Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
167	0.01994	0.3993	b1982	amn	-7.06	0.411594	174 -- 215	8 -- 54	AMP nucleosidase	_____________173______________________________________________216\n_____________\|________________________________________________\|\n5'-UUU...UGUGC_____U____________________CACACA___A____________UCCGG...GCA-3'\n______________GGUAA_UGU_AUGG___AACAGGAGA_______UG__AUAAUAAGGGC\n______________\|\|:\|\|_\|\|:_\|\|\|\|___\|\|\|\|\|:\|:\|_______\|\|__\|:\|\|\|\|\|:\|\|\|\n______________CCGUU_ACG_UACC___UUGUCUUUU_______AC__UGUUAUUUCCG\n3'-UUU...AGUCA_________U____GGG_________AUUUUAG__AC___________UAUAUUG-5'\n_____________\|________________________________________________\|\n_____________55_______________________________________________7\n	209 -- 215	8 -- 14	-29.9928 kcal/mol	10.9089 kcal/mol	12.019 kcal/mol	173 216@LB@ \| \|@LB@5'-UUU...UGUGC U CACACA A UCCGG...GCA-3'@LB@ GGUAA UGU AUGG AACAGGAGA UG AUAAUAAGGGC@LB@ \|\|:\|\| \|\|: \|\|\|\| \|\|\|\|\|:\|:\| \|\| \|:\|\|\|\|\|:\|\|\|@LB@ CCGUU ACG UACC UUGUCUUUU AC UGUUAUUUCCG@LB@3'-UUU...AGUCA U GGG AUUUUAG AC UAUAUUG-5'@LB@ \| \|@LB@ 55 7@LB@@LB@@LB@Energy -7.06 kcal/mol@LB@Hybridization Energy -29.9928 kcal/mol@LB@Unfolding Energy - mRNA 10.9089 kcal/mol@LB@Unfolding Energy - sRNA 12.019 kcal/mol@LB@@LB@Position - mRNA 174 -- 215@LB@Position - sRNA 8 -- 54@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 8 -- 14@LB@
176	0.02144	0.4097	b0948	rlmL	-6.91	0.434425	184 -- 201	13 -- 33	23S rRNA m(2)G2445 and m(7)G2069 methyltransferases SAM-dependent	_____________183___________________202\n_____________\|_____________________\|\n5'-GAC...CUCUU_____________________UGAAU...GUG-3'\n______________AGAGUAAAA___GUGACGAUA\n______________\|:\|:\|\|\|\|\|___\|\|\|\|\|:\|\|\|\n______________UUUUAUUUU___CACUGUUAU\n3'-UUU...UUGUC_________AGA_________UUCCG...UUG-5'\n_____________\|_____________________\|\n_____________34____________________12\n	195 -- 201	13 -- 19	-14.282 kcal/mol	2.4415 kcal/mol	4.9341 kcal/mol	183 202@LB@ \| \|@LB@5'-GAC...CUCUU UGAAU...GUG-3'@LB@ AGAGUAAAA GUGACGAUA@LB@ \|:\|:\|\|\|\|\| \|\|\|\|\|:\|\|\|@LB@ UUUUAUUUU CACUGUUAU@LB@3'-UUU...UUGUC AGA UUCCG...UUG-5'@LB@ \| \|@LB@ 34 12@LB@@LB@@LB@Energy -6.91 kcal/mol@LB@Hybridization Energy -14.282 kcal/mol@LB@Unfolding Energy - mRNA 2.4415 kcal/mol@LB@Unfolding Energy - sRNA 4.9341 kcal/mol@LB@@LB@Position - mRNA 184 -- 201@LB@Position - sRNA 13 -- 33@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 13 -- 19@LB@
116	0.0115	0.3326	b3770	ilvE	-6.73	0.460342	227 -- 277	1 -- 67	branched-chain amino acid aminotransferase	