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
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@
36	0.002273	0.2088	b4138	dcuA	-11.14	0.069498	259 -- 284	41 -- 65	C4-dicarboxylate antiporter	_____________258__________________________285\n_____________\|____________________________\|\n5'-AAC...AUUGG_______A___AUU___UU_________GGAUU...UGG-3'\n______________GGGGAAU_GGU___GGU__UGCA__GGC\n______________\|\|::\|\|\|_:\|\|___\|\|:__\|\|\|\|__\|\|\|\n______________CCUUUUA_UCA___CCG__ACGU__CCG\n3'-UUU...UACAA_______G_________UU____UA___GGUUG...UUG-5'\n_____________\|____________________________\|\n_____________66___________________________40\n	259 -- 265	59 -- 65	-20.3442 kcal/mol	3.39574 kcal/mol	5.80973 kcal/mol	258 285@LB@ \| \|@LB@5'-AAC...AUUGG A AUU UU GGAUU...UGG-3'@LB@ GGGGAAU GGU GGU UGCA GGC@LB@ \|\|::\|\|\| :\|\| \|\|: \|\|\|\| \|\|\|@LB@ CCUUUUA UCA CCG ACGU CCG@LB@3'-UUU...UACAA G UU UA GGUUG...UUG-5'@LB@ \| \|@LB@ 66 40@LB@@LB@@LB@Energy -11.14 kcal/mol@LB@Hybridization Energy -20.3442 kcal/mol@LB@Unfolding Energy - mRNA 3.39574 kcal/mol@LB@Unfolding Energy - sRNA 5.80973 kcal/mol@LB@@LB@Position - mRNA 259 -- 284@LB@Position - sRNA 41 -- 65@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 59 -- 65@LB@
134	0.01498	0.3759	b3388	damX	-9.22	0.174550	186 -- 204	42 -- 59	cell division protein that binds to the septal ring	_____________185__________________205\n_____________\|____________________\|\n5'-GGG...ACCUU_____________UA_____AUGAA...AAC-3'\n______________UUAGUGG_GGUGU__AAUGG\n______________\|:\|\|\|\|\|_::\|\|:__\|\|\|\|\|\n______________AGUCACC_UUACG__UUACC\n3'-UUU...CUUUU_______G____________GGGUU...UUG-5'\n_____________\|____________________\|\n_____________60___________________41\n	186 -- 192	53 -- 59	-16.4488 kcal/mol	3.53707 kcal/mol	3.69565 kcal/mol	185 205@LB@ \| \|@LB@5'-GGG...ACCUU UA AUGAA...AAC-3'@LB@ UUAGUGG GGUGU AAUGG@LB@ \|:\|\|\|\|\| ::\|\|: \|\|\|\|\|@LB@ AGUCACC UUACG UUACC@LB@3'-UUU...CUUUU G GGGUU...UUG-5'@LB@ \| \|@LB@ 60 41@LB@@LB@@LB@Energy -9.22 kcal/mol@LB@Hybridization Energy -16.4488 kcal/mol@LB@Unfolding Energy - mRNA 3.53707 kcal/mol@LB@Unfolding Energy - sRNA 3.69565 kcal/mol@LB@@LB@Position - mRNA 186 -- 204@LB@Position - sRNA 42 -- 59@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 53 -- 59@LB@
87	0.007653	0.2889	b1881	cheZ	-13.56	0.018568	164 -- 190	2 -- 28	chemotaxis regulator protein phosphatase for CheY	_____________163_________________________191\n_____________\|___________________________\|\n5'-AUU...UCAAC_______U___G__ACU__________GGAUG...GGG-3'\n______________AAAAUCU_UGA_AA___GGGCAUGUGA\n______________\|\|\|\|\|\|\|_\|\|\|_\|\|___:\|\|\|\|\|:\|:\|\n______________UUUUAGA_ACU_UU___UCCGUAUAUU\n3'-UUU...UUUUA_______C___G__AUU__________G-5'\n_____________\|___________________________\|\n_____________29__________________________1\n	