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
50	0.002273	0.1465	b4159	mscM	-6.32	0.162358	72 -- 90	16 -- 34	mechanosensitive channel protein miniconductance	_____________71__________________91\n_____________\|___________________\|\n5'-AAG...CUACC____CC_____________ACGCU...AGC-3'\n______________GAAA__UUUGUUACGCCAG\n______________:\|\|\|__\|\|:\|\|\|\|\|:\|\|\|\|\n______________UUUU__AAGCAAUGUGGUC\n3'-UUU...GUGAA____UU_____________CUUUA...CAA-5'\n_____________\|___________________\|\n_____________35__________________15\n	84 -- 90	16 -- 22	-19.9467 kcal/mol	4.98786 kcal/mol	8.63814 kcal/mol	71 91@LB@ \| \|@LB@5'-AAG...CUACC CC ACGCU...AGC-3'@LB@ GAAA UUUGUUACGCCAG@LB@ :\|\|\| \|\|:\|\|\|\|\|:\|\|\|\|@LB@ UUUU AAGCAAUGUGGUC@LB@3'-UUU...GUGAA UU CUUUA...CAA-5'@LB@ \| \|@LB@ 35 15@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -19.9467 kcal/mol@LB@Unfolding Energy - mRNA 4.98786 kcal/mol@LB@Unfolding Energy - sRNA 8.63814 kcal/mol@LB@@LB@Position - mRNA 72 -- 90@LB@Position - sRNA 16 -- 34@LB@Position Seed - mRNA 84 -- 90@LB@Position Seed - sRNA 16 -- 22@LB@
3	4.385e-06	0.004708	b3749	rbsA	-11.98	0.003917	29 -- 86	17 -- 57	D-ribose ABC transporter ATPase	_____________28_________________________________________________________87\n_____________\|__________________________________________________________\|\n5'-UAA...UGCUC___CAC________GCUGCAAAAACACCAG____A___CAUU________________CGCAU...UGG-3'\n______________ACU___CUUGAGCA________________GGAA_UAC____GAAAUUCGUUACACCA\n______________\|\|\|___\|\|\|:\|\|\|\|________________:\|\|\|_:\|\|____:\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________UGA___GAAUUCGU________________UCUU_GUG____UUUUAAGCAAUGUGGU\n3'-UUU...UACUU___AC_____________________________C___AAUU________________CCUUU...CAA-5'\n_____________\|__________________________________________________________\|\n_____________58_________________________________________________________16\n	80 -- 86	17 -- 23	-33.7219 kcal/mol	7.92362 kcal/mol	13.8209 kcal/mol	28 87@LB@ \| \|@LB@5'-UAA...UGCUC CAC GCUGCAAAAACACCAG A CAUU CGCAU...UGG-3'@LB@ ACU CUUGAGCA GGAA UAC GAAAUUCGUUACACCA@LB@ \|\|\| \|\|\|:\|\|\|\| :\|\|\| :\|\| :\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UGA GAAUUCGU UCUU GUG UUUUAAGCAAUGUGGU@LB@3'-UUU...UACUU AC C AAUU CCUUU...CAA-5'@LB@ \| \|@LB@ 58 16@LB@@LB@@LB@Energy -11.98 kcal/mol@LB@Hybridization Energy -33.7219 kcal/mol@LB@Unfolding Energy - mRNA 7.92362 kcal/mol@LB@Unfolding Energy - sRNA 13.8209 kcal/mol@LB@@LB@Position - mRNA 29 -- 86@LB@Position - sRNA 17 -- 57@LB@Position Seed - mRNA 80 -- 86@LB@Position Seed - sRNA 17 -- 23@LB@
136	0.01308	0.3087	b0131	panD	-6.12	0.181240	260 -- 282	17 -- 40	aspartate 1-decarboxylase	_____________259______________________283\n_____________\|________________________\|\n5'-AUU...GACCU_____AU_________________UUGAC...UUG-3'\n______________GCACU__GAAGGUUC_UUGCGCCA\n______________\|\|\|\|\|__:\|\|::\|\|\|_\|\|:\|:\|\|\|\n______________CGUGA__UUUUUAAG_AAUGUGGU\n3'-UUU...UUCUU_____AU________C________CCUUU...CAA-5'\n_____________\|________________________\|\n_____________41_______________________16\n	268 -- 274	26 -- 32	-23.1255 kcal/mol	7.80932 kcal/mol	9.19627 kcal/mol	259 283@LB@ \| \|@LB@5'-AUU...GACCU AU UUGAC...UUG-3'@LB@ GCACU GAAGGUUC UUGCGCCA@LB@ \|\|\|\|\| :\|\|::\|\|\| \|\|:\|:\|\|\|@LB@ CGUGA UUUUUAAG AAUGUGGU@LB@3'-UUU...UUCUU AU C CCUUU...CAA-5'@LB@ \| \|@LB@ 41 16@LB@@LB@@LB@Energy -6.12 kcal/mol@LB@Hybridization Energy -23.1255 kcal/mol@LB@Unfolding Energy - mRNA 7.80932 kcal/mol@LB@Unfolding Energy - sRNA 9.19627 kcal/mol@LB@@LB@Position - mRNA 260 -- 282@LB@Position - sRNA 17 -- 40@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 26 -- 32@LB@
