Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
95	0.005813	0.2147	b3450	ugpC	-12.76	0.087557	84 -- 111	1 -- 34	sn-glycerol-3-phosphate ABC transporter ATPase	_____________83_________________________________112\n_____________\|__________________________________\|\n5'-GUG...AGGCA___________A________U_____________GAUGU...UCG-3'\n______________CCACGGAAUGG__AC_UCAG_GA____UGGUGGC\n______________\|\|\|\|::\|\|\|\|\|__\|\|_\|\|\|:_\|\|____::\|\|\|\|\|\n______________GGUGUUUUACC__UG_AGUU_CU____GUCACCG\n3'-UUU...CCCGA___________CC__U____U__UUUC_______-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	105 -- 111	1 -- 7	-27.9886 kcal/mol	10.9582 kcal/mol	4.26884 kcal/mol	83 112@LB@ \| \|@LB@5'-GUG...AGGCA A U GAUGU...UCG-3'@LB@ CCACGGAAUGG AC UCAG GA UGGUGGC@LB@ \|\|\|\|::\|\|\|\|\| \|\| \|\|\|: \|\| ::\|\|\|\|\|@LB@ GGUGUUUUACC UG AGUU CU GUCACCG@LB@3'-UUU...CCCGA CC U U UUUC -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -12.76 kcal/mol@LB@Hybridization Energy -27.9886 kcal/mol@LB@Unfolding Energy - mRNA 10.9582 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 84 -- 111@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 1 -- 7@LB@
127	0.009277	0.2491	b2781	mazG	-12.70	0.090074	53 -- 69	8 -- 24	nucleoside triphosphate pyrophosphohydrolase	_____________52________________70\n_____________\|_________________\|\n5'-UGA...CAAGA__A___A__________AACAG...CGC-3'\n______________GG_GCA_CGAAGAAAGG\n______________\|\|_:\|\|_\|:\|\|\|\|\|\|:\|\n______________CC_UGU_GUUUCUUUUC\n3'-UUU...UUUAC__C___A__________GUCACCG-5'\n_____________\|_________________\|\n_____________25________________7\n	63 -- 69	8 -- 14	-16.258 kcal/mol	2.86814 kcal/mol	0.688982 kcal/mol	52 70@LB@ \| \|@LB@5'-UGA...CAAGA A A AACAG...CGC-3'@LB@ GG GCA CGAAGAAAGG@LB@ \|\| :\|\| \|:\|\|\|\|\|\|:\|@LB@ CC UGU GUUUCUUUUC@LB@3'-UUU...UUUAC C A GUCACCG-5'@LB@ \| \|@LB@ 25 7@LB@@LB@@LB@Energy -12.70 kcal/mol@LB@Hybridization Energy -16.258 kcal/mol@LB@Unfolding Energy - mRNA 2.86814 kcal/mol@LB@Unfolding Energy - sRNA 0.688982 kcal/mol@LB@@LB@Position - mRNA 53 -- 69@LB@Position - sRNA 8 -- 24@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 8 -- 14@LB@
128	0.00928	0.2491	b0491	fetB	-12.70	0.090276	178 -- 195	1 -- 17	iron export ABC transporter permease; peroxide resistance protein	_____________177________________196\n_____________\|__________________\|\n5'-GCC...CAUGC________U____GAA__ACGCU...AGA-3'\n______________CGGAGAAA_GCAG___GC\n______________\|::\|\|\|\|\|_\|\|\|\|___\|\|\n______________GUUUCUUU_CGUC___CG\n3'-UUU...CUGUA________U____AC___-5'\n_____________\|_________________\|\n_____________18________________1\n	179 -- 185	10 -- 16	-17.1669 kcal/mol	3.03232 kcal/mol	1.43853 kcal/mol	177 196@LB@ \| \|@LB@5'-GCC...CAUGC U GAA ACGCU...AGA-3'@LB@ CGGAGAAA GCAG GC@LB@ \|::\|\|\|\|\| \|\|\|\| \|\|@LB@ GUUUCUUU CGUC CG@LB@3'-UUU...CUGUA U AC -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -12.70 kcal/mol@LB@Hybridization Energy -17.1669 kcal/mol@LB@Unfolding Energy - mRNA 3.03232 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 178 -- 195@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 10 -- 16@LB@
105	0.007004	0.2333	b4034	malE	-12.62	0.093531	92 -- 123	2 -- 32	maltose transporter subunit	_____________91_________________________________124\n_____________\|__________________________________\|\n5'-AGG...ACAAA____C_________________C___G__GA___AAAGA...UGG-3'\n______________GCGA_GGUGGGG_CGU_AGGGG_AAG_AG__UGG\n______________:\|:\|_::\|\|\|\|\|_\|:\|_\|::\|:_\|\|\|_\|\|__\|\|\|\n______________UGUU_UUACCCC_GUA_UUUCU_UUC_UC__ACC\n3'-UUU...CGAGG____________U___G_____U___G_______G-5'\n_____________\|__________________________________\|\n_____________33_________________________________1\n	97 -- 103	22 -- 28	-24.1065 kcal/mol	8.94734 kcal/mol	2.53929 kcal/mol	91 124@LB@ \| \|@LB@5'-AGG...ACAAA C C G GA AAAGA...UGG-3'@LB@ GCGA GGUGGGG CGU AGGGG AAG AG UGG@LB@ :\|:\| ::\|\|\|\|\| \|:\| \|::\|: \|\|\| \|\| \|\|\|@LB@ UGUU UUACCCC GUA UUUCU UUC UC ACC@LB@3'-UUU...CGAGG U G U G G-5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -12.62 kcal/mol@LB@Hybridization Energy -24.1065 kcal/mol@LB@Unfolding Energy - mRNA 8.94734 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 92 -- 123@LB@Position - sRNA 2 -- 32@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 22 -- 28@LB@
79	0.004643	0.2062	b2264	menD	-12.62	0.093644	52 -- 86	1 -- 30	2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylate synthase; SEPHCHC synthase	_____________51_____________________________________87\n_____________\|______________________________________\|\n5'-CGU...GAGCA_______CAGGAAAUC____A_____C___________UGCGU...GUU-3'\n______________AGAGUGG_________GACA_CAAAG___GGCAG_GGC\n______________\|:\|:\|\|\|_________\|\|\|\|_\|\|\|\|\|___:\|\|\|\|_\|\|\|\n______________UUUUACC_________CUGU_GUUUC___UCGUC_CCG\n3'-UUU...AGGUG_______C____________A_____UUU_____A___-5'\n_____________\|_____________________________________\|\n_____________31____________________________________1\n	52 -- 58	24 -- 30	-24.8101 kcal/mol	9.6737 kcal/mol	2.51911 kcal/mol	51 87@LB@ \| \|@LB@5'-CGU...GAGCA CAGGAAAUC A C UGCGU...GUU-3'@LB@ AGAGUGG GACA CAAAG GGCAG GGC@LB@ \|:\|:\|\|\| \|\|\|\| \|\|\|\|\| :\|\|\|\| \|\|\|@LB@ UUUUACC CUGU GUUUC UCGUC CCG@LB@3'-UUU...AGGUG C A UUU A -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -12.62 kcal/mol@LB@Hybridization Energy -24.8101 kcal/mol@LB@Unfolding Energy - mRNA 9.6737 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 52 -- 86@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 24 -- 30@LB@
166	0.01216	0.2504	b4485	ytfR	-12.60	0.094393	18 -- 41	9 -- 34	putative sugar ABC transporter ATPase	_____________17_________________________42\n_____________\|__________________________\|\n5'-CCU...UGAUA________GAA_______________AGAAA...GCC-3'\n______________CCGCAAAA____GA_AUUAGAGAAGA\n______________\|\|:\|\|\|\|\|____\|\|_\|\|:\|:\|\|\|\|:\|\n______________GGUGUUUU____CU_UAGUUUCUUUU\n3'-UUU...CCCGA________ACCC__G___________CGUCACCG-5'\n_____________\|__________________________\|\n_____________35_________________________8\n	35 -- 41	9 -- 15	-17.8797 kcal/mol	1.35017 kcal/mol	3.92941 kcal/mol	17 42@LB@ \| \|@LB@5'-CCU...UGAUA GAA AGAAA...GCC-3'@LB@ CCGCAAAA GA AUUAGAGAAGA@LB@ \|\|:\|\|\|\|\| \|\| \|\|:\|:\|\|\|\|:\|@LB@ GGUGUUUU CU UAGUUUCUUUU@LB@3'-UUU...CCCGA ACCC G CGUCACCG-5'@LB@ \| \|@LB@ 35 8@LB@@LB@@LB@Energy -12.60 kcal/mol@LB@Hybridization Energy -17.8797 kcal/mol@LB@Unfolding Energy - mRNA 1.35017 kcal/mol@LB@Unfolding Energy - sRNA 3.92941 kcal/mol@LB@@LB@Position - mRNA 18 -- 41@LB@Position - sRNA 9 -- 34@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 9 -- 15@LB@
144	0.01052	0.2504	b1066	rimJ	-12.60	0.094480	174 -- 195	1 -- 22	ribosomal-protein-S5-alanine N-acetyltransferase	_____________173_____________________196\n_____________\|_______________________\|\n5'-AUU...UUAAA_______C___________A___AUAGA...AUU-3'\n______________GACGUUA_GGGAAGG_AGU_GGU\n______________\|\|\|:\|:\|_:\|:\|\|:\|_\|\|\|_\|\|:\n______________CUGUAGU_UCUUUUC_UCA_CCG\n3'-UUU...UACCC_______U_______G_______-5'\n_____________\|______________________\|\n_____________23_____________________1\n	182 -- 188	8 -- 14	-20.3318 kcal/mol	6.19349 kcal/mol	1.54023 kcal/mol	173 196@LB@ \| \|@LB@5'-AUU...UUAAA C A AUAGA...AUU-3'@LB@ GACGUUA GGGAAGG AGU GGU@LB@ \|\|\|:\|:\| :\|:\|\|:\| \|\|\| \|\|:@LB@ CUGUAGU UCUUUUC UCA CCG@LB@3'-UUU...UACCC U G -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -12.60 kcal/mol@LB@Hybridization Energy -20.3318 kcal/mol@LB@Unfolding Energy - mRNA 6.19349 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 174 -- 195@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 8 -- 14@LB@