183 -- 189	3 -- 9	-22.696 kcal/mol	4.24203 kcal/mol	4.89261 kcal/mol	163 191@LB@ \| \|@LB@5'-AUU...UCAAC U G ACU GGAUG...GGG-3'@LB@ AAAAUCU UGA AA GGGCAUGUGA@LB@ \|\|\|\|\|\|\| \|\|\| \|\| :\|\|\|\|\|:\|:\|@LB@ UUUUAGA ACU UU UCCGUAUAUU@LB@3'-UUU...UUUUA C G AUU G-5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -13.56 kcal/mol@LB@Hybridization Energy -22.696 kcal/mol@LB@Unfolding Energy - mRNA 4.24203 kcal/mol@LB@Unfolding Energy - sRNA 4.89261 kcal/mol@LB@@LB@Position - mRNA 164 -- 190@LB@Position - sRNA 2 -- 28@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 3 -- 9@LB@
6	0.0002023	0.1081	b1884	cheR	-8.31	0.257615	184 -- 205	1 -- 21	chemotaxis regulator protein-glutamate methyltransferase	_____________183____________________206\n_____________\|______________________\|\n5'-GCC...CUGAA_____UGA_______C______UUCAU...UGA-3'\n______________GUGAU___GAAGGCG_UAUGAC\n______________\|\|\|\|:___:\|\|\|\|\|:_\|\|\|:\|\|\n______________CACUG___UUUCCGU_AUAUUG\n3'-UUU...UUAGA_____UUA______________-5'\n_____________\|_____________________\|\n_____________22____________________1\n	192 -- 198	7 -- 13	-19.9838 kcal/mol	7.26541 kcal/mol	4.41334 kcal/mol	183 206@LB@ \| \|@LB@5'-GCC...CUGAA UGA C UUCAU...UGA-3'@LB@ GUGAU GAAGGCG UAUGAC@LB@ \|\|\|\|: :\|\|\|\|\|: \|\|\|:\|\|@LB@ CACUG UUUCCGU AUAUUG@LB@3'-UUU...UUAGA UUA -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -8.31 kcal/mol@LB@Hybridization Energy -19.9838 kcal/mol@LB@Unfolding Energy - mRNA 7.26541 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 184 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 7 -- 13@LB@
25	0.001369	0.1841	b2599	pheA	-10.09	0.116571	180 -- 205	1 -- 20	chorismate mutase and prephenate dehydratase P-protein	_____________179________________________206\n_____________\|__________________________\|\n5'-UGA...UUUAU______CAA_______ACAC______AUCGG...UCG-3'\n______________UGAUAA___AAAGGCA____UAUGAC\n______________\|\|\|:\|\|___\|\|\|\|\|\|\|____\|\|\|:\|\|\n______________ACUGUU___UUUCCGU____AUAUUG\n3'-UUU...UAGAC______A___________________-5'\n_____________\|_________________________\|\n_____________21________________________1\n	189 -- 195	7 -- 13	-16.49 kcal/mol	2.17136 kcal/mol	4.22784 kcal/mol	179 206@LB@ \| \|@LB@5'-UGA...UUUAU CAA ACAC AUCGG...UCG-3'@LB@ UGAUAA AAAGGCA UAUGAC@LB@ \|\|\|:\|\| \|\|\|\|\|\|\| \|\|\|:\|\|@LB@ ACUGUU UUUCCGU AUAUUG@LB@3'-UUU...UAGAC A -5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -10.09 kcal/mol@LB@Hybridization Energy -16.49 kcal/mol@LB@Unfolding Energy - mRNA 2.17136 kcal/mol@LB@Unfolding Energy - sRNA 4.22784 kcal/mol@LB@@LB@Position - mRNA 180 -- 205@LB@Position - sRNA 1 -- 20@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 7 -- 13@LB@
