Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
136	0.02238	0.526	b1883	cheB	-10.46	0.078180	185 -- 206	1 -- 23	fused chemotaxis regulator: protein-glutamate methylesterase in two-component regulatory system with CheA	_____________184______________________207\n_____________\|________________________\|\n5'-GGG...UGCGC_________A____C_________AAAAU...CGA-3'\n______________UAAGUAAGG_UUAA_GAUGA__GC\n______________\|\|\|:\|\|\|:\|_\|\|\|\|_\|\|\|\|\|__\|\|\n______________AUUUAUUUC_AAUU_CUACU__CG\n3'-UUU...CCAUU______________A_____AU__-5'\n_____________\|_______________________\|\n_____________24______________________1\n	187 -- 193	15 -- 21	-15.1436 kcal/mol	4.57462 kcal/mol	0.105066 kcal/mol	184 207@LB@ \| \|@LB@5'-GGG...UGCGC A C AAAAU...CGA-3'@LB@ UAAGUAAGG UUAA GAUGA GC@LB@ \|\|\|:\|\|\|:\| \|\|\|\| \|\|\|\|\| \|\|@LB@ AUUUAUUUC AAUU CUACU CG@LB@3'-UUU...CCAUU A AU -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -15.1436 kcal/mol@LB@Unfolding Energy - mRNA 4.57462 kcal/mol@LB@Unfolding Energy - sRNA 0.105066 kcal/mol@LB@@LB@Position - mRNA 185 -- 206@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 15 -- 21@LB@
36	0.003415	0.3114	b1849	purT	-10.41	0.080237	8 -- 43	29 -- 56	phosphoribosylglycinamide formyltransferase 2	_____________7_____________________________________44\n_____________\|_____________________________________\|\n____5'-UUUUGCU_______________UCUCUUCGCCCUCAC_______UACGU...GUC-3'\n______________GGUAAAC_GACAUUU_______________GAAUGAC\n______________\|\|\|\|\|\|\|_\|\|\|\|\|\|:_______________\|\|\|\|\|\|\|\n______________CCAUUUG_CUGUAAG_______________CUUACUG\n3'-UUU...UAUCC_______U_______UCUUUA________________CCAUU...UCG-5'\n_____________\|_____________________________________\|\n_____________57____________________________________28\n	37 -- 43	29 -- 35	-21.896 kcal/mol	5.20104 kcal/mol	6.28612 kcal/mol	7 44@LB@ \| \|@LB@ 5'-UUUUGCU UCUCUUCGCCCUCAC UACGU...GUC-3'@LB@ GGUAAAC GACAUUU GAAUGAC@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|: \|\|\|\|\|\|\|@LB@ CCAUUUG CUGUAAG CUUACUG@LB@3'-UUU...UAUCC U UCUUUA CCAUU...UCG-5'@LB@ \| \|@LB@ 57 28@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -21.896 kcal/mol@LB@Unfolding Energy - mRNA 5.20104 kcal/mol@LB@Unfolding Energy - sRNA 6.28612 kcal/mol@LB@@LB@Position - mRNA 8 -- 43@LB@Position - sRNA 29 -- 56@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 29 -- 35@LB@
192	0.03268	0.5507	b3532	bcsB	-10.41	0.080313	186 -- 199	1 -- 12	regulator of cellulose synthase cyclic di-GMP binding	_____________185____________200\n_____________\|______________\|\n5'-AAG...UCAAC__________AC__GAUGA...UCA-3'\n______________AAUGAUGAUA__GC\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\n______________UUACUACUAU__CG\n3'-UUU...UUCAA______________-5'\n_____________\|_____________\|\n_____________13____________1\n	189 -- 195	3 -- 9	-11.9692 kcal/mol	1.52301 kcal/mol	0.0394463 kcal/mol	185 200@LB@ \| \|@LB@5'-AAG...UCAAC AC GAUGA...UCA-3'@LB@ AAUGAUGAUA GC@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ UUACUACUAU CG@LB@3'-UUU...UUCAA -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -11.9692 kcal/mol@LB@Unfolding Energy - mRNA 1.52301 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 186 -- 199@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 3 -- 9@LB@
