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
3	2.244e-05	0.02513	b1107	nagZ	-17.54	0.010122	191 -- 218	37 -- 58	beta N-acetyl-glucosaminidase	_____________190__________________________219\n_____________\|____________________________\|\n5'-AUU...AAUAA___G_________GGUCC__________GAUGU...CGC-3'\n______________GGA_AGCAGUGUG_____AGUAAUGUUG\n______________\|\|\|_\|\|\|\|:\|\|\|\|_____\|\|:\|\|\|\|\|:\|\n______________CCU_UCGUUACAC_____UCGUUACAGC\n3'-UUU...UAUGA____________________________ACGAA...GCG-5'\n_____________\|____________________________\|\n_____________59___________________________36\n	212 -- 218	37 -- 43	-27.3301 kcal/mol	6.56806 kcal/mol	3.22699 kcal/mol	190 219@LB@ \| \|@LB@5'-AUU...AAUAA G GGUCC GAUGU...CGC-3'@LB@ GGA AGCAGUGUG AGUAAUGUUG@LB@ \|\|\| \|\|\|\|:\|\|\|\| \|\|:\|\|\|\|\|:\|@LB@ CCU UCGUUACAC UCGUUACAGC@LB@3'-UUU...UAUGA ACGAA...GCG-5'@LB@ \| \|@LB@ 59 36@LB@@LB@@LB@Energy -17.54 kcal/mol@LB@Hybridization Energy -27.3301 kcal/mol@LB@Unfolding Energy - mRNA 6.56806 kcal/mol@LB@Unfolding Energy - sRNA 3.22699 kcal/mol@LB@@LB@Position - mRNA 191 -- 218@LB@Position - sRNA 37 -- 58@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 37 -- 43@LB@
8	0.0004259	0.161	b4019	metH	-17.34	0.010954	191 -- 208	42 -- 58	homocysteine-N5-methyltetrahydrofolate transmethylase B12-dependent	_____________190________________209\n_____________\|__________________\|\n5'-UGA...GUGUC______A___________CAAAG...ACG-3'\n______________GGGAGC_AGUGUGAGCAG\n______________\|\|:\|\|\|_\|:\|\|\|\|\|\|\|\|:\n______________CCUUCG_UUACACUCGUU\n3'-UUU...UAUGA__________________ACAGC...GCG-5'\n_____________\|__________________\|\n_____________59_________________41\n	202 -- 208	42 -- 48	-25.1819 kcal/mol	4.63502 kcal/mol	3.2101 kcal/mol	190 209@LB@ \| \|@LB@5'-UGA...GUGUC A CAAAG...ACG-3'@LB@ GGGAGC AGUGUGAGCAG@LB@ \|\|:\|\|\| \|:\|\|\|\|\|\|\|\|:@LB@ CCUUCG UUACACUCGUU@LB@3'-UUU...UAUGA ACAGC...GCG-5'@LB@ \| \|@LB@ 59 41@LB@@LB@@LB@Energy -17.34 kcal/mol@LB@Hybridization Energy -25.1819 kcal/mol@LB@Unfolding Energy - mRNA 4.63502 kcal/mol@LB@Unfolding Energy - sRNA 3.2101 kcal/mol@LB@@LB@Position - mRNA 191 -- 208@LB@Position - sRNA 42 -- 58@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 42 -- 48@LB@
179	0.02212	0.4113	b3317	rplB	-11.24	0.118994	191 -- 218	39 -- 68	50S ribosomal subunit protein L2	_____________190____________________________219\n_____________\|______________________________\|\n5'-GCA...CGGAG_________AAU__________UUA_____AAACC...UGC-3'\n______________GAGUAAUAC____GGCAGU_UG___AAUGU\n______________:\|\|\|\|\|\|\|\|____:\|\|\|:\|_\|\|___\|\|\|\|\|\n______________UUCAUUAUG____UCGUUA_AC___UUACA\n3'-UUU...ACCGA_________ACCU______C__UCG_____GCACG...GCG-5'\n_____________\|______________________________\|\n_____________69_____________________________38\n	193 -- 199	60 -- 66	-19.7264 kcal/mol	5.17772 kcal/mol	3.30515 kcal/mol	190 219@LB@ \| \|@LB@5'-GCA...CGGAG AAU UUA AAACC...UGC-3'@LB@ GAGUAAUAC GGCAGU UG AAUGU@LB@ :\|\|\|\|\|\|\|\| :\|\|\|:\| \|\| \|\|\|\|\|@LB@ UUCAUUAUG UCGUUA AC UUACA@LB@3'-UUU...ACCGA ACCU C UCG GCACG...GCG-5'@LB@ \| \|@LB@ 69 38@LB@@LB@@LB@Energy -11.24 kcal/mol@LB@Hybridization Energy -19.7264 kcal/mol@LB@Unfolding Energy - mRNA 5.17772 kcal/mol@LB@Unfolding Energy - sRNA 3.30515 kcal/mol@LB@@LB@Position - mRNA 191 -- 218@LB@Position - sRNA 39 -- 68@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 60 -- 66@LB@