61	0.004706	0.2539	b3713	chrR	-11.93	0.045896	122 -- 163	8 -- 58	chromate reductase Class I flavoprotein	_____________121____________________________________________________164\n_____________\|______________________________________________________\|\n5'-ACG...CCUAC___CC__A_______UUUU_____________________CU___C________UUUUU...CGA-3'\n______________CAG__GG_UGAUGCG____GCCCAAC___________UCU___AC_GUGAAGGC\n______________\|\|\|__\|\|_::\|\|\|\|:____\|\|\|\|\|\|\|___________\|\|\|___\|\|_:\|:\|\|\|\|\|\n______________GUC__CC_GUUACGU____CGGGUUG___________AGA___UG_UAUUUCCG\n3'-UUU...UUUUA___A___________UAC________UCUUUUAUUUU___CAC__U________UAUAUUG-5'\n_____________\|______________________________________________________\|\n_____________59_____________________________________________________7\n	157 -- 163	8 -- 14	-33.8478 kcal/mol	9.79541 kcal/mol	12.1181 kcal/mol	121 164@LB@ \| \|@LB@5'-ACG...CCUAC CC A UUUU CU C UUUUU...CGA-3'@LB@ CAG GG UGAUGCG GCCCAAC UCU AC GUGAAGGC@LB@ \|\|\| \|\| ::\|\|\|\|: \|\|\|\|\|\|\| \|\|\| \|\| :\|:\|\|\|\|\|@LB@ GUC CC GUUACGU CGGGUUG AGA UG UAUUUCCG@LB@3'-UUU...UUUUA A UAC UCUUUUAUUUU CAC U UAUAUUG-5'@LB@ \| \|@LB@ 59 7@LB@@LB@@LB@Energy -11.93 kcal/mol@LB@Hybridization Energy -33.8478 kcal/mol@LB@Unfolding Energy - mRNA 9.79541 kcal/mol@LB@Unfolding Energy - sRNA 12.1181 kcal/mol@LB@@LB@Position - mRNA 122 -- 163@LB@Position - sRNA 8 -- 58@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 8 -- 14@LB@
20	0.0008987	0.1511	b2597	raiA	-11.08	0.071670	189 -- 211	11 -- 33	cold shock protein associated with 30S ribosomal subunit	_____________188_____________________212\n_____________\|_______________________\|\n5'-GCG...GACAA____________A__________CAUUA...AUC-3'\n______________GAGGUAAAAUUU_UGACAAUGAA\n______________:\|::\|\|\|\|\|\|:\|_\|\|\|\|\|\|\|:\|\|\n______________UUUUAUUUUAGA_ACUGUUAUUU\n3'-UUU...UUGUC____________C__________CCGUA...UUG-5'\n_____________\|_______________________\|\n_____________34______________________10\n	205 -- 211	11 -- 17	-19.0558 kcal/mol	3.03608 kcal/mol	4.94152 kcal/mol	188 212@LB@ \| \|@LB@5'-GCG...GACAA A CAUUA...AUC-3'@LB@ GAGGUAAAAUUU UGACAAUGAA@LB@ :\|::\|\|\|\|\|\|:\| \|\|\|\|\|\|\|:\|\|@LB@ UUUUAUUUUAGA ACUGUUAUUU@LB@3'-UUU...UUGUC C CCGUA...UUG-5'@LB@ \| \|@LB@ 34 10@LB@@LB@@LB@Energy -11.08 kcal/mol@LB@Hybridization Energy -19.0558 kcal/mol@LB@Unfolding Energy - mRNA 3.03608 kcal/mol@LB@Unfolding Energy - sRNA 4.94152 kcal/mol@LB@@LB@Position - mRNA 189 -- 211@LB@Position - sRNA 11 -- 33@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 11 -- 17@LB@
