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
164	0.02028	0.4072	b3295	rpoA	-11.98	0.089862	19 -- 43	66 -- 90	RNA polymerase alpha subunit	_____________18_________________________44\n_____________\|__________________________\|\n5'-GAA...CGCGU__________U__G_A__________CAGCG...GUG-3'\n______________GAAAGCC_GC_CU_G_GCUGGCUGAG\n______________:\|\|\|\|\|\|_\|\|_\|:_\|_\|\|\|\|\|\|\|:\|\|\n______________UUUUCGG_CG_GG_C_CGACCGAUUC\n___________3'-_______U__U__G____________AUUAU...GCG-5'\n______________\|_________________________\|\n______________90________________________65\n	37 -- 43	66 -- 72	-33.5627 kcal/mol	9.82436 kcal/mol	11.7544 kcal/mol	18 44@LB@ \| \|@LB@5'-GAA...CGCGU U G A CAGCG...GUG-3'@LB@ GAAAGCC GC CU G GCUGGCUGAG@LB@ :\|\|\|\|\|\| \|\| \|: \| \|\|\|\|\|\|\|:\|\|@LB@ UUUUCGG CG GG C CGACCGAUUC@LB@ 3'- U U G AUUAU...GCG-5'@LB@ \| \|@LB@ 90 65@LB@@LB@@LB@Energy -11.98 kcal/mol@LB@Hybridization Energy -33.5627 kcal/mol@LB@Unfolding Energy - mRNA 9.82436 kcal/mol@LB@Unfolding Energy - sRNA 11.7544 kcal/mol@LB@@LB@Position - mRNA 19 -- 43@LB@Position - sRNA 66 -- 90@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 66 -- 72@LB@
133	0.0147	0.3709	b3832	rmuC	-11.93	0.091595	31 -- 71	21 -- 63	DNA recombination protein	_____________30________________________________________________72\n_____________\|_________________________________________________\|\n5'-AAA...AAAUC___G_________________C______CU___GUAA___UC_______UGUCU...AGC-3'\n______________GUG_UGGAAGC______GGCG__GUCGU__GCU____UUC___UUCUCC\n______________:\|:_\|\|\|\|\|\|\|______:\|\|:__\|\|\|\|\|__\|\|\|____\|\|\|___\|\|\|\|\|\|\n______________UAU_ACCUUCG______UCGU__CAGCA__CGA____AAG___AAGAGG\n3'-UUU...UUCAU___G_______UUACAC____UA_________________UCC______CGCUC...GCG-5'\n_____________\|_________________________________________________\|\n_____________64________________________________________________20\n	35 -- 41	53 -- 59	-30.4211 kcal/mol	10.4952 kcal/mol	7.99187 kcal/mol	30 72@LB@ \| \|@LB@5'-AAA...AAAUC G C CU GUAA UC UGUCU...AGC-3'@LB@ GUG UGGAAGC GGCG GUCGU GCU UUC UUCUCC@LB@ :\|: \|\|\|\|\|\|\| :\|\|: \|\|\|\|\| \|\|\| \|\|\| \|\|\|\|\|\|@LB@ UAU ACCUUCG UCGU CAGCA CGA AAG AAGAGG@LB@3'-UUU...UUCAU G UUACAC UA UCC CGCUC...GCG-5'@LB@ \| \|@LB@ 64 20@LB@@LB@@LB@Energy -11.93 kcal/mol@LB@Hybridization Energy -30.4211 kcal/mol@LB@Unfolding Energy - mRNA 10.4952 kcal/mol@LB@Unfolding Energy - sRNA 7.99187 kcal/mol@LB@@LB@Position - mRNA 31 -- 71@LB@Position - sRNA 21 -- 63@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 53 -- 59@LB@
137	0.01545	0.379	b0881	clpS	-11.92	0.091960	57 -- 82	37 -- 62	regulatory protein for ClpA substrate specificity	_____________56_________________________83\n_____________\|__________________________\|\n5'-GCA...AACGC_____AC__G_______CA_______CUGAU...UCA-3'\n______________UAUUG__AG_AAUGUGA__GAUGUCG\n______________\|\|:\|\|__\|\|_\|\|\|\|\|\|\|__:\|\|\|\|\|\|\n______________AUGAC__UC_UUACACU__UUACAGC\n3'-UUU...UCAUU_____CU__G_______CG_______ACGAA...GCG-5'\n_____________\|__________________________\|\n_____________63_________________________36\n	76 -- 82	37 -- 43	-23.3317 kcal/mol	8.10565 kcal/mol	3.3026 kcal/mol	56 83@LB@ \| \|@LB@5'-GCA...AACGC AC G CA CUGAU...UCA-3'@LB@ UAUUG AG AAUGUGA GAUGUCG@LB@ \|\|:\|\| \|\| \|\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ AUGAC UC UUACACU UUACAGC@LB@3'-UUU...UCAUU CU G CG ACGAA...GCG-5'@LB@ \| \|@LB@ 63 36@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -23.3317 kcal/mol@LB@Unfolding Energy - mRNA 8.10565 kcal/mol@LB@Unfolding Energy - sRNA 3.3026 kcal/mol@LB@@LB@Position - mRNA 57 -- 82@LB@Position - sRNA 37 -- 62@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 37 -- 43@LB@
