACA__CG___CAGC_CGAAAGUCCA\n3'-UUU...CAUUA_____U________CU__UUA____A__________AGAGG...GCG-5'\n_____________\|____________________________________\|\n_____________62___________________________________25\n	250 -- 256	26 -- 32	-36.0496 kcal/mol	7.2648 kcal/mol	7.98122 kcal/mol	223 257@LB@ \| \|@LB@5'-CUU...GCCAC C UU G GCUGA...AUC-3'@LB@ GCUGG GGUAGUGU GU GUUG GUUUUCGGGU@LB@ :\|\|\|\| :\|:\|:\|\|\| \|: \|\|:\| \|:\|\|\|\|:\|\|\|@LB@ UGACC UCGUUACA CG CAGC CGAAAGUCCA@LB@3'-UUU...CAUUA U CU UUA A AGAGG...GCG-5'@LB@ \| \|@LB@ 62 25@LB@@LB@@LB@Energy -20.80 kcal/mol@LB@Hybridization Energy -36.0496 kcal/mol@LB@Unfolding Energy - mRNA 7.2648 kcal/mol@LB@Unfolding Energy - sRNA 7.98122 kcal/mol@LB@@LB@Position - mRNA 224 -- 256@LB@Position - sRNA 26 -- 61@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 26 -- 32@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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