122	0.01076	0.2828	b1908	yecA	-7.65	0.074805	79 -- 96	18 -- 40	UPF0149 family protein	_____________78_______________________97\n_____________\|________________________\|\n5'-UAC...UGCCU__A_____________________CUCCU...UGG-3'\n______________GC_ACUUG______UCGUUACACC\n______________\|\|_\|\|\|\|:______\|\|\|\|\|\|\|\|\|\|\n______________CG_UGAAU______AGCAAUGUGG\n3'-UUU...UUCUU________UUUUUA__________UCCUU...CAA-5'\n_____________\|________________________\|\n_____________41_______________________17\n	90 -- 96	18 -- 24	-19.1188 kcal/mol	2.30438 kcal/mol	9.1639 kcal/mol	78 97@LB@ \| \|@LB@5'-UAC...UGCCU A CUCCU...UGG-3'@LB@ GC ACUUG UCGUUACACC@LB@ \|\| \|\|\|\|: \|\|\|\|\|\|\|\|\|\|@LB@ CG UGAAU AGCAAUGUGG@LB@3'-UUU...UUCUU UUUUUA UCCUU...CAA-5'@LB@ \| \|@LB@ 41 17@LB@@LB@@LB@Energy -7.65 kcal/mol@LB@Hybridization Energy -19.1188 kcal/mol@LB@Unfolding Energy - mRNA 2.30438 kcal/mol@LB@Unfolding Energy - sRNA 9.1639 kcal/mol@LB@@LB@Position - mRNA 79 -- 96@LB@Position - sRNA 18 -- 40@LB@Position Seed - mRNA 90 -- 96@LB@Position Seed - sRNA 18 -- 24@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@
32	0.0009536	0.09599	b0637	rsfS	-12.32	0.003012	197 -- 230	23 -- 59	ribosomal silencing factor	_____________196___________________________________231\n_____________\|_____________________________________\|\n5'-AUU...GGGGA________A_______________CC____U______AUCGA...UCA-3'\n______________AAACUUGC__GGGUA__AAGCACU__AGGA_UUUGUU\n______________\|\|\|\|\|\|\|\|__::\|:\|__\|\|\|\|\|\|\|__\|::\|_\|\|:\|\|\|\n______________UUUGAACG__UUCGU__UUCGUGA__UUUU_AAGCAA\n3'-UUU...CCUAC________AA_____UC_______AU____U______UGUGG...CAA-5'\n_____________\|_____________________________________\|\n_____________60____________________________________22\n	211 -- 217	36 -- 42	-25.7611 kcal/mol	7.16036 kcal/mol	6.27609 kcal/mol	196 231@LB@ \| \|@LB@5'-AUU...GGGGA A CC U AUCGA...UCA-3'@LB@ AAACUUGC GGGUA AAGCACU AGGA UUUGUU@LB@ \|\|\|\|\|\|\|\| ::\|:\| \|\|\|\|\|\|\| \|::\| \|\|:\|\|\|@LB@ UUUGAACG UUCGU UUCGUGA UUUU AAGCAA@LB@3'-UUU...CCUAC AA UC AU U UGUGG...CAA-5'@LB@ \| \|@LB@ 60 22@LB@@LB@@LB@Energy -12.32 kcal/mol@LB@Hybridization Energy -25.7611 kcal/mol@LB@Unfolding Energy - mRNA 7.16036 kcal/mol@LB@Unfolding Energy - sRNA 6.27609 kcal/mol@LB@@LB@Position - mRNA 197 -- 230@LB@Position - sRNA 23 -- 59@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 36 -- 42@LB@
38	0.00143	0.1212	b3315	rplV	-7.95	0.062235	2 -- 19	23 -- 40	50S ribosomal subunit protein L22	_____________1__________________20\n_____________\|__________________\|\n__________5'-C________UCCCG_____CAACG...UGG-3'\n______________GCACUUGG_____UCGUU\n______________\|\|\|\|\|\|::_____\|\|\|\|\|\n______________CGUGAAUU_____AGCAA\n3'-UUU...UUCUU________UUUUA_____UGUGG...CAA-5'\n_____________\|__________________\|\n_____________41_________________22\n	3 -- 9	33 -- 39	-14.4443 kcal/mol	4.84591 kcal/mol	1.64885 kcal/mol	1 20@LB@ \| \|@LB@ 5'-C UCCCG CAACG...UGG-3'@LB@ GCACUUGG UCGUU@LB@ \|\|\|\|\|\|:: \|\|\|\|\|@LB@ CGUGAAUU AGCAA@LB@3'-UUU...UUCUU UUUUA UGUGG...CAA-5'@LB@ \| \|@LB@ 41 22@LB@@LB@@LB@Energy -7.95 kcal/mol@LB@Hybridization Energy -14.4443 kcal/mol@LB@Unfolding Energy - mRNA 4.84591 kcal/mol@LB@Unfolding Energy - sRNA 1.64885 kcal/mol@LB@@LB@Position - mRNA 2 -- 19@LB@Position - sRNA 23 -- 40@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 33 -- 39@LB@