193	0.02468	0.4226	b0642	leuS	-10.30	0.169116	191 -- 213	41 -- 61	leucyl-tRNA synthetase	_____________190_____________________214\n_____________\|_______________________\|\n5'-AAU...GGACC_____CU__C___CAA_______ACCGC...AGA-3'\n______________ACUGG__GC_AUG___GAGCAAU\n______________\|\|\|\|\|__\|\|_\|\|\|___\|\|\|\|\|\|\|\n______________UGACC__CG_UAC___CUCGUUA\n3'-UUU...CAUUA_____UU__U___A_________CAGCA...GCG-5'\n_____________\|_______________________\|\n_____________62______________________40\n	207 -- 213	41 -- 47	-20.8037 kcal/mol	7.20782 kcal/mol	3.30062 kcal/mol	190 214@LB@ \| \|@LB@5'-AAU...GGACC CU C CAA ACCGC...AGA-3'@LB@ ACUGG GC AUG GAGCAAU@LB@ \|\|\|\|\| \|\| \|\|\| \|\|\|\|\|\|\|@LB@ UGACC CG UAC CUCGUUA@LB@3'-UUU...CAUUA UU U A CAGCA...GCG-5'@LB@ \| \|@LB@ 62 40@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -20.8037 kcal/mol@LB@Unfolding Energy - mRNA 7.20782 kcal/mol@LB@Unfolding Energy - sRNA 3.30062 kcal/mol@LB@@LB@Position - mRNA 191 -- 213@LB@Position - sRNA 41 -- 61@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 41 -- 47@LB@
5	0.0002772	0.1521	b3365	nirB	-15.55	0.022306	192 -- 212	38 -- 57	nitrite reductase large subunit NAD(P)H-binding	_____________191___________________213\n_____________\|_____________________\|\n5'-AUC...AAAUC_______AAA_______A___AGACU...UUA-3'\n______________GAGGCAA___UGAGCAA_GUC\n______________\|\|:\|\|\|\|___\|\|\|\|\|\|\|_\|\|\|\n______________CUUCGUU___ACUCGUU_CAG\n3'-UUU...AUGAC_______AC________A___CACGA...GCG-5'\n_____________\|_____________________\|\n_____________58____________________37\n	202 -- 208	42 -- 48	-22.0527 kcal/mol	3.28811 kcal/mol	3.2161 kcal/mol	191 213@LB@ \| \|@LB@5'-AUC...AAAUC AAA A AGACU...UUA-3'@LB@ GAGGCAA UGAGCAA GUC@LB@ \|\|:\|\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ CUUCGUU ACUCGUU CAG@LB@3'-UUU...AUGAC AC A CACGA...GCG-5'@LB@ \| \|@LB@ 58 37@LB@@LB@@LB@Energy -15.55 kcal/mol@LB@Hybridization Energy -22.0527 kcal/mol@LB@Unfolding Energy - mRNA 3.28811 kcal/mol@LB@Unfolding Energy - sRNA 3.2161 kcal/mol@LB@@LB@Position - mRNA 192 -- 212@LB@Position - sRNA 38 -- 57@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 42 -- 48@LB@
97	0.0101	0.3393	b0192	nlpE	-13.07	0.059097	192 -- 230	40 -- 68	lipoprotein involved with copper homeostasis and adhesion	_____________191_____________________________________231\n_____________\|_______________________________________\|\n5'-UCA...AAAAG___GA___GA___UGAAAA_______A____CA______GCUGU...CGC-3'\n______________AAG__AUG__UGG______AAGCGAU_GUGA__GCGAUG\n______________\|\|\|__\|\|:__\|\|\|______\|\|\|\|:\|\|_\|\|\|\|__\|\|:\|\|\|\n______________UUC__UAU__ACC______UUCGUUA_CACU__CGUUAC\n3'-UUU...ACCGA___AU___G______________________________AGCAC...GCG-5'\n_____________\|_______________________________________\|\n_____________69______________________________________39\n	211 -- 217	50 -- 56	-20.8621 kcal/mol	4.48665 kcal/mol	3.30507 kcal/mol	191 231@LB@ \| \|@LB@5'-UCA...AAAAG GA GA UGAAAA A CA GCUGU...CGC-3'@LB@ AAG AUG UGG AAGCGAU GUGA GCGAUG@LB@ \|\|\| \|\|: \|\|\| \|\|\|\|:\|\| \|\|\|\| \|\|:\|\|\|@LB@ UUC UAU ACC UUCGUUA CACU CGUUAC@LB@3'-UUU...ACCGA AU G AGCAC...GCG-5'@LB@ \| \|@LB@ 69 39@LB@@LB@@LB@Energy -13.07 kcal/mol@LB@Hybridization Energy -20.8621 kcal/mol@LB@Unfolding Energy - mRNA 4.48665 kcal/mol@LB@Unfolding Energy - sRNA 3.30507 kcal/mol@LB@@LB@Position - mRNA 192 -- 230@LB@Position - sRNA 40 -- 68@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 50 -- 56@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@