61	0.005602	0.2905	b1778	msrB	-11.92	0.091967	166 -- 177	43 -- 54	methionine sulfoxide reductase B	_____________165__________178\n_____________\|____________\|\n5'-CUU...GUCAC____________CGAUU...GUC-3'\n______________GUAAUGUGAGCA\n______________\|:\|\|\|\|\|\|\|\|\|\|\n______________CGUUACACUCGU\n3'-UUU...ACCUU____________UACAG...GCG-5'\n_____________\|____________\|\n_____________55___________42\n	171 -- 177	43 -- 49	-18.0171 kcal/mol	2.89402 kcal/mol	3.19978 kcal/mol	165 178@LB@ \| \|@LB@5'-CUU...GUCAC CGAUU...GUC-3'@LB@ GUAAUGUGAGCA@LB@ \|:\|\|\|\|\|\|\|\|\|\|@LB@ CGUUACACUCGU@LB@3'-UUU...ACCUU UACAG...GCG-5'@LB@ \| \|@LB@ 55 42@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -18.0171 kcal/mol@LB@Unfolding Energy - mRNA 2.89402 kcal/mol@LB@Unfolding Energy - sRNA 3.19978 kcal/mol@LB@@LB@Position - mRNA 166 -- 177@LB@Position - sRNA 43 -- 54@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 43 -- 49@LB@
139	0.01578	0.3813	b3386	rpe	-11.91	0.092481	276 -- 300	34 -- 60	D-ribulose-5-phosphate 3-epimerase	_____________275_________________________300\n_____________\|___________________________\|\n5'-CGC...AAGCC____C_________C__U__________-3'\n______________CUGG_AGC__UG_G_GC_GAUGUCGUGC\n______________\|\|\|\|_\|\|\|__\|\|_\|_\|\|_:\|\|\|\|\|\|\|\|\|\n______________GACC_UCG__AC_C_CG_UUACAGCACG\n3'-UUU...AUUAU____U___UU__A_U_____________AAAGU...GCG-5'\n_____________\|____________________________\|\n_____________61___________________________33\n	294 -- 300	34 -- 40	-27.2321 kcal/mol	8.55668 kcal/mol	6.76671 kcal/mol	275 300@LB@ \| \|@LB@5'-CGC...AAGCC C C U -3'@LB@ CUGG AGC UG G GC GAUGUCGUGC@LB@ \|\|\|\| \|\|\| \|\| \| \|\| :\|\|\|\|\|\|\|\|\|@LB@ GACC UCG AC C CG UUACAGCACG@LB@3'-UUU...AUUAU U UU A U AAAGU...GCG-5'@LB@ \| \|@LB@ 61 33@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -27.2321 kcal/mol@LB@Unfolding Energy - mRNA 8.55668 kcal/mol@LB@Unfolding Energy - sRNA 6.76671 kcal/mol@LB@@LB@Position - mRNA 276 -- 300@LB@Position - sRNA 34 -- 60@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 34 -- 40@LB@
123	0.0134	0.3627	b3774	ilvC	-11.90	0.092739	9 -- 41	1 -- 25	ketol-acid reductoisomerase NAD(P)-binding	_____________8__________________________________42\n_____________\|__________________________________\|\n___5'-AUGGCGGC_______CAGAUGCAG__A_______A_______GUAAA...GCU-3'\n______________UUUCCGC_________GA_GGUUUUC__GAUCGC\n______________\|:\|\|\|\|\|_________\|\|_\|\|\|:\|\|\|__\|\|\|\|\|\|\n______________AGAGGCG_________CU_CCAGAAG__CUAGCG\n3'-UUU...GUCCA__________________C_______GA______-5'\n_____________\|_________________________________\|\n_____________26________________________________1\n	28 -- 34	9 -- 15	-28.1375 kcal/mol	8.51703 kcal/mol	7.71912 kcal/mol	8 42@LB@ \| \|@LB@ 5'-AUGGCGGC CAGAUGCAG A A GUAAA...GCU-3'@LB@ UUUCCGC GA GGUUUUC GAUCGC@LB@ \|:\|\|\|\|\| \|\| \|\|\|:\|\|\| \|\|\|\|\|\|@LB@ AGAGGCG CU CCAGAAG CUAGCG@LB@3'-UUU...GUCCA C GA -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -11.90 kcal/mol@LB@Hybridization Energy -28.1375 kcal/mol@LB@Unfolding Energy - mRNA 8.51703 kcal/mol@LB@Unfolding Energy - sRNA 7.71912 kcal/mol@LB@@LB@Position - mRNA 9 -- 41@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 9 -- 15@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@
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@
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@
103	0.0104	0.3393	b2711	norW	-11.75	0.098250	192 -- 208	42 -- 58	NADH:flavorubredoxin oxidoreductase	_____________191_______________209\n_____________\|_________________\|\n5'-GAA...GCAUC________AA_______CGGCA...UUG-3'\n______________GGAGGCAA__UGAGUAA\n______________\|\|\|:\|\|\|\|__\|\|\|\|:\|\|\n______________CCUUCGUU__ACUCGUU\n3'-UUU...UAUGA________AC_______ACAGC...GCG-5'\n_____________\|_________________\|\n_____________59________________41\n	202 -- 208	42 -- 48	-20.2467 kcal/mol	5.28663 kcal/mol	3.2101 kcal/mol	191 209@LB@ \| \|@LB@5'-GAA...GCAUC AA CGGCA...UUG-3'@LB@ GGAGGCAA UGAGUAA@LB@ \|\|\|:\|\|\|\| \|\|\|\|:\|\|@LB@ CCUUCGUU ACUCGUU@LB@3'-UUU...UAUGA AC ACAGC...GCG-5'@LB@ \| \|@LB@ 59 41@LB@@LB@@LB@Energy -11.75 kcal/mol@LB@Hybridization Energy -20.2467 kcal/mol@LB@Unfolding Energy - mRNA 5.28663 kcal/mol@LB@Unfolding Energy - sRNA 3.2101 kcal/mol@LB@@LB@Position - mRNA 192 -- 208@LB@Position - sRNA 42 -- 58@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 42 -- 48@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