_____________226__________________________________________________________________278\n_____________\|____________________________________________________________________\|\n5'-UUU...UACAU____U______A___G______________C_____________________CG____U_________GUCGC...GCA-3'\n______________UUGG____UCA_UGG_GA___GAUGGUUCG_UGGGAA___________GACG__AAGG_GCAUGUGAU\n______________\|\|\|\|____\|\|\|_\|\|\|_:\|___:\|\|\|\|::\|:_::\|:\|\|___________\|\|\|:__\|\|:\|_\|\|\|\|:\|:\|:\n______________AACC____AGU_ACC_UU___UUACCGGGU_GUCUUU___________CUGU__UUUC_CGUAUAUUG\n3'-UUU...UAUAC____UUUU___C___G__ACG_________U______UAUUUUAGACA____UA______________-5'\n_____________\|___________________________________________________________________\|\n_____________68__________________________________________________________________1\n	269 -- 275	3 -- 9	-35.2937 kcal/mol	16.4013 kcal/mol	12.1612 kcal/mol	226 278@LB@ \| \|@LB@5'-UUU...UACAU U A G C CG U GUCGC...GCA-3'@LB@ UUGG UCA UGG GA GAUGGUUCG UGGGAA GACG AAGG GCAUGUGAU@LB@ \|\|\|\| \|\|\| \|\|\| :\| :\|\|\|\|::\|: ::\|:\|\| \|\|\|: \|\|:\| \|\|\|\|:\|:\|:@LB@ AACC AGU ACC UU UUACCGGGU GUCUUU CUGU UUUC CGUAUAUUG@LB@3'-UUU...UAUAC UUUU C G ACG U UAUUUUAGACA UA -5'@LB@ \| \|@LB@ 68 1@LB@@LB@@LB@Energy -6.73 kcal/mol@LB@Hybridization Energy -35.2937 kcal/mol@LB@Unfolding Energy - mRNA 16.4013 kcal/mol@LB@Unfolding Energy - sRNA 12.1612 kcal/mol@LB@@LB@Position - mRNA 227 -- 277@LB@Position - sRNA 1 -- 67@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 3 -- 9@LB@
64	0.005005	0.2614	b3795	yifK	-6.27	0.531551	193 -- 206	51 -- 64	putative APC family amino acid transporter	_____________192____________207\n_____________\|______________\|\n5'-CAA...AACAC_______UA_____GAUAA...GGG-3'\n______________GAGGAUU__UGGCA\n______________\|\|::\|\|:__\|\|\|\|\|\n______________CUUUUAG__ACCGU\n3'-UUU...ACAAC_______UC_____UACGU...UUG-5'\n_____________\|______________\|\n_____________65_____________50\n	193 -- 199	58 -- 64	-12.618 kcal/mol	3.46106 kcal/mol	2.8882 kcal/mol	192 207@LB@ \| \|@LB@5'-CAA...AACAC UA GAUAA...GGG-3'@LB@ GAGGAUU UGGCA@LB@ \|\|::\|\|: \|\|\|\|\|@LB@ CUUUUAG ACCGU@LB@3'-UUU...ACAAC UC UACGU...UUG-5'@LB@ \| \|@LB@ 65 50@LB@@LB@@LB@Energy -6.27 kcal/mol@LB@Hybridization Energy -12.618 kcal/mol@LB@Unfolding Energy - mRNA 3.46106 kcal/mol@LB@Unfolding Energy - sRNA 2.8882 kcal/mol@LB@@LB@Position - mRNA 193 -- 206@LB@Position - sRNA 51 -- 64@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 58 -- 64@LB@
70	0.005852	0.2791	b3524	yhjG	-5.99	0.576071	198 -- 212	7 -- 18	putative inner membrane-anchored periplasmic AsmA family protein	_____________197_____________213\n_____________\|_______________\|\n5'-UUG...AGCGA_______GCA_____GGCAA...GAC-3'\n______________ACGAUGA___AGGCA\n______________\|\|:\|\|:\|___\|\|\|\|\|\n______________UGUUAUU___UCCGU\n3'-UUU...GACAC_______________AUAUUG-5'\n_____________\|_______________\|\n_____________19______________6\n	198 -- 204	12 -- 18	-10.9915 kcal/mol	1.73561 kcal/mol	3.26755 kcal/mol	197 213@LB@ \| \|@LB@5'-UUG...AGCGA GCA GGCAA...GAC-3'@LB@ ACGAUGA AGGCA@LB@ \|\|:\|\|:\| \|\|\|\|\|@LB@ UGUUAUU UCCGU@LB@3'-UUU...GACAC AUAUUG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -5.99 kcal/mol@LB@Hybridization Energy -10.9915 kcal/mol@LB@Unfolding Energy - mRNA 1.73561 kcal/mol@LB@Unfolding Energy - sRNA 3.26755 kcal/mol@LB@@LB@Position - mRNA 198 -- 212@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 12 -- 18@LB@
