Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
105	0.008762	0.2688	b2735	ygbI	-7.10	0.103888	185 -- 196	38 -- 49	DeoR family putative transcriptional regulator	_____________184__________197\n_____________\|____________\|\n5'-UUC...GGACA___G________AAAGU...AUA-3'\n______________AAG_AAGGAGCA\n______________\|\|\|_\|\|\|:\|\|\|\|\n______________UUC_UUCUUCGU\n3'-UUU...ACGAA___G________GAAUU...CAA-5'\n_____________\|____________\|\n_____________50___________37\n	190 -- 196	38 -- 44	-14.2659 kcal/mol	1.1364 kcal/mol	6.02696 kcal/mol	184 197@LB@ \| \|@LB@5'-UUC...GGACA G AAAGU...AUA-3'@LB@ AAG AAGGAGCA@LB@ \|\|\| \|\|\|:\|\|\|\|@LB@ UUC UUCUUCGU@LB@3'-UUU...ACGAA G GAAUU...CAA-5'@LB@ \| \|@LB@ 50 37@LB@@LB@@LB@Energy -7.10 kcal/mol@LB@Hybridization Energy -14.2659 kcal/mol@LB@Unfolding Energy - mRNA 1.1364 kcal/mol@LB@Unfolding Energy - sRNA 6.02696 kcal/mol@LB@@LB@Position - mRNA 185 -- 196@LB@Position - sRNA 38 -- 49@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 38 -- 44@LB@
161	0.01751	0.3504	b3394	hofN	-4.92	0.333288	275 -- 286	18 -- 29	DNA catabolic putative fimbrial assembly protein	_____________274__________287\n_____________\|____________\|\n5'-UGG...CUGAU____________UCUGC...CCG-3'\n______________GUUCGUUGCGCC\n______________:\|\|\|\|\|\|:\|:\|\|\n______________UAAGCAAUGUGG\n3'-UUU...UUUUU____________UCCUU...CAA-5'\n_____________\|____________\|\n_____________30___________17\n	275 -- 281	23 -- 29	-17.9024 kcal/mol	4.53191 kcal/mol	8.4513 kcal/mol	274 287@LB@ \| \|@LB@5'-UGG...CUGAU UCUGC...CCG-3'@LB@ GUUCGUUGCGCC@LB@ :\|\|\|\|\|\|:\|:\|\|@LB@ UAAGCAAUGUGG@LB@3'-UUU...UUUUU UCCUU...CAA-5'@LB@ \| \|@LB@ 30 17@LB@@LB@@LB@Energy -4.92 kcal/mol@LB@Hybridization Energy -17.9024 kcal/mol@LB@Unfolding Energy - mRNA 4.53191 kcal/mol@LB@Unfolding Energy - sRNA 8.4513 kcal/mol@LB@@LB@Position - mRNA 275 -- 286@LB@Position - sRNA 18 -- 29@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 23 -- 29@LB@
111	0.009564	0.2693	b2040	rfbD	-5.00	0.321114	87 -- 99	24 -- 42	dTDP-L-rhamnose synthase NAD(P)-dependent dTDP-4-dehydrorhamnose reductase subunit	_____________86__________________100\n_____________\|___________________\|\n5'-GAU...UUUGA___________________AAAAC...CUA-3'\n______________GAGCG______GGAUUCGU\n______________:\|\|\|:______::\|\|\|\|\|\|\n______________UUCGU______UUUAAGCA\n3'-UUU...CGUUC_____GAAUUU________AUGUG...CAA-5'\n_____________\|___________________\|\n_____________43__________________23\n	93 -- 99	24 -- 30	-9.51502 kcal/mol	2.86783 kcal/mol	1.64896 kcal/mol	86 100@LB@ \| \|@LB@5'-GAU...UUUGA AAAAC...CUA-3'@LB@ GAGCG GGAUUCGU@LB@ :\|\|\|: ::\|\|\|\|\|\|@LB@ UUCGU UUUAAGCA@LB@3'-UUU...CGUUC GAAUUU AUGUG...CAA-5'@LB@ \| \|@LB@ 43 23@LB@@LB@@LB@Energy -5.00 kcal/mol@LB@Hybridization Energy -9.51502 kcal/mol@LB@Unfolding Energy - mRNA 2.86783 kcal/mol@LB@Unfolding Energy - sRNA 1.64896 kcal/mol@LB@@LB@Position - mRNA 87 -- 99@LB@Position - sRNA 24 -- 42@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 24 -- 30@LB@