126	0.01361	0.3627	b2135	yohC	-14.18	0.038247	192 -- 212	38 -- 58	Yip1 family inner membrane protein	_____________191___________________213\n_____________\|_____________________\|\n5'-CAU...AACAA_________A_____C_____UGGGG...UUU-3'\n______________GGGGGCGGU_UGAGC_AUGUC\n______________\|\|::\|\|::\|_\|\|\|\|\|_\|\|\|\|\|\n______________CCUUCGUUA_ACUCG_UACAG\n3'-UUU...UAUGA_________C_____U_____CACGA...GCG-5'\n_____________\|_____________________\|\n_____________59____________________37\n	192 -- 198	52 -- 58	-26.6444 kcal/mol	9.24504 kcal/mol	3.21639 kcal/mol	191 213@LB@ \| \|@LB@5'-CAU...AACAA A C UGGGG...UUU-3'@LB@ GGGGGCGGU UGAGC AUGUC@LB@ \|\|::\|\|::\| \|\|\|\|\| \|\|\|\|\|@LB@ CCUUCGUUA ACUCG UACAG@LB@3'-UUU...UAUGA C U CACGA...GCG-5'@LB@ \| \|@LB@ 59 37@LB@@LB@@LB@Energy -14.18 kcal/mol@LB@Hybridization Energy -26.6444 kcal/mol@LB@Unfolding Energy - mRNA 9.24504 kcal/mol@LB@Unfolding Energy - sRNA 3.21639 kcal/mol@LB@@LB@Position - mRNA 192 -- 212@LB@Position - sRNA 38 -- 58@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 52 -- 58@LB@
168	0.02071	0.4072	b2431	yfeX	-10.86	0.137197	192 -- 213	24 -- 58	porphyrinogen oxidase cytoplasmic	_____________191_________________________________214\n_____________\|___________________________________\|\n5'-AUU...UUUCA_____AA____________________________AGAGU...CCA-3'\n______________GGAGG_________CAAUGUC______UCAGGUUC\n______________\|\|\|:\|_________\|\|\|\|\|\|\|______\|\|\|\|\|\|\|\|\n______________CCUUC_________GUUACAG______AGUCCAAG\n3'-UUU...UAUGA_____GUUACACUC_______CACGAA________AGGCG...GCG-5'\n_____________\|___________________________________\|\n_____________59__________________________________23\n	207 -- 213	24 -- 30	-23.408 kcal/mol	4.6321 kcal/mol	7.91302 kcal/mol	191 214@LB@ \| \|@LB@5'-AUU...UUUCA AA AGAGU...CCA-3'@LB@ GGAGG CAAUGUC UCAGGUUC@LB@ \|\|\|:\| \|\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CCUUC GUUACAG AGUCCAAG@LB@3'-UUU...UAUGA GUUACACUC CACGAA AGGCG...GCG-5'@LB@ \| \|@LB@ 59 23@LB@@LB@@LB@Energy -10.86 kcal/mol@LB@Hybridization Energy -23.408 kcal/mol@LB@Unfolding Energy - mRNA 4.6321 kcal/mol@LB@Unfolding Energy - sRNA 7.91302 kcal/mol@LB@@LB@Position - mRNA 192 -- 213@LB@Position - sRNA 24 -- 58@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 24 -- 30@LB@
55	0.005153	0.2905	b2727	hypB	-14.04	0.040392	194 -- 204	39 -- 49	GTP hydrolase involved in nickel liganding into hydrogenases	_____________193_________205\n_____________\|___________\|\n5'-GCC...CAGGA___________GUACA...CGG-3'\n______________GUGAGCGAUGU\n______________\|\|\|\|\|\|:\|\|\|\|\n______________CACUCGUUACA\n3'-UUU...CGUUA___________GCACG...GCG-5'\n_____________\|___________\|\n_____________50__________38\n	198 -- 204	39 -- 45	-18.0568 kcal/mol	2.85856 kcal/mol	1.15413 kcal/mol	193 205@LB@ \| \|@LB@5'-GCC...CAGGA GUACA...CGG-3'@LB@ GUGAGCGAUGU@LB@ \|\|\|\|\|\|:\|\|\|\|@LB@ CACUCGUUACA@LB@3'-UUU...CGUUA GCACG...GCG-5'@LB@ \| \|@LB@ 50 38@LB@@LB@@LB@Energy -14.04 kcal/mol@LB@Hybridization Energy -18.0568 kcal/mol@LB@Unfolding Energy - mRNA 2.85856 kcal/mol@LB@Unfolding Energy - sRNA 1.15413 kcal/mol@LB@@LB@Position - mRNA 194 -- 204@LB@Position - sRNA 39 -- 49@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 39 -- 45@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)

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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

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