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
18	0.0007186	0.1243	b3657	yicJ	-19.60	0.001218	184 -- 200	5 -- 21	putative transporter	_____________183_______________201\n_____________\|_________________\|\n5'-CAG...CUAUA_________________AUGAA...UGU-3'\n______________GCAUCAAGGAAAAGCAG\n______________:\|\|\|\|\|\|:\|\|\|\|\|\|\|\|\|\n______________UGUAGUUUCUUUUCGUC\n3'-UUU...ACCCC_________________ACCG-5'\n_____________\|_________________\|\n_____________22________________4\n	194 -- 200	5 -- 11	-25.6417 kcal/mol	4.53845 kcal/mol	1.5073 kcal/mol	183 201@LB@ \| \|@LB@5'-CAG...CUAUA AUGAA...UGU-3'@LB@ GCAUCAAGGAAAAGCAG@LB@ :\|\|\|\|\|\|:\|\|\|\|\|\|\|\|\|@LB@ UGUAGUUUCUUUUCGUC@LB@3'-UUU...ACCCC ACCG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -19.60 kcal/mol@LB@Hybridization Energy -25.6417 kcal/mol@LB@Unfolding Energy - mRNA 4.53845 kcal/mol@LB@Unfolding Energy - sRNA 1.5073 kcal/mol@LB@@LB@Position - mRNA 184 -- 200@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 5 -- 11@LB@
42	0.002133	0.1648	b0968	yccX	-12.44	0.101807	184 -- 198	5 -- 23	weak acylphosphatase	_____________183_________________199\n_____________\|___________________\|\n5'-GGC...AUUAA___________________CAAUG...CCG-3'\n______________GGAUA____AGGAGAGCAG\n______________\|\|\|:\|____\|\|:\|:\|\|\|\|\|\n______________CCUGU____UCUUUUCGUC\n3'-UUU...UUACC_____AGUU__________ACCG-5'\n_____________\|___________________\|\n_____________24__________________4\n	192 -- 198	5 -- 11	-17.1825 kcal/mol	3.17176 kcal/mol	1.57523 kcal/mol	183 199@LB@ \| \|@LB@5'-GGC...AUUAA CAAUG...CCG-3'@LB@ GGAUA AGGAGAGCAG@LB@ \|\|\|:\| \|\|:\|:\|\|\|\|\|@LB@ CCUGU UCUUUUCGUC@LB@3'-UUU...UUACC AGUU ACCG-5'@LB@ \| \|@LB@ 24 4@LB@@LB@@LB@Energy -12.44 kcal/mol@LB@Hybridization Energy -17.1825 kcal/mol@LB@Unfolding Energy - mRNA 3.17176 kcal/mol@LB@Unfolding Energy - sRNA 1.57523 kcal/mol@LB@@LB@Position - mRNA 184 -- 198@LB@Position - sRNA 5 -- 23@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 5 -- 11@LB@
179	0.01303	0.2504	b1276	acnA	-14.81	0.030801	184 -- 199	7 -- 22	aconitate hydratase 1; aconitase A	_____________183______________200\n_____________\|________________\|\n5'-CUU...ACCCU_U______________UAUGU...GCG-3'\n______________G_CAUUAAGGAGGAGC\n______________\|_\|\|\|:\|\|:\|\|::\|\|\|\n______________C_GUAGUUUCUUUUCG\n3'-UUU...UACCC_U______________UCACCG-5'\n_____________\|________________\|\n_____________23_______________6\n	193 -- 199	7 -- 13	-17.7225 kcal/mol	2.31939 kcal/mol	0.590875 kcal/mol	183 200@LB@ \| \|@LB@5'-CUU...ACCCU U UAUGU...GCG-3'@LB@ G CAUUAAGGAGGAGC@LB@ \| \|\|\|:\|\|:\|\|::\|\|\|@LB@ C GUAGUUUCUUUUCG@LB@3'-UUU...UACCC U UCACCG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -14.81 kcal/mol@LB@Hybridization Energy -17.7225 kcal/mol@LB@Unfolding Energy - mRNA 2.31939 kcal/mol@LB@Unfolding Energy - sRNA 0.590875 kcal/mol@LB@@LB@Position - mRNA 184 -- 199@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 7 -- 13@LB@