135	0.009724	0.2504	b1387	paaZ	-12.57	0.095542	174 -- 198	5 -- 30	oxepin-CoA hydrolase and 3-oxo-5 6-dehydrosuberyl-CoA semialdehyde dehydrogenase	_____________173_________________________199\n_____________\|___________________________\|\n5'-UAA...CAACA______U_AA_____U___________CGAUG...AAG-3'\n______________GAAAUG_G__ACAUC___GGAGAGUAG\n______________:\|\|\|\|\|_\|__\|\|\|\|\|___\|:\|:\|\|:\|\|\n______________UUUUAC_C__UGUAG___CUUUUCGUC\n3'-UUU...AGGUG________CC_____UUU_________ACCG-5'\n_____________\|___________________________\|\n_____________31__________________________4\n	192 -- 198	5 -- 11	-19.0129 kcal/mol	3.93627 kcal/mol	2.50278 kcal/mol	173 199@LB@ \| \|@LB@5'-UAA...CAACA U AA U CGAUG...AAG-3'@LB@ GAAAUG G ACAUC GGAGAGUAG@LB@ :\|\|\|\|\| \| \|\|\|\|\| \|:\|:\|\|:\|\|@LB@ UUUUAC C UGUAG CUUUUCGUC@LB@3'-UUU...AGGUG CC UUU ACCG-5'@LB@ \| \|@LB@ 31 4@LB@@LB@@LB@Energy -12.57 kcal/mol@LB@Hybridization Energy -19.0129 kcal/mol@LB@Unfolding Energy - mRNA 3.93627 kcal/mol@LB@Unfolding Energy - sRNA 2.50278 kcal/mol@LB@@LB@Position - mRNA 174 -- 198@LB@Position - sRNA 5 -- 30@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 5 -- 11@LB@
53	0.002642	0.1735	b0055	djlA	-12.56	0.096184	186 -- 227	1 -- 31	membrane-anchored DnaK co-chaperone DNA-binding protein	_____________185________________________________________228\n_____________\|__________________________________________\|\n5'-GAC...UGUGU___UU______AUAUAUGCAG____________AU__U____GUGGC...UUG-3'\n______________CGA__UGGGGA__________UAUUGGGGAAAA__CA_UGGC\n______________\|:\|__\|\|\|\|\|\|__________:\|\|::::\|\|\|\|\|__\|\|_\|\|\|\|\n______________GUU__ACCCCU__________GUAGUUUCUUUU__GU_ACCG\n3'-UUU...GAGGU___UU____________________________C___C____-5'\n_____________\|_________________________________________\|\n_____________32________________________________________1\n	212 -- 218	9 -- 15	-25.7115 kcal/mol	10.6128 kcal/mol	2.53929 kcal/mol	185 228@LB@ \| \|@LB@5'-GAC...UGUGU UU AUAUAUGCAG AU U GUGGC...UUG-3'@LB@ CGA UGGGGA UAUUGGGGAAAA CA UGGC@LB@ \|:\| \|\|\|\|\|\| :\|\|::::\|\|\|\|\| \|\| \|\|\|\|@LB@ GUU ACCCCU GUAGUUUCUUUU GU ACCG@LB@3'-UUU...GAGGU UU C C -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -12.56 kcal/mol@LB@Hybridization Energy -25.7115 kcal/mol@LB@Unfolding Energy - mRNA 10.6128 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 186 -- 227@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 9 -- 15@LB@
55	0.002823	0.1778	b3319	rplD	-12.54	0.096993	18 -- 45	1 -- 32	50S ribosomal subunit protein L4	_____________17________________________________46\n_____________\|_________________________________\|\n5'-UCA...UCCGG________U____________C___AAAA____AGGUC...UUG-3'\n______________GCAAAGUG______UCAAAGG_AAG____UGGC\n______________:\|\|\|\|:\|\|______\|\|\|\|\|\|:_\|\|\|____\|\|\|\|\n______________UGUUUUAC______AGUUUCU_UUC____ACCG\n3'-UUU...CGAGG________CCCUGU_______U___GUC_____-5'\n_____________\|________________________________\|\n_____________33_______________________________1\n	27 -- 33	12 -- 18	-19.13 kcal/mol	4.04955 kcal/mol	2.53929 kcal/mol	17 46@LB@ \| \|@LB@5'-UCA...UCCGG U C AAAA AGGUC...UUG-3'@LB@ GCAAAGUG UCAAAGG AAG UGGC@LB@ :\|\|\|\|:\|\| \|\|\|\|\|\|: \|\|\| \|\|\|\|@LB@ UGUUUUAC AGUUUCU UUC ACCG@LB@3'-UUU...CGAGG CCCUGU U GUC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -12.54 kcal/mol@LB@Hybridization Energy -19.13 kcal/mol@LB@Unfolding Energy - mRNA 4.04955 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 18 -- 45@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 12 -- 18@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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