86	0.007534	0.2889	b0189	rof	-5.95	0.582576	103 -- 121	40 -- 57	modulator of Rho-dependent transcription termination	_____________102_________________122\n_____________\|___________________\|\n5'-AGG...UUGAA____CUG____A_______GCCGA...GCG-3'\n______________AGUG___AAUG_AAUGGCU\n______________\|\|\|\|___\|\|\|\|_\|\|\|\|\|\|:\n______________UCAC___UUAC_UUACCGG\n3'-UUU...UUUAG____CG_____G_______GUUGU...UUG-5'\n_____________\|___________________\|\n_____________58__________________39\n	115 -- 121	40 -- 46	-14.9441 kcal/mol	3.94739 kcal/mol	5.04912 kcal/mol	102 122@LB@ \| \|@LB@5'-AGG...UUGAA CUG A GCCGA...GCG-3'@LB@ AGUG AAUG AAUGGCU@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\|\|:@LB@ UCAC UUAC UUACCGG@LB@3'-UUU...UUUAG CG G GUUGU...UUG-5'@LB@ \| \|@LB@ 58 39@LB@@LB@@LB@Energy -5.95 kcal/mol@LB@Hybridization Energy -14.9441 kcal/mol@LB@Unfolding Energy - mRNA 3.94739 kcal/mol@LB@Unfolding Energy - sRNA 5.04912 kcal/mol@LB@@LB@Position - mRNA 103 -- 121@LB@Position - sRNA 40 -- 57@LB@Position Seed - mRNA 115 -- 121@LB@Position Seed - sRNA 40 -- 46@LB@
146	0.01679	0.3828	b2699	recA	-5.90	0.590167	190 -- 206	40 -- 58	DNA recombination and repair protein; ssDNA-dependent ATPase; synaptase; ssDNA and dsDNA binding protein; ATP-dependent homologous DNA strand exchanger; recombinase A; LexA autocleavage cofactor	_____________189_________________207\n_____________\|___________________\|\n5'-UGC...CAUGA___GA____A_________AUCGA...ACC-3'\n______________CAG__GUAA___AAUGGCU\n______________\|\|\|__\|:\|\|___\|\|\|\|\|\|:\n______________GUC__CGUU___UUACCGG\n3'-UUU...UUUUA___AC____ACG_______GUUGU...UUG-5'\n_____________\|___________________\|\n_____________59__________________39\n	200 -- 206	40 -- 46	-15.424 kcal/mol	3.45581 kcal/mol	6.06808 kcal/mol	189 207@LB@ \| \|@LB@5'-UGC...CAUGA GA A AUCGA...ACC-3'@LB@ CAG GUAA AAUGGCU@LB@ \|\|\| \|:\|\| \|\|\|\|\|\|:@LB@ GUC CGUU UUACCGG@LB@3'-UUU...UUUUA AC ACG GUUGU...UUG-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -5.90 kcal/mol@LB@Hybridization Energy -15.424 kcal/mol@LB@Unfolding Energy - mRNA 3.45581 kcal/mol@LB@Unfolding Energy - sRNA 6.06808 kcal/mol@LB@@LB@Position - mRNA 190 -- 206@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 40 -- 46@LB@
194	0.0246	0.4256	b0211	mltD	-5.59	0.639593	30 -- 36	59 -- 65	putative membrane-bound lytic murein transglycosylase D	_____________29______37\n_____________\|_______\|\n5'-GAG...AGAAC_______AUUGA...GUC-3'\n______________GGAAGAU\n______________\|\|\|\|:\|\|\n______________CCUUUUA\n3'-UUU...UACAA_______GUCAC...UUG-5'\n_____________\|_______\|\n_____________66______58\n	30 -- 36	59 -- 65	-7.35578 kcal/mol	0.945124 kcal/mol	0.81955 kcal/mol	29 37@LB@ \| \|@LB@5'-GAG...AGAAC AUUGA...GUC-3'@LB@ GGAAGAU@LB@ \|\|\|\|:\|\|@LB@ CCUUUUA@LB@3'-UUU...UACAA GUCAC...UUG-5'@LB@ \| \|@LB@ 66 58@LB@@LB@@LB@Energy -5.59 kcal/mol@LB@Hybridization Energy -7.35578 kcal/mol@LB@Unfolding Energy - mRNA 0.945124 kcal/mol@LB@Unfolding Energy - sRNA 0.81955 kcal/mol@LB@@LB@Position - mRNA 30 -- 36@LB@Position - sRNA 59 -- 65@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 59 -- 65@LB@