160	0.01746	0.3504	b4542	yohO	-11.65	0.004993	133 -- 150	23 -- 41	putative membrane protein	_____________132_________________151\n_____________\|___________________\|\n5'-UCG...CACUC_________U_________AACAA...GUG-3'\n______________GGCAUUUAA__GAUUCGUU\n______________:\|\|\|:\|\|\|\|__:\|\|\|\|\|\|\|\n______________UCGUGAAUU__UUAAGCAA\n3'-UUU...GUUCU_________UU________UGUGG...CAA-5'\n_____________\|___________________\|\n_____________42__________________22\n	144 -- 150	23 -- 29	-16.4387 kcal/mol	3.13759 kcal/mol	1.64896 kcal/mol	132 151@LB@ \| \|@LB@5'-UCG...CACUC U AACAA...GUG-3'@LB@ GGCAUUUAA GAUUCGUU@LB@ :\|\|\|:\|\|\|\| :\|\|\|\|\|\|\|@LB@ UCGUGAAUU UUAAGCAA@LB@3'-UUU...GUUCU UU UGUGG...CAA-5'@LB@ \| \|@LB@ 42 22@LB@@LB@@LB@Energy -11.65 kcal/mol@LB@Hybridization Energy -16.4387 kcal/mol@LB@Unfolding Energy - mRNA 3.13759 kcal/mol@LB@Unfolding Energy - sRNA 1.64896 kcal/mol@LB@@LB@Position - mRNA 133 -- 150@LB@Position - sRNA 23 -- 41@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 23 -- 29@LB@
175	0.01993	0.3669	b0183	rnhB	-5.94	0.199165	195 -- 215	23 -- 41	ribonuclease HII degrades RNA of DNA-RNA hybrids	_____________194___________________216\n_____________\|_____________________\|\n5'-AAU...GAGUU_____AA___UC_________UAUCC...UCC-3'\n______________AGCAC__UGA__GAAUUUGUU\n______________\|\|\|\|\|__\|:\|__:\|\|\|\|:\|\|\|\n______________UCGUG__AUU__UUUAAGCAA\n3'-UUU...GUUCU_____A____U__________UGUGG...CAA-5'\n_____________\|_____________________\|\n_____________42____________________22\n	209 -- 215	23 -- 29	-11.3649 kcal/mol	3.77136 kcal/mol	1.64896 kcal/mol	194 216@LB@ \| \|@LB@5'-AAU...GAGUU AA UC UAUCC...UCC-3'@LB@ AGCAC UGA GAAUUUGUU@LB@ \|\|\|\|\| \|:\| :\|\|\|\|:\|\|\|@LB@ UCGUG AUU UUUAAGCAA@LB@3'-UUU...GUUCU A U UGUGG...CAA-5'@LB@ \| \|@LB@ 42 22@LB@@LB@@LB@Energy -5.94 kcal/mol@LB@Hybridization Energy -11.3649 kcal/mol@LB@Unfolding Energy - mRNA 3.77136 kcal/mol@LB@Unfolding Energy - sRNA 1.64896 kcal/mol@LB@@LB@Position - mRNA 195 -- 215@LB@Position - sRNA 23 -- 41@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 23 -- 29@LB@
14	0.0002995	0.06692	b4195	ulaC	-9.74	0.019405	182 -- 212	24 -- 54	L-ascorbate-specific enzyme IIA component of PTS	_____________181_______________________________213\n_____________\|_________________________________\|\n5'-GCG...CAGGA___G__________C____CAU_______A___GAUUC...UGG-3'\n______________UGU__AAGUAAGGA_GCGC____GAAAUU_CGU\n______________\|\|:__\|\|\|:\|\|\|:\|_\|\|:\|____:\|\|\|\|\|_\|\|\|\n______________ACG__UUCGUUCUU_CGUG____UUUUAA_GCA\n3'-UUU...UUUGA___AA______________AAUU__________AUGUG...CAA-5'\n_____________\|_________________________________\|\n_____________55________________________________23\n	187 -- 193	42 -- 48	-22.0137 kcal/mol	6.00518 kcal/mol	6.26866 kcal/mol	181 213@LB@ \| \|@LB@5'-GCG...CAGGA G C CAU A GAUUC...UGG-3'@LB@ UGU AAGUAAGGA GCGC GAAAUU CGU@LB@ \|\|: \|\|\|:\|\|\|:\| \|\|:\| :\|\|\|\|\| \|\|\|@LB@ ACG UUCGUUCUU CGUG UUUUAA GCA@LB@3'-UUU...UUUGA AA AAUU AUGUG...CAA-5'@LB@ \| \|@LB@ 55 23@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -22.0137 kcal/mol@LB@Unfolding Energy - mRNA 6.00518 kcal/mol@LB@Unfolding Energy - sRNA 6.26866 kcal/mol@LB@@LB@Position - mRNA 182 -- 212@LB@Position - sRNA 24 -- 54@LB@Position Seed - mRNA 187 -- 193@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