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
111	0.01184	0.3513	b0528	ybcJ	-13.49	0.050278	257 -- 272	44 -- 61	ribosome-associated protein; putative RNA-binding protein	_____________256________________273\n_____________\|__________________\|\n5'-AGG...CUGAA________GC________GAAAG...CGA-3'\n______________ACUGGAAG___UG_GAGC\n______________\|\|\|\|\|\|\|\|___\|\|_\|\|\|\|\n______________UGACCUUC___AC_CUCG\n3'-UUU...CAUUA________GUU__A____UUACA...GCG-5'\n_____________\|__________________\|\n_____________62_________________43\n	258 -- 264	54 -- 60	-19.8617 kcal/mol	3.07726 kcal/mol	3.29941 kcal/mol	256 273@LB@ \| \|@LB@5'-AGG...CUGAA GC GAAAG...CGA-3'@LB@ ACUGGAAG UG GAGC@LB@ \|\|\|\|\|\|\|\| \|\| \|\|\|\|@LB@ UGACCUUC AC CUCG@LB@3'-UUU...CAUUA GUU A UUACA...GCG-5'@LB@ \| \|@LB@ 62 43@LB@@LB@@LB@Energy -13.49 kcal/mol@LB@Hybridization Energy -19.8617 kcal/mol@LB@Unfolding Energy - mRNA 3.07726 kcal/mol@LB@Unfolding Energy - sRNA 3.29941 kcal/mol@LB@@LB@Position - mRNA 257 -- 272@LB@Position - sRNA 44 -- 61@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 54 -- 60@LB@
116	0.01242	0.3585	b0468	ybaN	-14.97	0.028033	230 -- 260	44 -- 78	DUF454 family inner membrane protein	_____________229___________________________________261\n_____________\|_____________________________________\|\n5'-GUC...AUUGG_______________________UAC___________GUGGU...UGC-3'\n______________CUGGCUGGC__GGUAGUGCUGGG___GC____UGGGC\n______________\|:\|\|\|\|\|\|\|__:\|\|\|:\|:\|\|\|\|:___\|\|____\|\|:\|\|\n______________GGCCGACCG__UCAUUAUGACCU___CG____ACUCG\n3'-UUU...UCGUG_________AU____________U____UUAC_____UUACA...GCG-5'\n_____________\|_____________________________________\|\n_____________79____________________________________43\n	244 -- 250	56 -- 62	-40.2392 kcal/mol	12.5705 kcal/mol	12.6976 kcal/mol	229 261@LB@ \| \|@LB@5'-GUC...AUUGG UAC GUGGU...UGC-3'@LB@ CUGGCUGGC GGUAGUGCUGGG GC UGGGC@LB@ \|:\|\|\|\|\|\|\| :\|\|\|:\|:\|\|\|\|: \|\| \|\|:\|\|@LB@ GGCCGACCG UCAUUAUGACCU CG ACUCG@LB@3'-UUU...UCGUG AU U UUAC UUACA...GCG-5'@LB@ \| \|@LB@ 79 43@LB@@LB@@LB@Energy -14.97 kcal/mol@LB@Hybridization Energy -40.2392 kcal/mol@LB@Unfolding Energy - mRNA 12.5705 kcal/mol@LB@Unfolding Energy - sRNA 12.6976 kcal/mol@LB@@LB@Position - mRNA 230 -- 260@LB@Position - sRNA 44 -- 78@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 56 -- 62@LB@
124	0.01356	0.3627	b2232	ubiG	-16.56	0.014945	261 -- 300	44 -- 89	bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase	_____________260_____________________________________________300\n_____________\|_______________________________________________\|\n5'-CUU...AAUUU_______U_____CCC______GG________________________-3'\n______________GAAGCCG_CGCCU___GCUGGU_____GAU_CUGGAAG____GUGAGU\n______________:\|\|\|\|\|:_\|:\|\|:___\|\|\|\|\|:_____:\|\|_\|\|\|\|\|\|\|____\|\|\|\|\|:\n______________UUUCGGU_GUGGG___CGACCG_____UUA_GACCUUC____CACUCG\n__________3'-U_______C_____C________AUUCA___U_______GUUA______UUACA...GCG-5'\n_____________\|________________________________________________\|\n_____________90_______________________________________________43\n	288 -- 294	54 -- 60	-44.5757 kcal/mol	13.1093 kcal/mol	14.9095 kcal/mol	260 300@LB@ \| \|@LB@5'-CUU...AAUUU U CCC GG -3'@LB@ GAAGCCG CGCCU GCUGGU GAU CUGGAAG GUGAGU@LB@ :\|\|\|\|\|: \|:\|\|: \|\|\|\|\|: :\|\| \|\|\|\|\|\|\| \|\|\|\|\|:@LB@ UUUCGGU GUGGG CGACCG UUA GACCUUC CACUCG@LB@ 3'-U C C AUUCA U GUUA UUACA...GCG-5'@LB@ \| \|@LB@ 90 43@LB@@LB@@LB@Energy -16.56 kcal/mol@LB@Hybridization Energy -44.5757 kcal/mol@LB@Unfolding Energy - mRNA 13.1093 kcal/mol@LB@Unfolding Energy - sRNA 14.9095 kcal/mol@LB@@LB@Position - mRNA 261 -- 300@LB@Position - sRNA 44 -- 89@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 54 -- 60@LB@
165	0.02037	0.4072	b1981	shiA	-10.79	0.140980	142 -- 153	44 -- 55	shikimate transporter	_____________141__________154\n_____________\|____________\|\n5'-CUG...UCGAC____________UACCU...UCG-3'\n______________GGCAAUGUGAGU\n______________:\|\|\|\|\|\|\|\|\|\|:\n______________UCGUUACACUCG\n3'-UUU...GACCU____________UUACA...GCG-5'\n_____________\|____________\|\n_____________56___________43\n	147 -- 153	44 -- 50	-18.9093 kcal/mol	4.9192 kcal/mol	3.20048 kcal/mol	141 154@LB@ \| \|@LB@5'-CUG...UCGAC UACCU...UCG-3'@LB@ GGCAAUGUGAGU@LB@ :\|\|\|\|\|\|\|\|\|\|:@LB@ UCGUUACACUCG@LB@3'-UUU...GACCU UUACA...GCG-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -10.79 kcal/mol@LB@Hybridization Energy -18.9093 kcal/mol@LB@Unfolding Energy - mRNA 4.9192 kcal/mol@LB@Unfolding Energy - sRNA 3.20048 kcal/mol@LB@@LB@Position - mRNA 142 -- 153@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 44 -- 50@LB@
166	0.02064	0.4072	b0429	cyoD	-11.77	0.097498	188 -- 206	44 -- 59	cytochrome o ubiquinol oxidase subunit IV	_____________187_________________207\n_____________\|___________________\|\n5'-UUC...UCUGA____________AAU____CAUUC...UCU-3'\n______________UGGGGGCGAUGU___GAGU\n______________\|\|\|::\|\|:\|\|\|\|___\|\|\|:\n______________ACCUUCGUUACA___CUCG\n3'-UUU...UUAUG___________________UUACA...GCG-5'\n_____________\|___________________\|\n_____________60__________________43\n	193 -- 199	48 -- 54	-20.4312 kcal/mol	5.39053 kcal/mol	3.27056 kcal/mol	187 207@LB@ \| \|@LB@5'-UUC...UCUGA AAU CAUUC...UCU-3'@LB@ UGGGGGCGAUGU GAGU@LB@ \|\|\|::\|\|:\|\|\|\| \|\|\|:@LB@ ACCUUCGUUACA CUCG@LB@3'-UUU...UUAUG UUACA...GCG-5'@LB@ \| \|@LB@ 60 43@LB@@LB@@LB@Energy -11.77 kcal/mol@LB@Hybridization Energy -20.4312 kcal/mol@LB@Unfolding Energy - mRNA 5.39053 kcal/mol@LB@Unfolding Energy - sRNA 3.27056 kcal/mol@LB@@LB@Position - mRNA 188 -- 206@LB@Position - sRNA 44 -- 59@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 48 -- 54@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@
192	0.02457	0.4226	b2689	yqaA	-16.30	0.016522	258 -- 300	44 -- 85	COG1238 family inner membrane protein	_____________257_________________________________________300\n_____________\|___________________________________________\|\n5'-CAC...CUACA___U________AACUCCG____C_______U________U___-3'\n______________CUA_UACCCGGC_______AAGU_GUGCUGG_GGCAAUGU__GC\n______________\|:\|_:\|\|\|\|\|\|\|_______\|\|\|\|_:\|:\|\|\|\|_:\|\|\|\|\|\|\|__\|\|\n______________GGU_GUGGGCCG_______UUCA_UAUGACC_UCGUUACA__CG\n______3'-UUUUC___C________ACCGA______U_______U________CU__UUACA...GCG-5'\n_____________\|____________________________________________\|\n_____________86___________________________________________43\n	291 -- 297	48 -- 54	-43.3701 kcal/mol	12.1561 kcal/mol	14.9093 kcal/mol	257 300@LB@ \| \|@LB@5'-CAC...CUACA U AACUCCG C U U -3'@LB@ CUA UACCCGGC AAGU GUGCUGG GGCAAUGU GC@LB@ \|:\| :\|\|\|\|\|\|\| \|\|\|\| :\|:\|\|\|\| :\|\|\|\|\|\|\| \|\|@LB@ GGU GUGGGCCG UUCA UAUGACC UCGUUACA CG@LB@ 3'-UUUUC C ACCGA U U CU UUACA...GCG-5'@LB@ \| \|@LB@ 86 43@LB@@LB@@LB@Energy -16.30 kcal/mol@LB@Hybridization Energy -43.3701 kcal/mol@LB@Unfolding Energy - mRNA 12.1561 kcal/mol@LB@Unfolding Energy - sRNA 14.9093 kcal/mol@LB@@LB@Position - mRNA 258 -- 300@LB@Position - sRNA 44 -- 85@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 48 -- 54@LB@