94	0.01566	0.5059	b3918	cdh	-10.38	0.081442	225 -- 238	1 -- 14	CDP-diacylglycerol phosphotidylhydrolase	_____________224____________239\n_____________\|______________\|\n5'-AUU...UUUUU______________UAUCG...CAU-3'\n______________UUGGUGAUGAUAGU\n______________\|\|::\|\|\|\|\|\|\|\|\|:\n______________AAUUACUACUAUCG\n3'-UUU...AUUUC______________-5'\n_____________\|_____________\|\n_____________15____________1\n	232 -- 238	1 -- 7	-16.1883 kcal/mol	5.76383 kcal/mol	0.0473494 kcal/mol	224 239@LB@ \| \|@LB@5'-AUU...UUUUU UAUCG...CAU-3'@LB@ UUGGUGAUGAUAGU@LB@ \|\|::\|\|\|\|\|\|\|\|\|:@LB@ AAUUACUACUAUCG@LB@3'-UUU...AUUUC -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -16.1883 kcal/mol@LB@Unfolding Energy - mRNA 5.76383 kcal/mol@LB@Unfolding Energy - sRNA 0.0473494 kcal/mol@LB@@LB@Position - mRNA 225 -- 238@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 1 -- 7@LB@
60	0.008489	0.4523	b3912	cpxR	-10.34	0.082729	218 -- 229	5 -- 16	response regulator in two-component regulatory system with CpxA	_____________217__________230\n_____________\|____________\|\n5'-UGA...CUGUU____________CCGAG...AUG-3'\n______________AGUUGAUGAUGA\n______________\|\|\|\|:\|\|\|\|\|\|\|\n______________UCAAUUACUACU\n3'-UUU...UUAUU____________AUCG-5'\n_____________\|____________\|\n_____________17___________4\n	223 -- 229	5 -- 11	-14.1725 kcal/mol	3.78244 kcal/mol	0.0462955 kcal/mol	217 230@LB@ \| \|@LB@5'-UGA...CUGUU CCGAG...AUG-3'@LB@ AGUUGAUGAUGA@LB@ \|\|\|\|:\|\|\|\|\|\|\|@LB@ UCAAUUACUACU@LB@3'-UUU...UUAUU AUCG-5'@LB@ \| \|@LB@ 17 4@LB@@LB@@LB@Energy -10.34 kcal/mol@LB@Hybridization Energy -14.1725 kcal/mol@LB@Unfolding Energy - mRNA 3.78244 kcal/mol@LB@Unfolding Energy - sRNA 0.0462955 kcal/mol@LB@@LB@Position - mRNA 218 -- 229@LB@Position - sRNA 5 -- 16@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 5 -- 11@LB@
160	0.02589	0.526	b3297	rpsK	-10.33	0.083340	178 -- 193	52 -- 64	30S ribosomal subunit protein S11	_____________177______________194\n_____________\|________________\|\n5'-CGA...AUCAA______AUC_______UUGAA...CUA-3'\n______________GAAAUA___GGGGUGA\n______________\|\|\|\|\|\|___\|\|\|\|\|:\|\n______________CUUUAU___CCCCAUU\n3'-UUU...GCCAA________________UGUCU...UCG-5'\n_____________\|________________\|\n_____________65_______________51\n	187 -- 193	52 -- 58	-13.1856 kcal/mol	2.77978 kcal/mol	0.0778991 kcal/mol	177 194@LB@ \| \|@LB@5'-CGA...AUCAA AUC UUGAA...CUA-3'@LB@ GAAAUA GGGGUGA@LB@ \|\|\|\|\|\| \|\|\|\|\|:\|@LB@ CUUUAU CCCCAUU@LB@3'-UUU...GCCAA UGUCU...UCG-5'@LB@ \| \|@LB@ 65 51@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -13.1856 kcal/mol@LB@Unfolding Energy - mRNA 2.77978 kcal/mol@LB@Unfolding Energy - sRNA 0.0778991 kcal/mol@LB@@LB@Position - mRNA 178 -- 193@LB@Position - sRNA 52 -- 64@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 52 -- 58@LB@
172	0.02805	0.531	b1912	pgsA	-10.33	0.083391	160 -- 169	52 -- 61	phosphatidylglycerophosphate synthetase	_____________159________170\n_____________\|__________\|\n5'-GUC...GCAAC__________UCUUA...UUG-3'\n______________AUAGGGGUAA\n______________\|\|\|\|\|\|\|\|\|\|\n______________UAUCCCCAUU\n3'-UUU...AACUU__________UGUCU...UCG-5'\n_____________\|__________\|\n_____________62_________51\n	163 -- 169	52 -- 58	-13.9577 kcal/mol	3.55629 kcal/mol	0.0747282 kcal/mol	159 170@LB@ \| \|@LB@5'-GUC...GCAAC UCUUA...UUG-3'@LB@ AUAGGGGUAA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UAUCCCCAUU@LB@3'-UUU...AACUU UGUCU...UCG-5'@LB@ \| \|@LB@ 62 51@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -13.9577 kcal/mol@LB@Unfolding Energy - mRNA 3.55629 kcal/mol@LB@Unfolding Energy - sRNA 0.0747282 kcal/mol@LB@@LB@Position - mRNA 160 -- 169@LB@Position - sRNA 52 -- 61@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 52 -- 58@LB@