86	0.005829	0.217	b2399	yfeD	-9.44	0.023742	136 -- 182	13 -- 56	DUF1323 family putative DNA-binding protein	_____________135______________________________________________183\n_____________\|________________________________________________\|\n5'-UGA...ACAUC_______CU________G_A___UC____________ACGC_______UUCGC...GGA-3'\n______________CUUGCUU__GCGGGAAG_G_UUA__GGAUU_GUUACA____UUAGGGA\n______________\|\|\|\|\|\|\|__\|\|::\|\|\|\|_:_\|\|\|__::\|\|\|_\|\|\|\|\|\|____::\|\|\|:\|\n______________GAACGAA__CGUUCUUC_U_AAU__UUUAA_CAAUGU____GGUCCUU\n3'-UUU...ACUUU_______UU________G_G___UU_____G_________________UAGAC...CAA-5'\n_____________\|________________________________________________\|\n_____________57_______________________________________________12\n	146 -- 152	40 -- 46	-35.8501 kcal/mol	12.5789 kcal/mol	13.8302 kcal/mol	135 183@LB@ \| \|@LB@5'-UGA...ACAUC CU G A UC ACGC UUCGC...GGA-3'@LB@ CUUGCUU GCGGGAAG G UUA GGAUU GUUACA UUAGGGA@LB@ \|\|\|\|\|\|\| \|\|::\|\|\|\| : \|\|\| ::\|\|\| \|\|\|\|\|\| ::\|\|\|:\|@LB@ GAACGAA CGUUCUUC U AAU UUUAA CAAUGU GGUCCUU@LB@3'-UUU...ACUUU UU G G UU G UAGAC...CAA-5'@LB@ \| \|@LB@ 57 12@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -35.8501 kcal/mol@LB@Unfolding Energy - mRNA 12.5789 kcal/mol@LB@Unfolding Energy - sRNA 13.8302 kcal/mol@LB@@LB@Position - mRNA 136 -- 182@LB@Position - sRNA 13 -- 56@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 40 -- 46@LB@
197	0.0237	0.3864	b4001	yjaH	-6.58	0.140477	149 -- 175	29 -- 57	DUF1481 family putative lipoprotein	_____________148____________________________176\n_____________\|______________________________\|\n5'-UGG...CCGGC________CU____________________CGCAG...AUA-3'\n______________AUUUGUUU__GGCA__AGGCACU_GAAAGA\n______________\|:\|\|\|:\|\|__:\|\|\|__\|:\|\|\|\|\|_:\|\|\|:\|\n______________UGAACGAA__UCGU__UUCGUGA_UUUUUU\n3'-UUU...UACUU________U_____UC_______A______AAGCA...CAA-5'\n_____________\|______________________________\|\n_____________58_____________________________28\n	163 -- 169	36 -- 42	-19.7163 kcal/mol	6.91297 kcal/mol	6.22375 kcal/mol	148 176@LB@ \| \|@LB@5'-UGG...CCGGC CU CGCAG...AUA-3'@LB@ AUUUGUUU GGCA AGGCACU GAAAGA@LB@ \|:\|\|\|:\|\| :\|\|\| \|:\|\|\|\|\| :\|\|\|:\|@LB@ UGAACGAA UCGU UUCGUGA UUUUUU@LB@3'-UUU...UACUU U UC A AAGCA...CAA-5'@LB@ \| \|@LB@ 58 28@LB@@LB@@LB@Energy -6.58 kcal/mol@LB@Hybridization Energy -19.7163 kcal/mol@LB@Unfolding Energy - mRNA 6.91297 kcal/mol@LB@Unfolding Energy - sRNA 6.22375 kcal/mol@LB@@LB@Position - mRNA 149 -- 175@LB@Position - sRNA 29 -- 57@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 36 -- 42@LB@