89	0.009246	0.3393	b1279	yciS	-12.08	0.086714	189 -- 204	46 -- 61	DUF1049 family inner membrane protein function unknown	_____________188______________205\n_____________\|________________\|\n5'-ACC...ACAUA__G_____________AAUAU...UGU-3'\n______________AC_GGAAGUAAUGUGA\n______________\|\|_\|\|\|\|\|:\|\|\|\|\|\|\|\n______________UG_CCUUCGUUACACU\n3'-UUU...CAUUA__A_____________CGUUA...GCG-5'\n_____________\|________________\|\n_____________62_______________45\n	198 -- 204	46 -- 52	-21.4875 kcal/mol	6.16612 kcal/mol	3.24422 kcal/mol	188 205@LB@ \| \|@LB@5'-ACC...ACAUA G AAUAU...UGU-3'@LB@ AC GGAAGUAAUGUGA@LB@ \|\| \|\|\|\|\|:\|\|\|\|\|\|\|@LB@ UG CCUUCGUUACACU@LB@3'-UUU...CAUUA A CGUUA...GCG-5'@LB@ \| \|@LB@ 62 45@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -21.4875 kcal/mol@LB@Unfolding Energy - mRNA 6.16612 kcal/mol@LB@Unfolding Energy - sRNA 3.24422 kcal/mol@LB@@LB@Position - mRNA 189 -- 204@LB@Position - sRNA 46 -- 61@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 46 -- 52@LB@
146	0.01749	0.3998	b1611	fumC	-5.84	0.669018	232 -- 244	46 -- 59	fumarate hydratase (fumarase C) aerobic Class II	_____________231____________245\n_____________\|______________\|\n5'-AGG...UUCGA______________UGUCC...UCC-3'\n______________UGGGGGCGAU_UGA\n______________\|\|\|::\|\|:\|\|_\|\|\|\n______________ACCUUCGUUA_ACU\n3'-UUU...UUAUG__________C___CGUUA...GCG-5'\n_____________\|______________\|\n_____________60_____________45\n	233 -- 239	52 -- 58	-14.3864 kcal/mol	5.35896 kcal/mol	3.18972 kcal/mol	231 245@LB@ \| \|@LB@5'-AGG...UUCGA UGUCC...UCC-3'@LB@ UGGGGGCGAU UGA@LB@ \|\|\|::\|\|:\|\| \|\|\|@LB@ ACCUUCGUUA ACU@LB@3'-UUU...UUAUG C CGUUA...GCG-5'@LB@ \| \|@LB@ 60 45@LB@@LB@@LB@Energy -5.84 kcal/mol@LB@Hybridization Energy -14.3864 kcal/mol@LB@Unfolding Energy - mRNA 5.35896 kcal/mol@LB@Unfolding Energy - sRNA 3.18972 kcal/mol@LB@@LB@Position - mRNA 232 -- 244@LB@Position - sRNA 46 -- 59@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 52 -- 58@LB@
198	0.02503	0.4226	b2544	yphB	-11.73	0.099011	68 -- 80	47 -- 61	mutarotase superfamily protein YphB family	_____________67______________81\n_____________\|_______________\|\n5'-CGG...GACGG_______________GCCGC...UAC-3'\n______________ACUGGAAGC__UGUG\n______________\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________UGACCUUCG__ACAC\n3'-UUU...CAUUA_________UU____UCGUU...GCG-5'\n_____________\|_______________\|\n_____________62______________46\n	70 -- 76	53 -- 59	-17.6322 kcal/mol	2.81046 kcal/mol	3.09217 kcal/mol	67 81@LB@ \| \|@LB@5'-CGG...GACGG GCCGC...UAC-3'@LB@ ACUGGAAGC UGUG@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UGACCUUCG ACAC@LB@3'-UUU...CAUUA UU UCGUU...GCG-5'@LB@ \| \|@LB@ 62 46@LB@@LB@@LB@Energy -11.73 kcal/mol@LB@Hybridization Energy -17.6322 kcal/mol@LB@Unfolding Energy - mRNA 2.81046 kcal/mol@LB@Unfolding Energy - sRNA 3.09217 kcal/mol@LB@@LB@Position - mRNA 68 -- 80@LB@Position - sRNA 47 -- 61@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 53 -- 59@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)

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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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