115	0.01846	0.5155	b4483	tatD	-10.31	0.084235	251 -- 265	1 -- 13	quality control of Tat-exported FeS proteins; Mg-dependent cytoplasmic DNase	_____________250_____________266\n_____________\|_______________\|\n5'-CUG...GACCG________UU_____GUGCG...UCA-3'\n______________UGAUGAUG__GUAGC\n______________\|:\|\|\|\|\|\|__:\|\|\|\|\n______________AUUACUAC__UAUCG\n3'-UUU...UUUCA_______________-5'\n_____________\|______________\|\n_____________14_____________1\n	252 -- 258	6 -- 12	-13.1693 kcal/mol	2.8194 kcal/mol	0.0446954 kcal/mol	250 266@LB@ \| \|@LB@5'-CUG...GACCG UU GUGCG...UCA-3'@LB@ UGAUGAUG GUAGC@LB@ \|:\|\|\|\|\|\| :\|\|\|\|@LB@ AUUACUAC UAUCG@LB@3'-UUU...UUUCA -5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -10.31 kcal/mol@LB@Hybridization Energy -13.1693 kcal/mol@LB@Unfolding Energy - mRNA 2.8194 kcal/mol@LB@Unfolding Energy - sRNA 0.0446954 kcal/mol@LB@@LB@Position - mRNA 251 -- 265@LB@Position - sRNA 1 -- 13@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 6 -- 12@LB@
188	0.03165	0.5492	b3247	rng	-10.28	0.085420	187 -- 220	10 -- 64	ribonuclease G	_____________186_____________________________________________________221\n_____________\|_______________________________________________________\|\n5'-GUU...CGUGA_________A____________________________C_______U________AAACG...CGC-3'\n______________GAAA_AGGG_UAAAC________________AUGACGG___UGAAU___GUUAGU\n______________\|\|\|\|_\|\|\|\|_\|\|\|\|\|________________\|\|\|\|\|\|\|___\|:\|\|\|___\|\|\|\|:\|\n______________CUUU_UCCC_AUUUG________________UACUGCC___AUUUA___CAAUUA\n3'-UUU...GCCAA____A____C_____UCUGUAAGUCUUUACU_______AUU_____UUU______CUACU...UCG-5'\n_____________\|_______________________________________________________\|\n_____________65______________________________________________________9\n	201 -- 207	27 -- 33	-22.7807 kcal/mol	6.16544 kcal/mol	6.33995 kcal/mol	186 221@LB@ \| \|@LB@5'-GUU...CGUGA A C U AAACG...CGC-3'@LB@ GAAA AGGG UAAAC AUGACGG UGAAU GUUAGU@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\| \|:\|\|\| \|\|\|\|:\|@LB@ CUUU UCCC AUUUG UACUGCC AUUUA CAAUUA@LB@3'-UUU...GCCAA A C UCUGUAAGUCUUUACU AUU UUU CUACU...UCG-5'@LB@ \| \|@LB@ 65 9@LB@@LB@@LB@Energy -10.28 kcal/mol@LB@Hybridization Energy -22.7807 kcal/mol@LB@Unfolding Energy - mRNA 6.16544 kcal/mol@LB@Unfolding Energy - sRNA 6.33995 kcal/mol@LB@@LB@Position - mRNA 187 -- 220@LB@Position - sRNA 10 -- 64@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 27 -- 33@LB@
122	0.01943	0.5155	b1842	holE	-10.27	0.085496	209 -- 257	4 -- 63	DNA polymerase III theta subunit	_____________208____________________________________________________________258\n_____________\|______________________________________________________________\|\n5'-GUC...CUGAA____CU__C_____U___U__AA_____________________________G____UC___UUGGC...UGC-3'\n______________GAAU__GG_UAAAC_GGA_CA__CAGAAAUG_____________GAUAAAGU_AAUG__GAU\n______________:\|\|\|__\|\|_\|\|\|\|\|_:\|\|_\|\|__\|\|\|\|\|\|\|\|_____________:\|\|\|\|\|\|\|_\|\|\|\|__\|\|\|\n______________UUUA__CC_AUUUG_UCU_GU__GUCUUUAC_____________UUAUUUCA_UUAC__CUA\n3'-UUU...CCAAC____UC__C____________AA________UUACUGCCAUUAU________A____UA___UCG-5'\n_____________\|______________________________________________________________\|\n_____________64_____________________________________________________________3\n	241 -- 247	14 -- 20	-26.5551 kcal/mol	9.93779 kcal/mol	6.34398 kcal/mol	208 258@LB@ \| \|@LB@5'-GUC...CUGAA CU C U U AA G UC UUGGC...UGC-3'@LB@ GAAU GG UAAAC GGA CA CAGAAAUG GAUAAAGU AAUG GAU@LB@ :\|\|\| \|\| \|\|\|\|\| :\|\| \|\| \|\|\|\|\|\|\|\| :\|\|\|\|\|\|\| \|\|\|\| \|\|\|@LB@ UUUA CC AUUUG UCU GU GUCUUUAC UUAUUUCA UUAC CUA@LB@3'-UUU...CCAAC UC C AA UUACUGCCAUUAU A UA UCG-5'@LB@ \| \|@LB@ 64 3@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -26.5551 kcal/mol@LB@Unfolding Energy - mRNA 9.93779 kcal/mol@LB@Unfolding Energy - sRNA 6.34398 kcal/mol@LB@@LB@Position - mRNA 209 -- 257@LB@Position - sRNA 4 -- 63@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 14 -- 20@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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