88	0.006209	0.2266	b1643	ydhI	-11.55	0.005389	141 -- 153	28 -- 40	DUF1656 family putative inner membrane efflux pump associated protein	_____________140___________154\n_____________\|_____________\|\n5'-UUU...UUUUC_____________AUUUA...GAU-3'\n______________GCACUUAAAGAAU\n______________\|\|\|\|\|\|\|\|\|:\|\|\|\n______________CGUGAAUUUUUUA\n3'-UUU...UUCUU_____________AGCAA...CAA-5'\n_____________\|_____________\|\n_____________41____________27\n	144 -- 150	31 -- 37	-15.2864 kcal/mol	2.10141 kcal/mol	1.63611 kcal/mol	140 154@LB@ \| \|@LB@5'-UUU...UUUUC AUUUA...GAU-3'@LB@ GCACUUAAAGAAU@LB@ \|\|\|\|\|\|\|\|\|:\|\|\|@LB@ CGUGAAUUUUUUA@LB@3'-UUU...UUCUU AGCAA...CAA-5'@LB@ \| \|@LB@ 41 27@LB@@LB@@LB@Energy -11.55 kcal/mol@LB@Hybridization Energy -15.2864 kcal/mol@LB@Unfolding Energy - mRNA 2.10141 kcal/mol@LB@Unfolding Energy - sRNA 1.63611 kcal/mol@LB@@LB@Position - mRNA 141 -- 153@LB@Position - sRNA 28 -- 40@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 31 -- 37@LB@
12	0.0001753	0.04706	b3676	yidH	-12.46	0.002725	279 -- 300	7 -- 26	DUF202 family inner membrane protein	_____________278___________________300\n_____________\|_____________________\|\n5'-GCC...GGAUC___AC__________UU_____-3'\n______________CGU__UGCACUAGGA__UCUGG\n______________\|\|\|__\|:\|\|\|:\|\|\|\|__\|\|\|\|:\n______________GCA__AUGUGGUCCU__AGACU\n3'-UUU...UUUAA_______________UU_____ACACAA-5'\n_____________\|______________________\|\n_____________27_____________________6\n	286 -- 292	15 -- 21	-23.8048 kcal/mol	2.98352 kcal/mol	8.36616 kcal/mol	278 300@LB@ \| \|@LB@5'-GCC...GGAUC AC UU -3'@LB@ CGU UGCACUAGGA UCUGG@LB@ \|\|\| \|:\|\|\|:\|\|\|\| \|\|\|\|:@LB@ GCA AUGUGGUCCU AGACU@LB@3'-UUU...UUUAA UU ACACAA-5'@LB@ \| \|@LB@ 27 6@LB@@LB@@LB@Energy -12.46 kcal/mol@LB@Hybridization Energy -23.8048 kcal/mol@LB@Unfolding Energy - mRNA 2.98352 kcal/mol@LB@Unfolding Energy - sRNA 8.36616 kcal/mol@LB@@LB@Position - mRNA 279 -- 300@LB@Position - sRNA 7 -- 26@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 15 -- 21@LB@