175	0.02099	0.4033	b2913	serA	-5.57	0.642321	190 -- 257	5 -- 65	D-3-phosphoglycerate dehydrogenase	_____________189_____________________________________________________________________258\n_____________\|_______________________________________________________________________\|\n5'-UGU...AGACA___UU____AAA______AG___UCGC___AGAAA________U____UU____C________________CACCA...CCA-3'\n______________GGA__GGGU___UGGCAA__GUA____UGG_____GACA_AGA_UAAG__UCUG_UGGUA__GAAGGCGUG\n______________\|\|\|__:::\|___\|\|\|\|\|\|__\|:\|____\|\|\|_____:\|\|\|_\|:\|_\|\|\|:__\|\|\|\|_\|\|::\|__:\|\|\|\|\|:\|:\n______________CCU__UUUA___ACCGUU__CGU____ACC_____UUGU_UUU_AUUU__AGAC_ACUGU__UUUCCGUAU\n3'-UUU...UACAA_________GUC______A____U______GGG______C___U____U___________UA_________AUUG-5'\n_____________\|_______________________________________________________________________\|\n_____________66______________________________________________________________________4\n	251 -- 257	5 -- 11	-32.5395 kcal/mol	14.8085 kcal/mol	12.157 kcal/mol	189 258@LB@ \| \|@LB@5'-UGU...AGACA UU AAA AG UCGC AGAAA U UU C CACCA...CCA-3'@LB@ GGA GGGU UGGCAA GUA UGG GACA AGA UAAG UCUG UGGUA GAAGGCGUG@LB@ \|\|\| :::\| \|\|\|\|\|\| \|:\| \|\|\| :\|\|\| \|:\| \|\|\|: \|\|\|\| \|\|::\| :\|\|\|\|\|:\|:@LB@ CCU UUUA ACCGUU CGU ACC UUGU UUU AUUU AGAC ACUGU UUUCCGUAU@LB@3'-UUU...UACAA GUC A U GGG C U U UA AUUG-5'@LB@ \| \|@LB@ 66 4@LB@@LB@@LB@Energy -5.57 kcal/mol@LB@Hybridization Energy -32.5395 kcal/mol@LB@Unfolding Energy - mRNA 14.8085 kcal/mol@LB@Unfolding Energy - sRNA 12.157 kcal/mol@LB@@LB@Position - mRNA 190 -- 257@LB@Position - sRNA 5 -- 65@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 5 -- 11@LB@
161	0.01858	0.3864	b3237	argR	-5.47	0.658327	53 -- 70	1 -- 21	l-arginine-responsive arginine metabolism regulon transcriptional regulator	_____________52____________________71\n_____________\|_____________________\|\n5'-ACA...AUGCC______C___________UU_UCAAU...UGC-3'\n______________GUGACG____AGGCAUGU__C\n______________\|\|\|\|\|:____\|\|\|\|\|\|:\|__\|\n______________CACUGU____UCCGUAUA__G\n3'-UUU...UUAGA______UAUU________UU_-5'\n_____________\|____________________\|\n_____________22___________________1\n	61 -- 67	4 -- 10	-16.8661 kcal/mol	6.97949 kcal/mol	4.41334 kcal/mol	52 71@LB@ \| \|@LB@5'-ACA...AUGCC C UU UCAAU...UGC-3'@LB@ GUGACG AGGCAUGU C@LB@ \|\|\|\|\|: \|\|\|\|\|\|:\| \|@LB@ CACUGU UCCGUAUA G@LB@3'-UUU...UUAGA UAUU UU -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -5.47 kcal/mol@LB@Hybridization Energy -16.8661 kcal/mol@LB@Unfolding Energy - mRNA 6.97949 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 53 -- 70@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 4 -- 10@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