18	0.0007704	0.1438	b4526	ydaE	-7.35	0.372707	186 -- 222	21 -- 54	conserved protein Rac prophage	_____________185___________________________________223\n_____________\|_____________________________________\|\n5'-ACU...GUAAA_____A__C_____GA____UA____________G__CUUAC...UAU-3'\n______________GGCGG_GU_AUGGU__UGAC__AGAAAAUAAAAU_UG\n______________\|\|\|::_\|:_\|\|\|\|:__::\|\|__\|\|\|\|\|\|\|\|\|\|\|\|_\|\|\n______________CCGUU_CG_UACCG__GUUG__UCUUUUAUUUUA_AC\n3'-UUU...AGUCA_____A__U_____G___________________G__ACUGU...UUG-5'\n_____________\|_____________________________________\|\n_____________55____________________________________20\n	212 -- 218	25 -- 31	-28.7009 kcal/mol	12.2907 kcal/mol	9.06413 kcal/mol	185 223@LB@ \| \|@LB@5'-ACU...GUAAA A C GA UA G CUUAC...UAU-3'@LB@ GGCGG GU AUGGU UGAC AGAAAAUAAAAU UG@LB@ \|\|\|:: \|: \|\|\|\|: ::\|\| \|\|\|\|\|\|\|\|\|\|\|\| \|\|@LB@ CCGUU CG UACCG GUUG UCUUUUAUUUUA AC@LB@3'-UUU...AGUCA A U G G ACUGU...UUG-5'@LB@ \| \|@LB@ 55 20@LB@@LB@@LB@Energy -7.35 kcal/mol@LB@Hybridization Energy -28.7009 kcal/mol@LB@Unfolding Energy - mRNA 12.2907 kcal/mol@LB@Unfolding Energy - sRNA 9.06413 kcal/mol@LB@@LB@Position - mRNA 186 -- 222@LB@Position - sRNA 21 -- 54@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 25 -- 31@LB@
40	0.00261	0.2088	b3008	metC	-11.48	0.058180	224 -- 274	11 -- 59	cystathionine beta-lyase PLP-dependent	_____________223___________________________________________________275\n_____________\|_____________________________________________________\|\n5'-CGA...GAUAC___AC____G__________A_G_____A______CAC___C_GC________UAGCG...CGC-3'\n______________UCA__UGGU_AAUGCA__GG_C_CAGCA_AAAAUA___UCU_G__GCGGUAAA\n______________\|\|\|__\|\|\|:_\|\|\|\|\|\|__\|\|_\|_\|\|:\|\|_\|\|\|\|\|\|___\|\|\|_\|__:\|::\|\|\|\|\n______________AGU__ACCG_UUACGU__CC_G_GUUGU_UUUUAU___AGA_C__UGUUAUUU\n3'-UUU...CUUUU___C____________UA____G_____C______UUU_____AC________CCGUA...UUG-5'\n_____________\|_____________________________________________________\|\n_____________60____________________________________________________10\n	268 -- 274	11 -- 17	-31.6805 kcal/mol	9.07324 kcal/mol	11.1233 kcal/mol	223 275@LB@ \| \|@LB@5'-CGA...GAUAC AC G A G A CAC C GC UAGCG...CGC-3'@LB@ UCA UGGU AAUGCA GG C CAGCA AAAAUA UCU G GCGGUAAA@LB@ \|\|\| \|\|\|: \|\|\|\|\|\| \|\| \| \|\|:\|\| \|\|\|\|\|\| \|\|\| \| :\|::\|\|\|\|@LB@ AGU ACCG UUACGU CC G GUUGU UUUUAU AGA C UGUUAUUU@LB@3'-UUU...CUUUU C UA G C UUU AC CCGUA...UUG-5'@LB@ \| \|@LB@ 60 10@LB@@LB@@LB@Energy -11.48 kcal/mol@LB@Hybridization Energy -31.6805 kcal/mol@LB@Unfolding Energy - mRNA 9.07324 kcal/mol@LB@Unfolding Energy - sRNA 11.1233 kcal/mol@LB@@LB@Position - mRNA 224 -- 274@LB@Position - sRNA 11 -- 59@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 11 -- 17@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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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

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