60	0.00317	0.1645	b0466	ybaM	-6.37	0.157728	143 -- 158	25 -- 40	DUF2496 family protein	_____________142_______________159\n_____________\|_________________\|\n5'-GCA...GCCAU_____GG__________AAAAC...CGC-3'\n______________GCGCU__AAAAAAU_CG\n______________\|\|:\|\|__\|\|\|\|\|\|\|_\|\|\n______________CGUGA__UUUUUUA_GC\n3'-UUU...UUCUU_____A________A__AAUGU...CAA-5'\n_____________\|_________________\|\n_____________41________________24\n	150 -- 156	28 -- 34	-11.3444 kcal/mol	3.32327 kcal/mol	1.64821 kcal/mol	142 159@LB@ \| \|@LB@5'-GCA...GCCAU GG AAAAC...CGC-3'@LB@ GCGCU AAAAAAU CG@LB@ \|\|:\|\| \|\|\|\|\|\|\| \|\|@LB@ CGUGA UUUUUUA GC@LB@3'-UUU...UUCUU A A AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -6.37 kcal/mol@LB@Hybridization Energy -11.3444 kcal/mol@LB@Unfolding Energy - mRNA 3.32327 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 143 -- 158@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 28 -- 34@LB@
169	0.01902	0.3625	b0858	ybjO	-5.59	0.239654	140 -- 156	25 -- 43	DUF2593 family inner membrane protein	_____________139__________________157\n_____________\|____________________\|\n5'-AUG...UGGCU____A_______________CCAAC...UUA-3'\n______________GAAG_CACU___AAAAUUUG\n______________\|\|\|\|_\|\|\|\|___\|\|\|\|\|\|:\|\n______________CUUC_GUGA___UUUUAAGC\n3'-UUU...UCGUU_________AUU________AAUGU...CAA-5'\n_____________\|____________________\|\n_____________44___________________24\n	150 -- 156	25 -- 31	-11.6219 kcal/mol	2.26879 kcal/mol	3.76226 kcal/mol	139 157@LB@ \| \|@LB@5'-AUG...UGGCU A CCAAC...UUA-3'@LB@ GAAG CACU AAAAUUUG@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\|\|:\|@LB@ CUUC GUGA UUUUAAGC@LB@3'-UUU...UCGUU AUU AAUGU...CAA-5'@LB@ \| \|@LB@ 44 24@LB@@LB@@LB@Energy -5.59 kcal/mol@LB@Hybridization Energy -11.6219 kcal/mol@LB@Unfolding Energy - mRNA 2.26879 kcal/mol@LB@Unfolding Energy - sRNA 3.76226 kcal/mol@LB@@LB@Position - mRNA 140 -- 156@LB@Position - sRNA 25 -- 43@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 25 -- 31@LB@
130	0.01234	0.3033	b2958	yggN	-5.61	0.236844	227 -- 233	35 -- 41	DUF2884 family putative periplasmic protein	_____________226_____234\n_____________\|_______\|\n5'-ACG...GCGGC_______UCAGU...UUG-3'\n______________AGCACUU\n______________\|\|\|\|\|\|\|\n______________UCGUGAA\n3'-UUU...GUUCU_______UUUUU...CAA-5'\n_____________\|_______\|\n_____________42______34\n	227 -- 233	35 -- 41	-8.1936 kcal/mol	0.976472 kcal/mol	1.6033 kcal/mol	226 234@LB@ \| \|@LB@5'-ACG...GCGGC UCAGU...UUG-3'@LB@ AGCACUU@LB@ \|\|\|\|\|\|\|@LB@ UCGUGAA@LB@3'-UUU...GUUCU UUUUU...CAA-5'@LB@ \| \|@LB@ 42 34@LB@@LB@@LB@Energy -5.61 kcal/mol@LB@Hybridization Energy -8.1936 kcal/mol@LB@Unfolding Energy - mRNA 0.976472 kcal/mol@LB@Unfolding Energy - sRNA 1.6033 kcal/mol@LB@@LB@Position - mRNA 227 -- 233@LB@Position - sRNA 35 -- 41@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 35 -- 41@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