98	0.006107	0.2179	b3822	recQ	-9.35	0.343777	185 -- 205	1 -- 22	ATP-dependent DNA helicase	_____________184_____________________206\n_____________\|_______________________\|\n5'-CGC...UUUCA___A_______U___U_______GCAGG...UUA-3'\n______________GGC_AUCGGGG_GAA___GUGGC\n______________\|:\|_\|\|\|:::\|_:\|\|___\|\|\|\|\|\n______________CUG_UAGUUUC_UUU___CACCG\n3'-UUU...UACCC___________U___CGU_____-5'\n_____________\|______________________\|\n_____________23_____________________1\n	189 -- 195	13 -- 19	-17.8698 kcal/mol	6.98341 kcal/mol	1.54023 kcal/mol	184 206@LB@ \| \|@LB@5'-CGC...UUUCA A U U GCAGG...UUA-3'@LB@ GGC AUCGGGG GAA GUGGC@LB@ \|:\| \|\|\|:::\| :\|\| \|\|\|\|\|@LB@ CUG UAGUUUC UUU CACCG@LB@3'-UUU...UACCC U CGU -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -9.35 kcal/mol@LB@Hybridization Energy -17.8698 kcal/mol@LB@Unfolding Energy - mRNA 6.98341 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 185 -- 205@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 13 -- 19@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@
89	0.005593	0.2147	b3398	yrfF	-14.72	0.032340	186 -- 206	1 -- 31	putative RcsCDB-response attenuator inner membrane protein	_____________185______________________________207\n_____________\|________________________________\|\n5'-UUA...CUAAG_____________________________A__ACCAU...GGA-3'\n______________UAAGAUGGGGA__________AAGCA_UG_GC\n______________:\|\|:\|\|\|\|\|\|\|__________\|\|\|\|\|_\|\|_\|\|\n______________GUUUUACCCCU__________UUCGU_AC_CG\n3'-UUU...GAGGU___________GUAGUUUCUU_____C_____-5'\n_____________\|_______________________________\|\n_____________32______________________________1\n	190 -- 196	21 -- 27	-21.8606 kcal/mol	4.59782 kcal/mol	2.53929 kcal/mol	185 207@LB@ \| \|@LB@5'-UUA...CUAAG A ACCAU...GGA-3'@LB@ UAAGAUGGGGA AAGCA UG GC@LB@ :\|\|:\|\|\|\|\|\|\| \|\|\|\|\| \|\| \|\|@LB@ GUUUUACCCCU UUCGU AC CG@LB@3'-UUU...GAGGU GUAGUUUCUU C -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -14.72 kcal/mol@LB@Hybridization Energy -21.8606 kcal/mol@LB@Unfolding Energy - mRNA 4.59782 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 186 -- 206@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 21 -- 27@LB@
60	0.003101	0.1789	b1849	purT	-10.92	0.194410	188 -- 196	17 -- 25	phosphoribosylglycinamide formyltransferase 2	_____________187_______197\n_____________\|_________\|\n5'-UUU...AAUCA_________CGUUA...GUC-3'\n______________GGGGAUAUU\n______________\|\|\|\|\|:\|\|:\n______________CCCCUGUAG\n3'-UUU...UUUUA_________UUUCU...CCG-5'\n_____________\|_________\|\n_____________26________16\n	190 -- 196	17 -- 23	-14.1846 kcal/mol	2.60139 kcal/mol	0.664736 kcal/mol	187 197@LB@ \| \|@LB@5'-UUU...AAUCA CGUUA...GUC-3'@LB@ GGGGAUAUU@LB@ \|\|\|\|\|:\|\|:@LB@ CCCCUGUAG@LB@3'-UUU...UUUUA UUUCU...CCG-5'@LB@ \| \|@LB@ 26 16@LB@@LB@@LB@Energy -10.92 kcal/mol@LB@Hybridization Energy -14.1846 kcal/mol@LB@Unfolding Energy - mRNA 2.60139 kcal/mol@LB@Unfolding Energy - sRNA 0.664736 kcal/mol@LB@@LB@Position - mRNA 188 -- 196@LB@Position - sRNA 17 -- 25@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 17 -- 23@LB@
5	2.356e-05	0.01653	b1123	potD	-19.53	0.001282	190 -- 207	9 -- 25	spermidine/putrescine ABC transporter periplasmic binding protein	_____________189________________208\n_____________\|__________________\|\n5'-GAC...ACACA____________U_____AAUGG...ACU-3'\n______________GGGGACGUUAAA_GAAAA\n______________\|\|\|\|\|\|:\|:\|\|\|_\|\|\|\|\|\n______________CCCCUGUAGUUU_CUUUU\n3'-UUU...UUUUA__________________CGUCACCG-5'\n_____________\|__________________\|\n_____________26_________________8\n	195 -- 201	14 -- 20	-22.5319 kcal/mol	2.32696 kcal/mol	0.671024 kcal/mol	189 208@LB@ \| \|@LB@5'-GAC...ACACA U AAUGG...ACU-3'@LB@ GGGGACGUUAAA GAAAA@LB@ \|\|\|\|\|\|:\|:\|\|\| \|\|\|\|\|@LB@ CCCCUGUAGUUU CUUUU@LB@3'-UUU...UUUUA CGUCACCG-5'@LB@ \| \|@LB@ 26 8@LB@@LB@@LB@Energy -19.53 kcal/mol@LB@Hybridization Energy -22.5319 kcal/mol@LB@Unfolding Energy - mRNA 2.32696 kcal/mol@LB@Unfolding Energy - sRNA 0.671024 kcal/mol@LB@@LB@Position - mRNA 190 -- 207@LB@Position - sRNA 9 -- 25@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 14 -- 20@LB@
88	0.005527	0.2147	b3525	yhjH	-13.65	0.056862	190 -- 212	5 -- 23	cyclic-di-GMP phosphodiesterase FlhDC-regulated	_____________189_____________________213\n_____________\|_______________________\|\n5'-UUA...ACACA_______UUU__UGAU_______GUUAU...CCU-3'\n______________GGACAUC___GA____AAGGCAG\n______________\|\|\|\|\|\|\|___\|\|____\|\|:\|\|\|\|\n______________CCUGUAG___CU____UUUCGUC\n3'-UUU...UUACC_______UUU_____________ACCG-5'\n_____________\|_______________________\|\n_____________24______________________4\n	206 -- 212	5 -- 11	-19.0549 kcal/mol	3.83037 kcal/mol	1.57523 kcal/mol	189 213@LB@ \| \|@LB@5'-UUA...ACACA UUU UGAU GUUAU...CCU-3'@LB@ GGACAUC GA AAGGCAG@LB@ \|\|\|\|\|\|\| \|\| \|\|:\|\|\|\|@LB@ CCUGUAG CU UUUCGUC@LB@3'-UUU...UUACC UUU ACCG-5'@LB@ \| \|@LB@ 24 4@LB@@LB@@LB@Energy -13.65 kcal/mol@LB@Hybridization Energy -19.0549 kcal/mol@LB@Unfolding Energy - mRNA 3.83037 kcal/mol@LB@Unfolding Energy - sRNA 1.57523 kcal/mol@LB@@LB@Position - mRNA 190 -- 212@LB@Position - sRNA 5 -- 23@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 5 -- 11@LB@
120	0.00842	0.2462	b1068	yceM	-12.88	0.082928	190 -- 205	9 -- 24	putative oxidoreductase	_____________189______________206\n_____________\|________________\|\n5'-GCG...CAUCU____G_______U___AAAAU...GAG-3'\n______________GGGA_AUUAAAG_GAA\n______________\|\|\|\|_\|\|:\|\|\|\|_:\|\|\n______________CCCU_UAGUUUC_UUU\n3'-UUU...UUUAC____G_______U___CGUCACCG-5'\n_____________\|________________\|\n_____________25_______________8\n	195 -- 201	13 -- 19	-15.5519 kcal/mol	2.0153 kcal/mol	0.659805 kcal/mol	189 206@LB@ \| \|@LB@5'-GCG...CAUCU G U AAAAU...GAG-3'@LB@ GGGA AUUAAAG GAA@LB@ \|\|\|\| \|\|:\|\|\|\| :\|\|@LB@ CCCU UAGUUUC UUU@LB@3'-UUU...UUUAC G U CGUCACCG-5'@LB@ \| \|@LB@ 25 8@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -15.5519 kcal/mol@LB@Unfolding Energy - mRNA 2.0153 kcal/mol@LB@Unfolding Energy - sRNA 0.659805 kcal/mol@LB@@LB@Position - mRNA 190 -- 205@LB@Position - sRNA 9 -- 24@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 13 -- 19@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching